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Results 1 - 10 of about 662 for BRB ArrayTools. (0.17 seconds) 

[BOOK] Design and Analysis of DNA Microarray Investigations
RM Simon - 2003 - Springer
... We thank Amy Peng Lam for her development of BRB-ArrayTools in collaboration with
Richard Simon, and for her many contributions to our microarray analyses. ...
Cited by 120 - Related Articles - Web Search - Full-Text Plus!

Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data - all 7 versions »
LM McShane, MD Radmacher, B Freidlin, R Yu, MC Li, … - Bioinformatics, 2002 - Oxford Univ Press
... Availability: Software to implement these methods is contained in BRB ArrayTools
microarray analysis package available from http://linus.nci.nih.gov./BRB ...
Cited by 107 - Related Articles - Web Search - BL Direct

A random variance model for detection of differential gene expression in small microarray … - all 4 versions »
GW Wright, RM Simon - Bioinformatics, 2003 - Oxford Univ Press
... positives. Availability:This method is incorporated into BRB-ArrayTools
version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 110 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Molecular Classification of Tamoxifen-Resistant Breast Carcinomas by Gene Expression Profiling - all 6 versions »
MPHM Jansen, JA Foekens, IL van Staveren, MM … - Journal of Clinical Oncology, 2005 - jcojournal.org
... packages BRB Array Tools, developed by the Biometric Research Branch of the US National
Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html) and ...
Cited by 108 - Related Articles - Web Search - Full-Text Plus!

De Novo Kidney Transplantation Without Use of Calcineurin Inhibitors Preserves Renal Structure and … - all 6 versions »
SM Flechner, SM Kurian, K Solez, DJ Cook, JT Burke … - American Journal of Transplantation, 2004 - Blackwell Synergy
... BRB ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html) was used to perform
class comparisons between the two drug treatment or Banff score-defined ...
Cited by 134 - Related Articles - Web Search - BL Direct

Laser Capture Microdissection and Microarray Expression Analysis of Lung Adenocarcinoma Reveals … - all 3 versions »
K Miura, ED Bowman, R Simon, AC Peng, AI Robles, … - Cancer Research, 2002 - AACR
... The analyses were performed using BRB-ArrayTools. 5. Hierarchical Clustering. ... 5 Simon,
R., and Peng, A. BRB-ArrayTools Users Guide. National Cancer Institute. ...
Cited by 108 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Kidney Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and Peripheral Blood … - all 5 versions »
SM Flechner, SM Kurian, SR Head, SM Sharp, TC … - American Journal of Transplantation, 2004 - Blackwell Synergy
... We used six class predictors implemented in BRB ArrayTools for determining to ... six
class prediction algorithms currently available in BRB Array Tools for both ...
Cited by 56 - Related Articles - Web Search - BL Direct

Gene expression patterns for doxorubicin (Adriamycin) and cyclophosphamide (Cytoxan)(AC) response … - all 4 versions »
S Cleator, A Tsimelzon, A Ashworth, M Dowsett, T … - Breast Cancer Research and Treatment, 2006 - Springer
... and analyzed by dChip (http://www.dchip.org) [7] and classifiers were constructed
with BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) [8]. ...
Cited by 21 - Related Articles - Web Search - Full-Text Plus! - BL Direct

[PDF] Analysis of gene expression data using BRB-Array Tools - all 4 versions »
R Simon, A Lam, MC Li, M Ngan, S Menenzes, Y Zhao - Cancer Informatics, 2007 - la-press.com
... converted to BRB-ArrayTools format. In addition to importing the single or dual
channel intensities for each gene on each array, BRB-Array- Tools imports an ...
Cited by 10 - Related Articles - View as HTML - Web Search

Expression Profiling of Serous Low Malignant Potential, Low-Grade, and High-Grade Tumors of the … - all 3 versions »
T Bonome, JY Lee, DC Park, M Radonovich, C Pise- … - Cancer Research, 2005 - AACR
... BRB ArrayTools is a multifunctional Excel add-in that contains utilities for processing
and analyzing microarray data using the R version 2.0.1 environment (R ...
Cited by 41 - Related Articles - Web Search - Full-Text Plus! - BL Direct

10

Gene expression in peripheral blood mononuclear cells from patients with chronic fatigue syndrome - all 10 versions »
N Kaushik, D Fear, SCM Richards, CR McDermott, EF … - British Medical Journal, 2005 - jcp.bmj.com
... by Dr R Simon and A Peng (http://linus.nci.nih.gov/BRB-ArrayTools.html). ... CFS; n =
25) and normal persons (n = 25) identified by analysis in BRB Array Tools. ...
Cited by 46 - Related Articles - Web Search - BL Direct

Analysis of gene expression in cancer cell lines identifies candidate markers for pancreatic … - all 3 versions »
E Missiaglia, E Blaveri, B Terris, YH Wang, E … - International Journal of Cancer, 2004 - doi.wiley.com
... Statistical class comparison The data were also analyzed using BRB-ArrayTools (version
3.0; http://linus.nci.nih.gov/BRB-ArrayTools.html) developed by Dr. ...
Cited by 47 - Related Articles - Web Search - Full-Text Plus! - BL Direct

The p53 Tumor Suppressor Network Is a Key Responder to Microenvironmental Components of Chronic … - all 5 versions »
F Staib, AI Robles, L Varticovski, XW Wang, BR … - Cancer Research, 2005 - AACR
... the following software for data analysis: BRB Array Tools developed by Dr. Richard
Simon and Amy Peng Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html), High ...
Cited by 23 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene Microarray Analysis of Peripheral Blood Cells in Pulmonary Arterial Hypertension - all 5 versions »
TM Bull, CD Coldren, M Moore, SM Sotto-Santiago, … - American Journal of Respiratory and Critical Care Medicine, 2004 - Am Thoracic Soc
... The array data were analyzed with BRB ArrayTools v3.0.2E developed by Dr. Richard
Simon and Amy Tan. ... and class prediction functions of BRB ArrayTools. ...
Cited by 32 - Related Articles - Web Search - BL Direct

Cancer-associated molecular signature in the tissue samples of patients with cirrhosis - all 4 versions »
JW Kim, Q Ye, M Forgues, Y Chen, A Budhu, J Sime, … - Hepatology, 2004 - doi.wiley.com
... All analyses were performed using the BRB ArrayTools (version 3.0 ... that more complex
SVMs perform less well for this application (R. Simon, BRB Array Tools manual ...
Cited by 33 - Related Articles - Web Search - Full-Text Plus!

Laparoscopic Donor Nephrectomy Gene Expression Profiling Reveals Upregulation of Stress and Ischemia … - all 3 versions »
SM Kurian, SM Flechner, J Kaouk, C Modlin, D … - Transplantation, 2005 - transplantjournal.com
... comparison between the control and LDN kidneys using BRB Array Tools on all ... Clustering
was done in BRB ArrayTools using centered correlation and average linkage ...
Cited by 12 - Related Articles - Web Search - Full-Text Plus!

Analysis of Orthologous Gene Expression between Human Pulmonary Adenocarcinoma and a Carcinogen- … - all 6 versions »
RS Stearman, L Dwyer-Nield, L Zerbe, SA Blaine, Z … - American Journal of Pathology, 2005 - ASIP
... BRB-ArrayTools has several classification/prediction modes we used for ... Further,
BRB-Array Tools includes five different algorithms for class prediction that ...
Cited by 24 - Related Articles - Web Search - BL Direct

Breast cancer classification and prognosis based on gene expression profiles from a population-based … - all 9 versions »
C Sotiriou, SY Neo, LM McShane, EL Korn, PM Long, … - Proceedings of the National Academy of Sciences, 2003 - National Acad Sciences
... agglomerative clustering using the statistical package BRB-ARRAYTOOLS software
(available at http://linus.nci.nih.gov/BRB-ArrayTools.html) was applied to these ...
Cited by 437 - Related Articles - Web Search - BL Direct

Development and Evaluation of Therapeutically Relevant Predictive Classifiers Using Gene Expression … - all 7 versions »
R Simon - jnci, 2006 - jnci.oxfordjournals.org
... are included in the BRB-ArrayTools software package, freely available for noncommercial
purposes from the National Cancer Institute at http://linus.nci.nih.gov ...
Cited by 23 - Related Articles - Web Search - Full-Text Plus! - BL Direct

 

20

Expression Profiles of Osteosarcoma That Can Predict Response to Chemotherapy - all 3 versions »
TK Man, M Chintagumpala, J Visvanathan, J Shen, L … - Cancer Research, 2005 - AACR
... experiments were subjected to data analysis using BRB Array Tools 3.1.0 developed
by R. Simon and A. Pang Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 18 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Condensin binding at distinct and specific chromosomal sites in the Saccharomyces cerevisiae genome - all 4 versions »
BD Wang, D Eyre, M Basrai, M Lichten, A Strunnikov - Mol. Cell. Biol, 2005 - pubmedcentral.nih.gov
... BRB-Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) software was used
to validate the reproducibility of hybridization replicas (within each array ...
Cited by 22 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Evaluation of a linear amplification method for small samples used on high-density oligonucleotide … - all 3 versions »
CI Dumur, CT Garrett, KJ Archer, S Nasim, DS … - Analytical Biochemistry, 2004 - Elsevier
... we applied to identify differentially expressed genes was the paired t test as
implemented in the Class Comparison tool available in BRB-ArrayTools v3.0.2 [15 ...
Cited by 22 - Related Articles - Web Search - Full-Text Plus!

Alterations in the expression of DEAD-box and other RNA binding proteins during HIV-1 replication - all 9 versions »
V Krishnan, SL Zeichner - Retrovirology, 2004 - retrovirology.com
... Using BRB -ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools webcite, the data
were subjected to statistical analyses using univariate parametric and ...
Cited by 18 - Related Articles - Cached - Web Search - Full-Text Plus!

Gene profiling of scleroderma skin reveals robust signatures of disease that are imperfectly … - all 3 versions »
H Gardner, JR Shearstone, R Bandaru, T Crowell, M … - Arthritis Rheum, 2006 - doi.wiley.com
... Data were analyzed using the BRB ArrayTools system. When appropriate, findings were
followed up with immunohistochemical analysis or TaqMan studies. Results. ...
Cited by 17 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Downregulation in components of the mitochondrial electron transport chain in the postmortem frontal … - all 6 versions »
X Sun, JF Wang, M Tseng, LT Young - Journal of Psychiatry and Neuroscience, 2006 - pubmedcentral.nih.gov
... Analyses were performed using BRB ArrayTools developed by Dr. Richard Simon and
Amy Peng Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html, Biometric Research ...
Cited by 16 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Cryptococcus neoformans Gene Expression during Murine Macrophage Infection - all 6 versions »
W Fan, PR Kraus, MJ Boily, J Heitman - Eukaryotic Cell, 2005 - ec.highwire.org
... Pro v 4.0 and BRB array tools (developed by Richard Simon and Amy Peng Lam at the
National Cancer Institute; http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 28 - Related Articles - Web Search - BL Direct

Lung Adenocarcinoma Global Profiling Identifies Type II Transforming Growth Factor-{beta} Receptor … - all 5 versions »
AC Borczuk, HK Kim, HA Yegen, RA Friedman, CA … - American Journal of Respiratory and Critical Care Medicine, 2005 - 171.66.122.149
... supervised analysis using an F test within BRB array tools (developed by Richard
Simon and Amy Peng Lam; http://linus.nci.nih.gov/BRB-ArrayTools.html) to ...
Cited by 14 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Signatures of differentially regulated interferon gene expression and vasculotrophism in the … - all 5 versions »
FK Tan, X Zhou, MD Mayes, P Gourh, X Guo, C Marcum … - Rheumatology, 2006 - Br Soc Rheumatology
... The program BRB ArrayTools v. 3.2, designed by Richard Simon and Amy Peng Lam ... Next,
using BRB Array Tools, we examined known biological pathways in order to ...
Cited by 26 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Distinct Transcriptional Changes in Donor Kidneys upon Brain Death Induction in Rats: Insights in … - all 3 versions »
TA Schuurs, F Gerbens, JAB van der Hoeven, PJ … - American Journal of Transplantation, 2004 - Blackwell Synergy
... To account for dye bias, resulting data were normalized by intensity-dependent
regression (Lowess) of the log-transformed ratios by BRB ArrayTools version 3.0 ...
Cited by 19 - Related Articles - Web Search - Full-Text Plus!

30

Gene expression profile of cervical tissue compared to exfoliated cells: Impact on biomarker … - all 5 versions »
M Steinau, DR Lee, MS Rajeevan, SD Vernon, MT … - feedback, 2005 - biomedcentral.com
... (1) BRB Array Tools 3.2 http://linus.nci.nih.gov/BRB-ArrayTools: Log 2 transformed
sARM values were normalized over the median of each array and subjected to a ...
Cited by 12 - Related Articles - Cached - Web Search - Full-Text Plus!

Molecular mechanisms of West Nile virus pathogenesis in brain cell - all 4 versions »
WL Koh, ML Ng - Emerg Infect Dis, 2005 - cdc.gov
... Analyses of the scanned microarray images were performed with BRB ArrayTools version
3.1 (developed by R. Simon and AP Lam, National Cancer Institute, Bethesda ...
Cited by 11 - Related Articles - Cached - Web Search - Full-Text Plus!

Gene Expression Profiles in Paraffin-Embedded Core Biopsy Tissue Predict Response to Chemotherapy in … - all 9 versions »
L Gianni, M Zambetti, K Clark, J Baker, M Cronin, … - Journal of Clinical Oncology, 2005 - jco.ascopubs.org
... Statistical analysis was performed by using the BRB-Arraytools software package
(http://linus.nci.nih.gov/BRB-ArrayTools.html). RESULTS. ...
Cited by 115 - Related Articles - Web Search - Full-Text Plus!

Gene Expression Profiling of Microsatellite Unstable and Microsatellite Stable Endometrial Cancers … - all 3 versions »
JI Risinger, GL Maxwell, GVR Chandramouli, O … - Cancer Research, 2005 - AACR
... BRB Array tools ver. 3.0c, Richard Simon, Amy Peng, Biometric research branch, National
Cancer Institute, NIH; http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 13 - Related Articles - Web Search - Full-Text Plus!

Differential gene alteration among hepatoma cell lines demonstrated by cDNA microarray-based … - all 4 versions »
K Kawaguchi, M Honda, T Yamashita, Y Shirota, S … - Biochemical and Biophysical Research Communications, 2005 - Elsevier
... BRB-Array Tools Ver. 3.1.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html) were used
to compare gene amplification in AFP-producing and AFP-negative hepatoma ...
Cited by 11 - Related Articles - Web Search - Full-Text Plus!

Unique microRNA molecular profiles in lung cancer diagnosis and prognosis - all 14 versions »
N Yanaihara, N Caplen, E Bowman, M Seike, K … - Cancer Cell, 2006 - Elsevier
... A univariate Cox proportional hazard regression model with global permutation test
in BRB-ArrayTools indicated that eight miRNAs (hsa-mir-155, hsa-mir-17-3p ...
Cited by 193 - Related Articles - Web Search

Molecular Heterogeneity of Inflammatory Breast Cancer: A Hyperproliferative Phenotype - all 3 versions »
DM Nguyen, K Sam, A Tsimelzon, X Li, H Wong, S … - Clinical Cancer Research, 2006 - AACR
... We used three software packages: dChip (http://www.dchip.org), BRB Array Tools
(http://linus.nci.nih.gov/BRB-ArrayTools.html), and Array Analyzer (http://www ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Elevated Levels of the 64-kDa Cleavage Stimulatory Factor (CstF-64) in Lipopolysaccharide-stimulated … - all 3 versions »
SA Shell, C Hesse, SM Morris Jr, C Milcarek - Journal of Biological Chemistry, 2005 - ASBMB
... was performed as described under "Materials and Methods" using BRB Array Tools
developed by the National Cancer Institute (linus.nci.nih.gov/BRB-ArrayTools.html ...
Cited by 15 - Related Articles - Web Search - Full-Text Plus! - BL Direct

 

40

Exercise responsive genes measured in peripheral blood of women with Chronic Fatigue Syndrome and … - all 7 versions »
T Whistler, JF Jones, ER Unger, SD Vernon - feedback, 2005 - biomedcentral.com
... The Class Comparison analysis method in BRB ArrayTools [24] uses this approach,
applying ... We used the Gene Ontology comparison module of BRB Array tools [24] as ...
Cited by 12 - Related Articles - Cached - Web Search - Full-Text Plus!

Differential Gene Expression Profiles in Stage I Primary Biliary Cirrhosis - all 3 versions »
M Honda, H Kawai, Y Shirota, T Yamashita, S Kaneko - The American Journal of Gastroenterology, 2005 - Blackwell Synergy
... Hierarchical clustering of gene expression of the patients was performed by
BRB-ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Hepatocellular carcinoma in HCV-infected patients awaiting liver transplantation: Genes involved in … - all 3 versions »
VR Mas, DG Maluf, R Stravitz, CI Dumur, B Clark, C … - Liver Transplantation, 2004 - doi.wiley.com
... we created 3 expression-value data sets for every pool of samples, which were then
converted by taking loga- rithms of base 2 using BRB ArrayTools version 3.0.2 ...
Cited by 13 - Related Articles - Web Search - Full-Text Plus!

A Paradigm for Class Prediction Using Gene Expression Profiles - all 8 versions »
MD Radmacher, LM McShane, R Simon - Journal of Computational Biology, 2002 - liebertonline.com
... value is closer to C 2 . Compound covariate prediction is implemented in BRB ArrayTools,
a visualization and statistical analysis software package for ...
Cited by 119 - Related Articles - Web Search - BL Direct

Molecular profiling of malignant peritoneal mesothelioma identifies the ubiquitin–proteasome … - all 5 versions »
AC Borczuk, GCA Cappellini, HK Kim, M Hesdorffer, … - Oncogene, 2007 - nature.com
... agglomerative hierarchical clustering within BRB array tools (developed by Richard
Simon and Amy Peng Lam; http://linus.nci.nih.gov/BRB-ArrayTools.html) using ...
Cited by 9 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Activation of Murine CD4+ and CD8+ T Lymphocytes Leads to Dramatic Remodeling of N-Linked Glycans - all 3 versions »
EM Comelli, M Sutton-Smith, Q Yan, M Amado, M … - The Journal of Immunology, 2006 - Am Assoc Immnol
... Unsupervised hierarchical clustering by sample was performed with BRB ArrayTools
using the default settings for correlation and linkage ( http://linus.nci.nih ...
Cited by 12 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Metastasis Predictive Signature Profiles Pre-exist in Normal Tissues - all 5 versions »
H Yang, N Crawford, L Lukes, R Finney, M Lancaster … - Clinical and Experimental Metastasis, 2005 - Springer
... normalization and statistical analysis was performed using BRB-Array Tools v3.2.0 ...
were then determined using the class prediction function of BRB ArrayTools. ...
Cited by 11 - Related Articles - Web Search - BL Direct

Identification by real-time PCR of 13 mature microRNAs differentially expressed in colorectal cancer … - all 8 versions »
E Bandres, E Cubedo, X Agirre, R Malumbres, R … - Mol Cancer, 2006 - molecular-cancer.com
...
We attempted to use the class prediction tool (BRB-Array tools) that creates a ... data,
raw data Ct was normalized and analyzed using BRB ArrayTools version 3.3.2 ...
Cited by 66 - Related Articles - Cached - Web Search - Full-Text Plus!

Human immunodeficiency virus type 1 Vpr-dependent cell cycle arrest through a mitogen-activated … - all 5 versions »
N Yoshizuka, Y Yoshizuka-Chadani, V Krishnan, SL … - J. Virol, 2005 - pubmedcentral.nih.gov
... was performed with univariate parametric and multivariate permutation tests based
on the one-sample random-variance statistic in BRB-ArrayTools (http://linus ...
Cited by 11 - Related Articles - Web Search - Full-Text Plus! - BL Direct

A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with … - all 19 versions »
XJ Ma, Z Wang, PD Ryan, SJ Isakoff, A Barmettler, … - Cancer Cell, 2004 - Elsevier
... Identification and permutation testing for significance of differential gene expression
were performed using BRB ArrayTools, developed by Richard Simon and Amy ...
Cited by 236 - Related Articles - Web Search

 

50

The gene expression profile of nodal peripheral T-cell lymphoma demonstrates a molecular link … - all 2 versions »
L de Leval, DS Rickman, C Thielen, A Reynies, YL … - Blood, 2007 - bloodjournal.hematologylibrary.org
... Univariate t tests (BRB ArrayTools v3.4.beta2, http://linus.nci.nih.gov/BRB-ArrayTools.
html) were used to define the differentially expressed gene lists with a ...
Cited by 11 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression … - all 19 versions »
A Subramanian, P Tamayo, VK Mootha, S Mukherjee, … - Proceedings of the National Academy of Sciences, 2005 - National Acad Sciences
... Home page, Bioinformatics Home page X. Xu, Y. Zhao, and R. Simon Gene Set Expression
Comparison kit for BRB-ArrayTools Bioinformatics, January 1, 2008; 24(1 ...
Cited by 551 - Related Articles - Web Search - BL Direct

GENOME-WIDE MONOCYTIC mRNA EXPRESSION IN POLYTRAUMA PATIENTS FOR IDENTIFICATION OF CLINICAL OUTCOME. - all 4 versions »
P Biberthaler, V Bogner, HV Baker, MC López, P … - Shock, 2005 - shockjournal.com
... were performed using algorithms within the software packages dChip and BRB Array
Tools (for details, see http://linus.nci.nih.gov/BRB-ArrayTools.html ) (12). ...
Cited by 13 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Analysis of gene expression profiles of hepatocellular carcinomas with regard to 18 F- … - all 3 versions »
JD Lee, M Yun, JM Lee, Y Choi, YH Choi, JS Kim, SJ … - European Journal of Nuclear Medicine and Molecular Imaging, 2004 - Springer
... al. [13] and BRB ArrayTools ver- sion 3.0 developed by Simon and Lam
(http://linus.nci.nih.gov/ BRB-ArrayTools.html). The class ...
Cited by 13 - Related Articles - Web Search - Full-Text Plus!

Gene Alterations Identified by Expression Profiling in Tumor-Associated Endothelial Cells from … - all 3 versions »
C Lu, T Bonome, Y Li, AA Kamat, LY Han, R Schmandt … - Cancer Research, 2007 - AACR
... before downstream analyses. 5 Biometric Research Branch (BRB) ArrayTools
version 3.2.2 software, developed by Drs. Richard Simon and ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene expression profiling of chemically induced rat mammary gland cancer - all 6 versions »
L Shan, M Yu, EG Snyderwine - Carcinogenesis, 2005 - Oxford Univ Press
... carcinomas could be distinguished by array tools, including hierarchical ... total intensity
normalization (50th percentile)] using BRB-ArrayTools software version ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus!

Detection of Differentially Expressed Glycogenes in Trabecular Meshwork of Eyes with Primary Open- … - all 4 versions »
S Diskin, J Kumar, Z Cao, JS Schuman, T Gilmartin, … - Investigative ophthalmology & visual science, 2006 - pubmedcentral.nih.gov
... Hierarchical clustering was preformed based on all analyzed genes using centered
correlation and average linkage with the software BRB ArrayTools 3.2.2 (http ...
Cited by 8 - Related Articles - Web Search - Full-Text Plus! - BL Direct

High-protein and high-carbohydrate breakfasts differentially change the transcriptome of human blood … - all 4 versions »
MJ van Erk, WAM Blom, B van Ommen, HFJ Hendriks - American Journal of Clinical Nutrition, 2006 - Am Soc Nutrition
... Statistical analysis to test for differences between gene expression profiles was
performed in BRB ArrayTools (software for microarray data analysis developed ...
Cited by 11 - Related Articles - Web Search - Full-Text Plus! - BL Direct

60

cDNA microarray analysis of autoimmune hepatitis, primary biliary cirrhosis and consecutive disease … - all 3 versions »
M Honda, H Kawai, Y Shirota, T Yamashita, T … - Journal of Autoimmunity, 2005 - Elsevier
... Hierarchical clustering and principal component analysis of gene expression were
performed by BRB-ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus!

Expression profiling defines a recurrence signature in lung squamous cell carcinoma - all 5 versions »
JE Larsen, SJ Pavey, LH Passmore, R Bowman, BE … - Carcinogenesis, 2007 - Oxford Univ Press
... we use Cox proportional hazards modeling, leave-one-out cross-validation (LOOCV),
and class prediction using 1-nearest neighbor (BRB ArrayTools Version 3.5 ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Abnormal Alveolar Development Associated with Elevated Adenine Nucleosides - all 5 versions »
SK Banerjee, HWJ Young, A Barczak, DJ Erle, MR … - American Journal of Respiratory Cell and Molecular Biology, 2004 - Am Thoracic Soc
... 2 Simon, R., and Peng, A. BRB-Array tools Users Guide. National Cancer Institute.
Internet address: http://linus.nci.nih.gov/BRB-ArrayTools.html period. ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene Expression Profiles of BRCA1-Linked, BRCA2-Linked, and Sporadic Ovarian Cancers - all 7 versions »
AA Jazaeri, CJ Yee, C Sotiriou, KR Brantley, J … - jnci, 2002 - jnci.oxfordjournals.org
... Statistical comparison between tumor groups was performed with BRB Array Tools software
(http://linus.nci.nih.gov/~brb/tool.htm), consisting of a modified F ...
Cited by 108 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Methamphetamine-induced gene expression profiles in the striatum of male rat pups exposed to the … - all 4 versions »
PAH Noailles, KG Becker, WH Wood, D Teichberg, JL … - Developmental Brain Research, 2003 - Elsevier
... The array data were analyzed by BRB ArrayTools (NIH/NCI). ... 3.1. Filtering and cluster
analysis.
We used BRB Array Tools software to filter the 17,000 genes. ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus!

Exquisite sensitivity of TP53 mutant and basal breast cancers to a dose-dense epirubicin- … - all 5 versions »
P Bertheau, E Turpin, DS Rickman, M Espie, A de … - PLoS Med, 2007 - medicine.plosjournals.org
... of freedom (this criterion is used in the BRB Array Tools filtering tool, described
in the user's manual [http: / /linus.nci.nih.gov /BRB-ArrayTools.html]) and ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus!

[PDF] Gene expression profiles derived from fine needle aspiration correlate with response to systemic … - all 11 versions »
C Sotiriou, TJ Powles, M Dowsett, AA Jazaeri, AL … - Breast Cancer Res, 2002 - biomedcentral.com
... Data analysis Expression profiles were analyzed with BRB Array tools, version 1.03
(Molecular ... Simon and Dr Amy Peng, who provided the BRB ArrayTools software. ...
Cited by 157 - Related Articles - View as HTML - Web Search - Full-Text Plus!

 

70

Selective deficits in the expression of striatal-enriched mRNAs in Huntington's disease. - all 4 versions »
PA Desplats, KE Kass, T Gilmartin, GD Stanwood, EL … - Journal of Neurochemistry, 2006 - pt.wkhealth.com
... Using the 'Present list' and their respective RMA expression signal values,
hierarchical clustering by sample was performed with BRB-ArrayTools software (http ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Serum Proteome to Predict Virologic Response in Patients With Hepatitis C Treated by Pegylated … - all 3 versions »
V Paradis, T Asselah, D Dargere, MP Ripault, M … - Gastroenterology, 2006 - Elsevier
... For class prediction, we used the class prediction tool from BRB-ArrayTools, version
3.1.0 (available at http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 9 - Related Articles - Web Search - Full-Text Plus!

Spontaneous differentiation of mouse embryonic stem cells in vitro: Characterization by global gene … - all 4 versions »
J Heo, JS Lee, IS Chu, Y Takahama, SS Thorgeirsson - Biochemical and Biophysical Research Communications, 2005 - Elsevier
... A data set for analysis was produced using BRB Array Tools version 3.0
(http://linus.nci.nih.gov/BRB-ArrayTools.html) from the raw data set that had been ...
Cited by 4 - Related Articles - Web Search - Full-Text Plus!

[CITATION] Independent Validation of Prognostic Relevance of a Previously Reported Gene-Expression Signature in …
G Marcucci, MD Radmacher, AS Ruppert, K Mrozek, JE … - Blood, 2005 - 2005, The American Society of Hematology
Cited by 5 - Related Articles - Web Search

Global Gene Expression Profiles During Acute Pathogen-Induced Pulmonary Inflammation Reveal … - all 4 versions »
NG Sandler, MM Mentink-Kane, AW Cheever, TA Wynn - The Journal of Immunology, 2003 - Am Assoc Immnol
... Image analysis was performed using GeneSpring (Silicon Genetics, Redwood City, CA),
BRB Array Tools (Biometric Research Branch, National Cancer Institute), and ...
Cited by 63 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Brain pH has a significant impact on human postmortem hippocampal gene expression profiles - all 3 versions »
S Mexal, R Berger, CE Adams, RG Ross, R Freedman, … - Brain Research, 2006 - Elsevier
User Name: Password: Remember me on this computer, Forgotten password? ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus!

Influence of BrpA on Critical Virulence Attributes of Streptococcus mutans - all 6 versions »
ZT Wen, HV Baker, RA Burne - Journal of Bacteriology, 2006 - Am Soc Microbiol
... array tools (version 3.01, developed by Richard Simon and Amy Peng Lam, National
Cancer Institute, Bethesda, MD; http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 8 - Related Articles - Web Search - BL Direct

Emphysema lung tissue gene expression profiling - all 4 versions »
HA Golpon, CD Coldren, MR Zamora, GP Cosgrove, MD … - American Journal of Respiratory Cell and Molecular Biology, 2004 - Am Thoracic Soc
... was further analyzed with BRB ArrayTools v2.1d1 developed by Dr. Richard
Simon and Amy Tan. Gene Ontology analysis was conducted ...
Cited by 39 - Related Articles - Web Search - Full-Text Plus!

Molecular Profiling Improves Diagnoses of Rejection and Infection in Transplanted Organs - all 4 versions »
A Morgun, N Shulzhenko, A Perez-Diez, RVZ Diniz, … - Circulation Research, 2006 - Am Heart Assoc
... Analyses of the remaining data were performed using BRB ArrayTools (version 3.0)
developed by Dr Richard Simon and Amy Peng Lam (http://linus.nci.nih.gov/BRB ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus!

Alterations of Gene Expression in the Development of Early Hyperplastic Precursors of Breast Cancer - all 7 versions »
S Lee, D Medina, A Tsimelzon, SK Mohsin, S Mao, Y … - American Journal of Pathology, 2007 - ASIP
... BRB Array Tools software (http://linus.nci.nih.gov/BRB-ArrayTools.html) was used
for pathway comparisons using the functional class scoring analysis algorithm ...
Cited by 7 - Related Articles - Web Search - BL Direct

 

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 Adaptive Signature Design - all 5 versions »
B Freidlin, R Simon - Clinical Cancer Research, 2005 - linus.nci.nih.gov
... in press).
Predictive Classifiers in BRB-ArrayTools. Classifiers: ... Radmacher;
Sudhir Varma; Yingdong Zhao; BRB-ArrayTools Development Team.
Cited by 20 - Related Articles - View as HTML - Web Search - Full-Text Plus! - BL Direct

Human T-Cell Leukemia Virus Type 1 Integration Target Sites in the Human Genome: Comparison with Those … - all 4 versions »
D Derse, B Crise, Y Li, G Princler, N Lum, C … - Journal of Virology, 2007 - Am Soc Microbiol
... BRB-arrayTools 3.3.0 software (http://linus.nci.nih.gov/BRB-ArrayTools.
html) was used to cluster viral integration site profiles. ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Membrane Composition Changes and Physiological Adaptation by Streptococcus mutans Signal Recognition … - all 7 versions »
A Hasona, K Zuobi-Hasona, PJ Crowley, J Abranches, … - Journal of Bacteriology, 2007 - Am Soc Microbiol
... A statistical analysis was carried out using BRB array tools (http://linus.nci.nih.
gov/BRB-ArrayTools.html) with a cutoff P value of 0.01 for class prediction ...
Cited by 7 - Related Articles - Web Search - BL Direct

Identification of carboxypeptidase E and γ-glutamyl hydrolase as biomarkers for pulmonary … - all 3 versions »
P He, L Varticovski, ED Bowman, J Fukuoka, JA … - Human Pathology, 2004 - Elsevier
... which is part of the microarray analysis software BRB-ArrayTools, version 3.0 ... We
used the class comparison within BRB array tools to compare fold expression of ...
Cited by 17 - Related Articles - Web Search - Full-Text Plus!

cDNA microarray profiling of rat mammary gland carcinomas induced by 2-amino-1-methyl-6- … - all 4 versions »
L Shan, M He, M Yu, C Qiu, NH Lee, ET Liu, EG … - Carcinogenesis, 2002 - Oxford Univ Press
... BRB Array Tools analysis further confirmed that 21 clones showed statistically
significance differences in expression between PhIP- and DMBA-induced carcinomas ...
Cited by 39 - Related Articles - Web Search - Full-Text Plus! - BL Direct

A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells - all 6 versions »
JS Lee, J Heo, L Libbrecht, IS Chu, P Kaposi-Novak … - Nature Medicine, 2006 - nature.com
... To select genes that were differentially expressed between two groups of tissues,
we used a class-comparison tool in BRB ArrayTools (v3.2) as a method for the ...
Cited by 55 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Molecular Signatures in Biopsy Specimens of Lung Cancer - all 8 versions »
AC Borczuk, L Shah, GDN Pearson, KL Walter, L Wang … - American Journal of Respiratory and Critical Care Medicine, 2004 - Am Thoracic Soc
... Analyses were performed with BRB ArrayTools (version 3.01; R. Simon and AP Lam,
National Cancer Institute, Bethesda, MD) (17, 18) and with the Maximum ...
Cited by 29 - Related Articles - Web Search - BL Direct

Gene expression correlates of unexplained fatigue - all 6 versions »
T Whistler, R Taylor, RC Craddock, G Broderick, N … - Pharmacogenomics, 2006 - Future Medicine
... fatigue, physical fatigue, mental fatigue, motivation reduction and activity reduction
using quantitative trait analysis performed with BRB Arraytools v3.30 ...
Cited by 7 - Related Articles - Web Search

Overexpression of folate binding protein and mesothelin are associated with uterine serous carcinoma - all 3 versions »
LA Dainty, JI Risinger, C Morrison, GVR … - Gynecologic Oncology, 2007 - Elsevier
... BRB Array tools software (BRB Array tools ver. 3.0c, Richard Simon, Amy Peng, Biometric
research branch, NCI, NIH, http://linus.nci.nih.gov/BRB-ArrayTools.html ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus!

 

90

Molecular profiling of platinum resistant ovarian cancer - all 3 versions »
J Helleman, MP Jansen, PN Span, IL van Staveren, … - Int J Cancer, 2006 - doi.wiley.com
... Data analysis and statistics Data analysis was done with BRB-Array Tools v2.1d1
(http:// linus.nci.nih.gov/BRB-ArrayTools.html), Significance Analysis of ...
Cited by 30 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Genes for systemic vascular complications are differentially expressed in the livers of Type 2 … - all 4 versions »
T Takamura, M Sakurai, T Ota, H Ando, M Honda, S … - Diabetologia, 2004 - Springer
... of numbers and frequencies of genes or Cy5:Cy3 ratios, we used supervised analyses
with the permuta- tion-based method (BRB-ArrayTools, http://linus.nci.nih.gov ...
Cited by 17 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Tcl1 Expression in Chronic Lymphocytic Leukemia Is Regulated by miR-29 and miR-181 - all 4 versions »
Y Pekarsky, U Santanam, A Cimmino, A Palamarchuk, … - Cancer Research, 2006 - AACR
... To identify statistically significant differentially expressed microRNA, class
prediction analyses were done using BRB ArrayTools developed by Dr. Richard Simm ...
Cited by 49 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Enrichment of low molecular weight fraction of serum for MS analysis of peptides associated with … - all 3 versions »
E Orvisky, SK Drake, BM Martin, M Abdel-Hamid, HW … - Proteomics, 2006 - doi.wiley.com
... These functions were per- formed in BRB-ArrayTools 3.1 software (NCI, Bethesda,
MD, USA ... the HCC cases and controls by random variance t-test (BRB Array Tools 3.1 ...
Cited by 17 - Related Articles - Web Search - Full-Text Plus! - BL Direct

[PDF] Gene expression in blood changes rapidly in neutrophils and monocytes after ischemic stroke in … - all 5 versions »
Y Tang, H Xu, X Du, L Lit, W Walker, A Lu, R Ran, … - J Cereb Blood Flow Metab, 2006 - med.stanford.edu
... were significantly regulated between different time points after stroke (5 versus
3 h, 24 versus 5 h), a class comparison tool (BRB-Array Tools 2.0, developed ...
Cited by 28 - Related Articles - View as HTML - Web Search - Full-Text Plus! - BL Direct

Host Cell Gene Expression during Human Immunodeficiency Virus Type 1 Latency and Reactivation and … - all 6 versions »
V Krishnan, SL Zeichner - Journal of Virology, 2004 - Am Soc Microbiol
... was performed with univariate parametric and multivariate permutation tests based
on the one-sample random variance t statistic in BRB-ArrayTools (http://linus ...
Cited by 28 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Quantitative gene expression in Budd-Chiari syndrome: a molecular approach to the pathogenesis of … - all 8 versions »
V Paradis, I Bieche, D Dargere, D Cazals-Hatem, I … - British Medical Journal, 2005 - gut.bmj.com
... ArrayTools Ver.3.1.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html) was ... A three
dimensional scaling plot was performed using the 35 genes and BRB array tools. ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Different Roles of EIIABMan and EIIGlc in Regulation of Energy Metabolism, Biofilm Development, and … - all 4 versions »
J Abranches, MM Candella, ZT Wen, HV Baker, RA … - Journal of Bacteriology, 2006 - Am Soc Microbiol
... Statistical analysis was carried out using BRB array tools (http://linus.nci.
nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001. ...
Cited by 18 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene Set Expression Comparison kit for BRB-ArrayTools - all 4 versions »
X Xu, Y Zhao, R Simon - Bioinformatics, 2008 - Oxford Univ Press
... The Gene Set Expression Comparison kit is developed as a module of BRB-ArrayTools. ...
Simon RM, et al. Analysis of gene expression data using BRB-Array Tools. ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Study design considerations in clinical outcome research of lung cancer using microarray analysis - all 3 versions »
P Yang, Z Sun, MC Aubry, F Kosari, W Bamlet, C … - Lung Cancer, 2004 - Elsevier
... The MAS5, MBEI PM, and MBEI PM/MM data created in the pre-process step were analyzed
directly in Dchip or imported into Dchip (MAS5), BRB ArrayTools 3.0.2 ...
Cited by 12 - Related Articles - Web Search - Full-Text Plus!

100

Molecular Characterization of the Acute Inflammatory Response to Infections with Gram-Negative … - all 8 versions »
RJ Feezor, C Oberholzer, HV Baker, D Novick, M … - Infection and Immunity, 2003 - iai.highwire.org
... The hybridization signal intensities of the genes passing the initial expression
filter were analyzed (in part) with BRB Array Tools 3.01 (developed by Richard ...
Cited by 50 - Related Articles - Web Search - BL Direct

Comparative Proteomic Analysis of Intra-and Interindividual Variation in Human Cerebrospinal Fluid* … - all 3 versions »
Y Hu, JP Malone, AM Fagan, RR Townsend, DM … - Molecular & Cellular Proteomics, 2005 - ASBMB
... BRB Arraytools (linus.nci.nih.gov/BRB-ArrayTools.html) were used for multidimensional
scaling analysis. Euclidean distance was used to measure similarity. ...
Cited by 19 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Increased Expression of Metallothionein Is Associated with Irinotecan Resistance in Gastric Cancer - all 5 versions »
JH Chun, HK Kim, E Kim, IH Kim, JH Kim, HJ Chang, … - Cancer Research, 2004 - AACR
... present’ (P) Affymetrix Microarray Analysis Suite (MAS) detection calls in all 16
samples (B). Clustering was performed by BRB-ArrayTools software (National ...
Cited by 19 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Bayesian hierarchical error model for analysis of gene expression data - all 7 versions »
HJ Cho, JK Lee - Bioinformatics, 2004 - Oxford Univ Press
... on such within-gene ANOVA modeling for identify- ing microarray expression patterns
under multiple conditions (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 20 - Related Articles - Web Search - Full-Text Plus! - BL Direct

BRCA1-mediated repression of select X chromosome genes - all 10 versions »
AA Jazaeri, GVR Chandramouli, O Aprelikova, UA … - Journal of Translational Medicine, 2004 - translational-medicine.com
... Statistical comparison between tumor groups was performed with the "BRB Array Tools"
software http://linus.nci.nih.gov/~brb/tool.htm webcite, consisting of a ...
Cited by 9 - Related Articles - Cached - Web Search - Full-Text Plus!

DNA microarray analysis of the correlation between gene expression patterns and acquired resistance … - all 4 versions »
HK Kim, IJ Choi, HS Kim, JH Kim, E Kim, IS Park, … - Biochemical and Biophysical Research Communications, 2004 - Elsevier
... The preprocessed data were then subjected to unsupervised clustering and supervised
classification analyses using the BRB-ArrayTools version 3.0 (Molecular ...
Cited by 14 - Related Articles - Web Search - Full-Text Plus!

Analysis of proteome and transcriptome of tumor necrosis factor Æ stimulated vascular smooth muscle … - all 3 versions »
WG Jang, HS Kim, KG Park, YB Park, KH Yoon, SW Han … - Proteomics, 2004 - doi.wiley.com
... Analyses were performed using Cluster developed by Eisen [16] and BRB ArrayTools
developed by Simon and Peng (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Statistical Issues in the Design and Analysis of Gene Expression Microarray Studies of Animal Models - all 6 versions »
LM McShane, JH Shih, AM Michalowska - Journal of Mammary Gland Biology and Neoplasia, 2003 - Springer
Page 1. Journal of Mammary Gland Biology and Neoplasia, Vol. 8, No. 3, July 2003 (
C 2003) Statistical Issues in the Design and Analysis of Gene ...
Cited by 15 - Related Articles - Web Search - BL Direct

Expression profiling of mucinous tumors of the ovary identifies genes of clinicopathologic … - all 5 versions »
FW Wamunyokoli - The Womenʼs Oncology Review, 2006 - informaworld.com
... DOI: 10.1080/14733400600674227 Page 2. (BRB ArrayTools). Faint spots and
spots present in 550% of the experiments were excluded. . ...
Cited by 15 - Related Articles - Web Search - Full-Text Plus! - BL Direct

110

A Gene Expression Signature Associated with Metastatic Outcome in Human Leiomyosarcomas - all 3 versions »
YF Lee, M John, A Falconer, S Edwards, J Clark, P … - Cancer Research, 2004 - AACR
... BRB-ArrayTools (Biometric Research Branch, National Cancer Institute, Bethesda,
MD) was used for class comparison analyses (univariate F test/two-sample t test ...
Cited by 25 - Related Articles - Web Search - Full-Text Plus! - BL Direct

HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL … - all 2 versions »
J Soulier, E Clappier, JM Cayuela, A Regnault, M … - Blood, 2005 - bloodjournal.hematologylibrary.org
... on the quantile-normalized data using dChip1.3 (http://biosun1.harvard.edu/complab/
dchip/) and BRB (http://linus.nci.nih.gov/BRB-ArrayTools.html) software, as ...
Cited by 48 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Valproic acid blood genomic expression patterns in children with epilepsy-a pilot study. - all 5 versions »
Y Tang, TA Glauser, DL Gilbert, AD Hershey, MD … - Acta Neurologica Scandinavica, 2004 - pt.wkhealth.com
... To determine if there was an expression profile in blood corresponding to a particular
phenotype, the class comparison tool in BRB-Array Tools 2.0 (developed ...
Cited by 26 - Related Articles - Web Search - Full-Text Plus! - BL Direct

 

120

Endothelial monocyte activating polypeptide-II induced gene expression changes in endothelial cells - all 3 versions »
AT Tandle, C Mazzanti, HR Alexander, DD Roberts, … - Cytokine, 2005 - Elsevier
... expression (0 h) vs. expression at 0.5, 1, 2, 4 and 8 h were drawn on 8382
genes using BRB Array Tools (Fig. 2). The lines indicate ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus!

Gene expression profiling of ATP-binding cassette (ABC) transporters as a predictor of the … - all 3 versions »
S Park, C Shimizu, T Shimoyama, M Takeda, M Ando, … - Breast Cancer Research and Treatment, 2006 - Springer
... the random variance t-test to data using the BRB Array Tools and was ... gene expression
profiles, we used the class prediction tools of BRB ArrayTools in which ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Development of a Highly Specialized cDNA Array for the Study and Diagnosis of Epithelial Ovarian … - all 3 versions »
GP Sawiris, CA Sherman-Baust, KG Becker, C Cheadle … - Cancer Research, 2002 - AACR
... Silicon Genetics, San Carlos, CA). All of the MDS analyses were performed
using BRB ArrayTools developed previously (15) . RESULTS. ...
Cited by 86 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Inflammatory gene signature in ulcerative colitis with cDNA macroarray analysis - all 5 versions »
S Okahara, Y Arimura, T Yabana, K Kobayashi, A … - Alimentary Pharmacology & Therapeutics, 2005 - Blackwell Synergy
... 3.2.1 (http://linus.nci.nih.gov/BRB-ArrayTools.html) with the following parameters ...
t-test and SAM in our analyses were performed using BRB-ARRAY TOOLS v3.2.1 ...
Cited by 13 - Related Articles - Web Search - Full-Text Plus!

High Frequency of Loss of Heterozygosity in Imprinted, Compared with Nonimprinted, Genomic Regions … - all 4 versions »
MS Sarquis, F Weber, L Shen, CE Broelsch, SM … - Journal of Clinical Endocrinology & Metabolism, 2006 - Endocrine Soc
... 2. Multidimensional scaling function of the BRB Array Tools software package,
visualizing the ... developed by Li and Wong and the BRB ArrayTools developed by Dr ...
Cited by 9 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Isolation and Angiogenesis by Endothelial Progenitors in the Fetal Liver - all 5 versions »
S Cherqui, SM Kurian, O Schussler, JA Hewel, JR … - Stem Cells, 2006 - stemcells.com
... We used RMA Express for signal normalization [25], BRB ArrayTools for class comparisons
(http://linus.nci.nih.gov/BRB-ArrayTools.html), and Cluster/TreeView ...
Cited by 12 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Analysis of gene expression in Egr-1 transfected human fibrosarcoma cells - all 3 versions »
YG Liu, J Gano, R Huang, Y Lin, SM Wang, RP Huang - Journal of Surgical Oncology, 2002 - doi.wiley.com
... using the Pathway2.01softwarepackage(www.resgen.com).Scatter plots and Pearson’s
correlation were analyzed using the BRB ArrayTools software package 2.0 ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus! - BL Direct

MicroRNA Expression Profiles Associated With Prognosis and Therapeutic Outcome in Colon … - all 3 versions »
AJ Schetter, SY Leung, JJ Sohn, KA Zanetti, ED … - JAMA, 2008 - Am Med Assoc
... ray tools 3.5.0 (http://linus.nci.nih.gov /BRB-ArrayTools.html) for ... Class prediction
algo- rithms in BRB array tools were used to determine whether microRNA ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Multiple Gene Expression Classifiers from Different Array Platforms Predict Poor Prognosis of … - all 3 versions »
YH Lin, J Friederichs, MA Black, J Mages, R … - Clinical Cancer Research, 2007 - AACR
... Multigene classifiers and cross-validation Classifiers based solely on gene expression
information were constructed using the BRB Array Tools package. ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus! - BL Direct

 

130

Differential expression of Rac1 identifies its target genes and its contribution to progression of … - all 3 versions »
T Gómez del Pulgar, E Bandrés, C Espina, F Valdés … - International Journal of Biochemistry and Cell Biology, 2007 - Elsevier
... The BRB-ArrayTools software (http://linus.nci.nih.gov/BRBArrayTools.html), an
integrated package for the visualization and statistical analysis of cDNA ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus!

Evaluation of normalization methods for microarray data - all 7 versions »
T Park, SG Yi, SH Kang, SY Lee, YS Lee, R Simon - feedback, 2004 - biomedcentral.com
... Software for intensity dependent normalization is available on desktop packages
such as BRB-ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools and via the ...
Cited by 78 - Related Articles - Cached - Web Search - Full-Text Plus!

Identification of a plasma proteomic signature to distinguish pediatric osteosarcoma from benign … - all 3 versions »
Y Li, TA Dang, J Shen, L Perlaky, J Hicks, J … - Proteomics, 2006 - doi.wiley.com
... 681) identified by Ciphergen Express 3.0 software (background subtracted and normalized)
were log 2 trans- formed and imported to BRB ArrayTools 3.01 developed ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Ischemic and Nephrotoxic Acute Renal Failure are Distinguished by their Broad Transcriptomic … - all 3 versions »
PST Yuen, SK Jo, MK Holly, X Hu, RA Star - Physiological Genomics, 2006 - Am Physiological Soc
... Differences between treatment groups was assessed using 1- and 2-variable ANOVA
(Partek), and BRB ArrayTools (http://linus.nci.nih.gov/BRB- Page 8. ...
Cited by 11 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene-expression profiling and array-based CGH classify CD4+ CD56+ hematodermic neoplasm and … - all 3 versions »
R Dijkman, R van Doorn, K Szuhai, R Willemze, MH … - Blood, 2007 - bloodjournal.hematologylibrary.org
... Normalization of the data and analysis of the gene-expression patterns were done
using BRB ArrayTools v3.3.0 11 and the DNA Chip Analyzer, 12,13 and results ...
Cited by 8 - Related Articles - Web Search - Full-Text Plus! - BL Direct

[PDF] Bioinformatics and whole genome technologies - all 2 versions »
R Simon - linus.nci.nih.gov
... by biologists.
BRB-Array Tools is also intended as a tool for helping
to educated ... 2.Simon R, Peng A. BRB-ArrayTools Users Guide. ...
Cited by 2 - Related Articles - View as HTML - Web Search

Identification of Tumor-Specific Molecular Signatures in Intracranial Ependymoma and Association … - all 4 versions »
P Modena, E Lualdi, F Facchinetti, J Veltman, JF … - Journal of Clinical Oncology, 2006 - jco.ascopubs.org
... class comparison analyses to identify differentially imbalanced clones according
to clinicopathologic criteria, using the BRB ArrayTools software (http://linus ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus!

Novel candidate targets of Wnt/β-catenin signaling in hepatoma cells - all 3 versions »
HS Lee, MH Park, SJ Yang, KC Park, NS Kim, YS Kim, … - Life Sciences, 2007 - Elsevier
... the normalized M values, we applied hierarchical clustering analysis using Cluster
and TreeView (Eisen et al., 1998), and, then, the BRB-ArrayTools Version 3.1 ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus!

Different signaling pathways in the livers of patients with chronic hepatitis B or chronic hepatitis … - all 4 versions »
M Honda, T Yamashita, T Ueda, H Takatori, R … - Hepatology, 2006 - doi.wiley.com
... 1124 HONDA ET AL. HEPATOLOGY, November 2006 Page 4. rayTools (http://linus.
nci.nih.gov/BRB-ArrayTools.htm). The filtered data were ...
Cited by 5 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Alpha-Fetoprotein Controls Female Fertility and Prenatal Development of the Gonadotropin-Releasing … - all 6 versions »
C De Mees, JF Laes, J Bakker, J Smitz, B Hennuy, P … - Molecular and Cellular Biology, 2006 - pubmedcentral.nih.gov
... All data were then collected by BRB 3.1 software, developed by Richard Simon and
Amy Peng Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 12 - Related Articles - Web Search - BL Direct

140

Transcriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida - all 3 versions »
P Gong, X Guan, LS Inouye, Y Deng, M Pirooznia, EJ … - BMC Genomics, 2008 - biomedcentral.com
... the control and the treated groups was performed using the BRB Array Tools version
3.6.0 beta_2 release (http://linus.nci.nih.gov/BRB-ArrayTools.html webcite). ...
Cited by 2 - Related Articles - Cached - Web Search

Gene Expression Profiling of Primary Cutaneous Melanoma and Clinical Outcome - all 8 versions »
V Winnepenninckx, V Lazar, S Michiels, P Dessen, M … - jnci, 2006 - jnci.oxfordjournals.org
... The default gene selection procedure from BRB ArrayTools was used, in which the
sequences that were differentially expressed at a statistical significance ...
Cited by 41 - Related Articles - Web Search - BL Direct

Interrelation between polyploidization and megakaryocyte differentiation: a gene profiling approach - all 3 versions »
H Raslova, A Kauffmann, D Sekkai, H Ripoche, F … - Blood, 2007 - bloodjournal.hematologylibrary.org
... The class prediction option of BrB ArrayTools software, version 3.2 (http://linus.
nci.nih.gov/BRB-ArrayTools.html), was applied to discover genes that best ...
Cited by 11 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene expression profiling of mouse postnatal cerebellar development using oligonucleotide … - all 3 versions »
FI Smith, Q Qu, SJ Hong, KS Kim, TJ Gilmartin, SR … - Gene Expression Patterns, 2005 - Elsevier
... In order to identify specific genes differentially expressed between classes, we
performed a class comparison analysis using BRB-ArrayTools 3.1.0 software. ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus!

Microarray analysis of gene expression associated with extrapulmonary dissemination of tuberculosis - all 4 versions »
DK KIM, GM PARK, YI HWANG, HJ KIM, SK HAN, YS SHIM … - Respirology, 2006 - Blackwell Synergy
... with CLUSTER (http://rana.lbl.gov/EisenSoftware.htm) and the results were visualized
with the BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Differential modulation of gene expression in the NMDA postsynaptic density of schizophrenic and … - all 3 versions »
S Mexal, M Frank, R Berger, CE Adams, RG Ross, R … - Molecular Brain Research, 2005 - Elsevier
... BRB ArrayTools version 3.0.1 (http://linus.nci.nih.gov/BRB-ArrayTools.html) was
utilized to perform 5000 random permutations of the normalized microarray data ...
Cited by 15 - Related Articles - Web Search - Full-Text Plus!

Quality prediction of cell substrate using gene expression profiling - all 3 versions »
J Han, RL Farnsworth, JL Tiwari, J Tian, H Lee, P … - Genomics, 2006 - Elsevier
... subjected to a scatter-plot analysis. BRB-Array/Tools were utilized to compare
various phenotype classes. The average log ratio of gene ...
Cited by 4 - Related Articles - Web Search - Full-Text Plus!

Gene Expression Profiling of Acute Myeloid Leukemia with Translocation t (8; 16)(p11; p13) and MYST3 … - all 3 versions »
M Camos, J Esteve, P Jares, D Colomer, M Rozman, N … - Cancer Research, 2006 - AACR
... significant differences in their expression level among different AML categories,
we used a random-variance F test as described in BRB ArrayTools software (BRB ...
Cited by 13 - Related Articles - Web Search - Full-Text Plus! - BL Direct

cDNA microarray and bioinformatic analysis of nuclear factor-kappaB related genes in squamous cell … - all 4 versions »
Z Chen, TL Lee, XP Yang, G Dong, A Loercher, C Van … - Cancer Genomics and Proteomics: Methods and Protocols - Springer
... of the data from the hierarchical clustering was performed using BRB-Array Tools
2.0 (NCI ...
Gene Data Commercial http://www.genedata.com/ BRB Arraytools NCI/NIH ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus! - BL Direct

11q22. 3 deletion in B-chronic lymphocytic leukemia is specifically associated with bulky … - all 5 versions »
JD Dickinson, J Gilmore, J Iqbal, W Sanger, JC … - Leukemia and Lymphoma, 2006 - informaworld.com
... Quantitative trait analysis (BRB Array Tools, developed by Simon and Lom, NCI, NIH,
Bethesda, MD version 3.2) was then performed to identify genes whose ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus! - BL Direct

 

150

Analysis of microarray experiments for pulmonary fibrosis - all 4 versions »
NB Dave, N Kaminski - Methods Mol Med, 2005 - Springer
... GEDA www.bioinformatics.upmc.edu/GE2/GEDA.html XX Cancer Institute NCI/Biometric
Research BRB Array www.linus.nci.nih.gov/BRB-ArrayTools.html XX X Branch Tools ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Epigenetic Inactivation of the HOXA Gene Cluster in Breast Cancer - all 4 versions »
P Novak, T Jensen, MM Oshiro, RJ Wozniak, M … - Cancer Research, 2006 - AACR
... Normalized log 2 ratios were analyzed using BRB ArrayTools 6 to find CpG ... between
normal and cancerous tissues were identified using BRB array tools with a ...
Cited by 9 - Related Articles - Web Search - Full-Text Plus! - BL Direct

The Pep4p vacuolar proteinase contributes to the turnover of oxidized proteins but PEP4 … - all 3 versions »
M Marques, D Mojzita, MA Amorim, T Almeida, S … - Microbiology, 2006 - Soc General Microbiol
... Statistical analysis of the microarray data was performed by using BRB ArrayTools
(version 3.3.0 beta1) developed by Richard Simon and Amy Peng Lam (http ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus! - BL Direct

The Nuclear Receptor Coactivator AIB1 Mediates Insulin-like Growth Factor I-induced Phenotypic … - all 3 versions »
A Oh, HJ List, R Reiter, A Mani, Y Zhang, E Gehan, … - Cancer Research, 2004 - AACR
... such that the median log intensity of each of the eight arrays is equal to the median
log intensity for the reference array (BRB array tools arbitrarily choose ...
Cited by 29 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with … - all 3 versions »
JC Chang, EC Wooten, A Tsimelzon, SG Hilsenbeck, … - The Lancet, 2003 - Elsevier
... We eliminated genes that were not present in at least 30% of samples, and exported
expression data for the remaining 6849 genes to BRB Arraytools version 2.1c ...
Cited by 409 - Related Articles - Web Search - Full-Text Plus!

Hepatic triglyceride contents are genetically determined in mice: results of a strain survey - all 5 versions »
X Lin, P Yue, Z Chen, G Schonfeld - American Journal of Physiology- Gastrointestinal and Liver …, 2005 - Am Physiological Soc
... Further analysis was performed by using BRB-Array Tools (version 3.1, http://linus.
nci.nih.gov/BRB-ArrayTools.html) according to the instructions provided. ...
Cited by 5 - Related Articles - Web Search - Full-Text Plus!

Molecular Classification of Parathyroid Neoplasia by Gene Expression Profiling - all 5 versions »
C Morrison, W Farrar, J Kneile, N Williams, Y Liu- … - American Journal of Pathology, 2004 - ASIP
... Acknowledgements. We thank Dr. Richard Simon and Amy Peng for developing the BRB
ArrayTools used during the performance of analyses. Footnotes. ...
Cited by 8 - Related Articles - Web Search - BL Direct

Apoptotic Signaling Pathways Induced by Nitric Oxide in Human Lymphoblastoid Cells Expressing Wild- … - all 3 versions »
CQ Li, AI Robles, CL Hanigan, LJ Hofseth, LJ … - Cancer Research, 2004 - AACR
... We used the BRB Array Tools software developed by the Biometric Research ... analyses
of microarray experiments were performed using BRB ArrayTools developed by Dr ...
Cited by 33 - Related Articles - Web Search - Full-Text Plus! - BL Direct

 

160

Delineation of a 1Mb breakpoint region at 1p13 in Wilms tumors by fine-tiling oligonucleotide array … - all 2 versions »
R Natrajan, RD Williams, A Grigoriadis, A Mackay, … - Genes Chromosomes Cancer, 2007 - doi.wiley.com
... Data were filtered and normalized using BRB ArrayTools (http://linus.nci.nih.gov/
BRB- ArrayTools.html), and annotated with a custom Perl script (available from ...
Cited by 5 - Related Articles - Web Search - Full-Text Plus! - BL Direct

A new paradigm for profiling testicular gene expression during normal and disturbed human … - all 5 versions »
C Feig, C Kirchhoff, R Ivell, O Naether, W Schulze … - Molecular Human Reproduction, 2007 - Oxford Univ Press
... Using BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html), which calls
compiled Fortran code for speed, extensive permutation analysis was first ...
Cited by 4 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Expression Profiling of PeripheralBlood Mononuclear Cells from Patients with Chronic Hepatitis C … - all 4 versions »
M Tateno, M Honda, T Kawamura, H Honda, S Kaneko - The Journal of Infectious Diseases, 2007 - UChicago Press
... Hierarchical clustering of gene expression in patients was performed using
BRB
ArrayTools software (version 3.3.0; available at: http://linus.nci.nih.gov/BRB ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature … - all 3 versions »
L De Cecco, L Marchionni, M Gariboldi, JF Reid, MS … - Oncogene, 2004 - nature.com
... randomized variance model and FDR correction using BRB Array Tools (McShane et ... and
class comparison analysis were performed using BRB ArrayTools (developed by ...
Cited by 25 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Preliminary evidence of mitochondrial dysfunction associated with post-infective fatigue after acute … - all 8 versions »
SD Vernon, T Whistler, B Cameron, IB Hickie, WC … - BMC Infect Dis, 2006 - biomedcentral.com
... The Class Comparison analyses were performed using BRB ArrayTools [17] developed
by Dr. Richard Simon and Amy Peng Lam to determine if gene expression profiles ...
Cited by 9 - Related Articles - Cached - Web Search

Gingival Epithelial Cell Transcriptional Responses to Commensal and Opportunistic Oral Microbial … - all 5 versions »
Y Hasegawa, JJ Mans, S Mao, MC Lopez, HV Baker, M … - Infection and Immunity, 2007 - Am Soc Microbiol
... the initial expression filters and were correlated using BRB Array Tools (R. Simon ...
set of differentially expressed genes (P < 0.001, BRB ArrayTools) with the ...
Cited by 5 - Related Articles - Web Search - BL Direct

Blood Gene Expression Profiling of Neurologic Diseases A Pilot Microarray Study - all 5 versions »
Y Tang, DL Gilbert, TA Glauser, AD Hershey, FR … - Archives of Neurology, 2005 - Am Med Assoc
... As an internal means of validation, we performed permutation analysis (BRB ArrayTools;
developed by Richard Simon, DSc, and Amy Peng Lam), which determines the ...
Cited by 32 - Related Articles - Web Search - Full-Text Plus!

Met-regulated expression signature defines a subset of human hepatocellular carcinomas with poor … - all 6 versions »
P Kaposi-Novak, JS Lee, L Gomez-Quiroz, C … - J Clin Invest, 2006 - pubmedcentral.nih.gov
... between groups of Met KO and Cre-control hepatocyte samples were identified by a
multivariate permutation t test using the BRB ArrayTools 3.3 software package ...
Cited by 19 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Gene Expression Profiles in Peripheral Lymphocytes by Arsenic Exposure and Skin Lesion Status in a … - all 4 versions »
M Argos, MG Kibriya, F Parvez, F Jasmine, M … - Cancer Epidemiology Biomarkers & Prevention, 2006 - AACR
... All analyses were done using BRB ArrayTools version 3.3.0 Beta 2 (49). ... [Abstract/
Free Full Text]; Simon R, Lam A. BRB ArrayTools User Guide, version 3.3.
...
Cited by 6 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Using bioinformatics and genome analysis for new therapeutic interventions - all 3 versions »
DW Mount, R Pandey - Molecular Cancer Therapeutics, 2005 - AACR
... BRB-array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html), SAM (http://www-
stat.stanford.edu/~tibs/SAM/), and GeneCluster (http://www.broad.mit.edu/cancer ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus!

 

170

Slow and Fast Fiber Isoform Gene Expression Is Systematically Altered in Skeletal Muscle of the Sox6 … - all 3 versions »
N Hagiwara, B Ma, A Ly - development, 2005 - doi.wiley.com
... GenBank accession numbers listed in the table correspond to those listed by Affymetrix.
Fold changes and p-values were calculated by BRB Array Tools. ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Comparative proteomic and transcriptomic profiling of the human hepatocellular carcinoma - all 3 versions »
H Minagawa, M Honda, K Miyazaki, Y Tabuse, R … - Biochemical and Biophysical Research Communications, 2007 - Elsevier
... data. Hierarchical clustering of gene expression was done with BRB-ArrayTools
(http://linus.nci.nih.gov/BRB-ArrayTools.htm). The ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus!

Effects of Oxygen on Virulence Traits of Streptococcus mutans - all 3 versions »
SJ Ahn, ZT Wen, RA Burne - Journal of Bacteriology, 2007 - Am Soc Microbiol
... Statistical analysis was carried out with BRB array tools (http://linus.nci.
nih.gov/BRB-ArrayTools.html/) with a cutoff P value of 0.001. ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Independent confirmation of a prognostic gene-expression signature in adult acute myeloid leukemia … - all 3 versions »
MD Radmacher, G Marcucci, AS Ruppert, K Mrozek, SP … - Blood, 2006 - bloodjournal.hematologylibrary.org
... Cambridge, MA). The log 2 MBEIs were exported to BRB-ArrayTools v3.2.3 (National
Cancer Institute, Bethesda, MD) for further analysis. ...
Cited by 20 - Related Articles - Web Search - BL Direct

MicroRNA expression profiles of esophageal cancer - all 3 versions »
A Feber, L Xi, JD Luketich, A Pennathur, RJ … - The Journal of Thoracic and Cardiovascular Surgery, 2008 - Elsevier
... gene analysis among the groups, and prediction analysis of microarray (PAM) were
performed with the National Cancer Insitute BRB-ArrayTools Version 3.4 (BRB ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus!

[PDF] Transcriptional profiling reveals evidence for signaling and oligodendroglial abnormalities in the … - all 5 versions »
C Aston, L Jiang, BP Sokolov - Molecular Psychiatry, 2005 - mcrcr4.med.nyu.edu
... 29 was calculated using BRB ArrayTools (http://linus.nci.- nih.gov/BRB-ArrayTools.
html), with a confidence level of false discovery rate assessment of 95%). ...
Cited by 36 - Related Articles - View as HTML - Web Search - Full-Text Plus!

Npr1-regulated gene pathways contributing to cardiac hypertrophy and fibrosis - all 3 versions »
LJ Ellmers, NJA Scott, J Piuhola, N Maeda, O … - Journal of Molecular Endocrinology, 2007 - Soc Endocrinology
... by the statistical software BRB Array Tools (Biometric Research Branch, National
Cancer Institute, MD, USA, http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus!

[PDF] MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia - all 2 versions »
R Garzon, S Volinia, CG Liu, C Fernandez-Cymering, … - Blood, 2008 - bloodjournal.hematologylibrary.org
... subtracted; log2 transformed and normalized using a set of housekeeping genes (Table
S1) and the BRB Array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html ...
Cited by 3 - Related Articles - View as HTML - Web Search - Full-Text Plus!

CD34 expression on murine marrow-derived mesenchymal stromal cells: impact on neovascularization - all 2 versions »
I Copland, K Sharma, L Lejeune, N Eliopoulos, D … - Experimental Hematology, 2008 - Elsevier
... Data sets on each GeneChip were then imported into BRB ArrayTools version 3.2.2,
developed by Dr. Richard Simon and Amy Peng Lam (http://linus.nci.nih.gov/BRB ...
Cited by 3 - Related Articles - Web Search - Full-Text Plus!

Bulky lymphadenopathy with poor clinical outcome is associated with ATM downregulation in B-cell … - all 3 versions »
AD Joshi, JD Dickinson, GV Hegde, WG Sanger, JO … - Cancer Genetics and Cytogenetics, 2007 - Elsevier
... The GenePix microarray data files of all B-CLL patients were collated and further
analyzed using BRB ArrayTools software (US National Cancer Institute ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus!

 

180

Gene Expression Profiling of Breast Cancer - all 2 versions »
MCU Cheang, M van de Rijn, TO Nielsen - Annual Review of Pathology: Mechanisms of Disease - Annual Reviews
... harvard.edu/complab/dchip/) and BRB ArrayTools (http://linus.nci.nih.gov/BRB-
ArrayTools.html). 70 Cheang · van de Rijn · Nielsen Page 5. ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus!

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data - all 8 versions »
JM Vaquerizas, L Conde, P Yankilevich, A Cabezon, … - Nucleic Acids Res, 2005 - Oxford Univ Press
... There are also different initiatives such as BASE (30), Bioconductor (31) and BRB
tools (http://linus.nci.nih.gov/BRB-ArrayTools.html), but these are in some ...
Cited by 50 - Related Articles - Web Search

Radiation-Induced Changes in Gene-Expression Profiles for the SCC VII Tumor Cells Grown In Vitro and … - all 2 versions »
JA Cook, EY Chuang, MH Tsai, D Coffin, W Degraff, … - Antioxidants & Redox Signaling, 2006 - liebertonline.com
... after radiation at which mRNA was col- lected were 0, 1, 3, 6, 12, and 24 h. Analyses
were performed by using BRB ArrayTools, developed by Dr. Richard Simon ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Isc1p Plays a Key Role in Hydrogen Peroxide Resistance and Chronological Lifespan through Modulation … - all 2 versions »
T Almeida, M Marques, D Mojzita, MA Amorim, RD … - Molecular Biology of the Cell, 2008 - Am Soc Cell Biol
... Statistical analysis of the microarray data was performed by using BRB ArrayTools
(version 3.3.0 beta 1) developed by Dr. Richard Simon and Amy Peng Lam (http ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus!

Parallel analysis of transcript and translation profiles: identification of metastasis-related … - all 4 versions »
H Yang, LR Yu, M Yi, DA Lucas, L Lukes, M … - Journal of proteome research, 2006 - pubmedcentral.nih.gov
... were processed using the RMA function of the BRB-ArrayTools ver 3.2.0. Normalization
and statistical analysis were performed using the BRB-Array Tools (8, 9 ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus!

Selection of control genes for quantitative RT-PCR based on microarray data - all 4 versions »
N Shulzhenko, A Yambartsev, A Goncalves-Primo, M … - Biochemical and Biophysical Research Communications, 2005 - Elsevier
... Differentially expressed genes (manuscript submitted) were revealed using BRB
ArrayTools (version 3.0) developed by Dr. Richard Simon and Amy Peng. ...
Cited by 6 - Related Articles - Web Search - Full-Text Plus!

Analysis of gene expression in Lassa virus-infected HuH-7 cells - all 4 versions »
S Muller, R Geffers, S Gunther - Journal of General Virology, 2007 - Soc General Microbiol
... ACKNOWLEDGEMENTS. Analyses were performed using BRB ArrayTools developed by Dr Richard
Simon and Amy Peng Lam. We thank Andreas Dotzauer for providing HAV. ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus! - BL Direct

The Porphyromonas gingivalis clpB gene is involved in cellular invasion in vitro and virulence in … - all 4 versions »
L Yuan, PH Rodrigues, M Belanger, W Dunn, A … - FEMS Immunology & Medical Microbiology, 2007 - Blackwell Synergy
... automatically discarded. Final statistical analysis was carried out using BRB
array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html). A ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus!

Functional and genomic implications of global gene expression profiles in cell lines from human … - all 3 versions »
J Lee… - Hepatology, 2002 - doi.wiley.com
... 2,3,13 The mul- tidimensional scaling (MDS) was performed using BRB ArrayTools,
which was developed by Richard Simon and his colleagues in the Biometric ...
Cited by 60 - Related Articles - Web Search - Full-Text Plus! - BL Direct

 

190

Expression Patterns of a2, 3 Sialyltransferases and a1, 3 Fucosyltransferases Determine the Mode of … - all 2 versions »
JR Brown, MM Fuster, JD Esko - Journal of Biological Chemistry - ASBMB
... performed with the software BRB ArrayTools (http://linus.nci.nih.gov/BRB-
ArrayTools.html) developed by Dr. Richard Simon and Amy Peng at ...
Cited by 2 - Related Articles - Web Search

Gene expression and functional evidence of epithelial-to-mesenchymal transition in papillary thyroid … - all 4 versions »
V Vasko, AV Espinosa, W Scouten, H He, H Auer, S … - Proceedings of the National Academy of Sciences, 2007 - National Acad Sciences
... central tumor groups and central–invasive groups were performed with BRB Array Tools
software (http://linus.nci.nih.gov/BRB-ArrayTools.html) consisting of a ...
Cited by 15 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Identification of Novel Genes Regulated by Chorionic Gonadotropin in Baboon Endometrium during the … - all 3 versions »
JRA Sherwin, AM Sharkey, P Cameo, PM Mavrogianis, … - Endocrinology, 2007 - Endocrine Soc
... data analyses were performed using Biometric Research Branch Array Tools developed
by ... Treatment and Diagnosis) (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 9 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Effects of Globin mRNA Reduction Methods on Gene Expression Profiles from Whole Blood - all 4 versions »
J Liu, E Walter, D Stenger, D Thach - Journal of Molecular Diagnostics, 2006 - ASIP
... scaling of gene expression data were performed in Arraytools 3.3.0 beta 3a developed
by Richard Simon and Amy Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html ...
Cited by 9 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Distinctive characteristics of transcriptional profiles from two epithelial cell lines upon … - all 5 versions »
JJ Mans, HV Baker, D Oda, RJ Lamont, M Handfield - Oral Microbiology and Immunology, 2006 - Blackwell Synergy
... raw signal intensities were log-transformed for all probe-sets that passed the initial
expression filters and were correlated using BRB Array Tools (Simon and ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Identification of expressed genes characterizing long-term survival in malignant glioma patients - all 3 versions »
R Yamanaka, T Arao, N Yajima, N Tsuchiya, J Homma, … - Oncogene, 2006 - nature.com
... normalization and survival analysis were performed using the BRB Array Tools software
ver. 3.3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html) developed by Dr ...
Cited by 10 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Role of RelA of Streptococcus mutans in Global Control of Gene Expression - all 3 versions »
MM Nascimento, JA Lemos, J Abranches, VK Lin, RA … - Journal of Bacteriology, 2008 - Am Soc Microbiol
... Statistical analysis was carried out by using BRB ArrayTools (http://linus.
nci.nih.gov/BRB-ArrayTools.html) with a P value of 0.001. ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus!

The effect of chronic exposure to highly aggressive mice on hippocampal gene expression of non- … - all 3 versions »
DEM Feldker, MC Morsink, AH Veenema, NA Datson, V … - Brain Research, 2006 - Elsevier
... downregulated.
Both the ANOVA/FDR and the class comparison analyses from
the BRB ArrayTools package confirmed this finding. All ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus!

Effects of Co-administration of Antioxidants and Arsenicals on the Rat Urinary Bladder Epithelium - all 6 versions »
M Wei, L Arnold, M Cano, SM Cohen - Toxicological Sciences, 2005 - Soc Toxicology
... One-sample t-test was performed using BRB ArrayTools developed by Dr. Richard Simon
and Amy Peng Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html) to identify ...
Cited by 5 - Related Articles - Web Search - Full-Text Plus!

Survival prediction of stage I lung adenocarcinomas by expression of 10 genes - all 3 versions »
F Bianchi, P Nuciforo, M Vecchi, L Bernard, L … - Journal of Clinical Investigation, 2007 - Am Soc Clin Investig
... Analyses of gene expression data were performed using BRB ArrayTools version
3.3.1 (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 5 - Related Articles - Web Search - Full-Text Plus! - BL Direct

 

200

Genomics and microarrays
M Sarwal, F Alemi - Measuring Immunity: Basic Biology and Clinical Assessment, 2005 - books.google.com
... R: Statistics for microarray analysis Cluster and Treeview (Eisen Lab) Xcluster
(Sherlock lab, Stanford) BRB Array Tools (NIH informatics ... gov/BRB-ArrayTools. ...
Cited by 1 - Related Articles - Web Search

GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology - all 5 versions »
J Zhu, J Wang, Z Guo, M Zhang, D Yang, YH Li, D … - BMC Genomics, 2007 - pubmedcentral.nih.gov
... Entrez Gene) respectively, of which 318 and 3388 are differentially expressed genes
(DEGs) identified by t-test with FDR 1%, calculated by BRB ArrayTools [22]. ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus!

Informatics-assisted Protein Profiling in a Transgenic Mouse Model of Amyotrophic Lateral Sclerosis - all 3 versions »
TJ Lukas, WW Luo, H Mao, N Cole, T Siddique - Molecular & Cellular Proteomics, 2006 - ASBMB
... Microarray data were analyzed with BRB ArrayTools developed by Dr. Richard Simon
and Amy Peng Lam (Biometric Research Branch, NCI, National Institutes of Health ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus! - BL Direct

CpG-mediated changes in gene expression in murine spleen cells identified by microarray analysis - all 2 versions »
S Klaschik, I Gursel, DM Klinman - Molecular Immunology, 2007 - Elsevier
... the mAdb database (Microarray Database, a collaboration of CIT/BIMAS and NCI/CCR
at the NIH) and formatted via the export function for use with BRB ArrayTools. ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus!

Baseline Gene Expression Predicts Sensitivity to Gefitinib in Non-Small Cell Lung Cancer Cell Lines - all 3 versions »
CD Coldren, BA Helfrich, SE Witta, M Sugita, R … - Molecular Cancer Research, 2006 - AACR
... training set were used for classification of these 28 cell lines based on six different
prediction algorithms employed in BRB-ArrayTools: compound covariate ...
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Gene expression profiles are influenced by ISS, MOF, and clinical outcome in multiple injured … - all 3 versions »
V Bogner, C Kirchhoff, HV Baker, JC Stegmaier, LL … - Langenbeck's Archives of Surgery, 2007 - Springer
... were calculated using algorithms of the software packages dChip and BRB Array Tools
(for details, see: http://www.linus.nci.nih.gov/BRB-ArrayTools.html, [8]). ...
Cited by 4 - Related Articles - Web Search - Full-Text Plus! - BL Direct

A method for computing the overall statistical significance of a treatment effect among a group of … - all 5 versions »
R Delongchamp, T Lee, C Velasco - feedback, 2006 - biomedcentral.com
... 15.
Simon R, Lam AP: BRB Array-Tools User's Guide, Version 3.3: (National Cancer
Institute Biometric Research Branch, Bethesda, MD) Technical Report. ...
Cited by 9 - Related Articles - Cached - Web Search - Full-Text Plus!

Celecoxib Treatment Alters the Gene Expression Profile of Normal Colonic Mucosa - all 3 versions »
OK Glebov, LM Rodriguez, P Lynch, S Patterson, H … - Cancer Epidemiology Biomarkers & Prevention, 2006 - AACR
... Several multivariate classification methods available in BRB ArrayTools 3.2 (compound
covariate predictor, diagonal linear discriminant analysis, nearest ...
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Mect1-Maml2 Fusion Oncogene Linked to the Aberrant Activation of Cyclic AMP/CREB Regulated Genes - all 3 versions »
A Coxon, E Rozenblum, YS Park, N Joshi, J … - Cancer Research, 2005 - AACR
... Statistical analyses were done using the BRB ArrayTools Version 3.2.0 (BRB-Array
Tools Users Guide, version 3.2; R. Simon and A. Peng Lam, Biometric Research ...
Cited by 13 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, … - all 7 versions »
ET Hayes, JC Wilks, P Sanfilippo, E Yohannes, DP … - BMC Microbiology, 2006 - pubmedcentral.nih.gov
... The gene expression profiles of the arrays were visualized in two-dimensional
Euclidian space, by using BRB ArrayTools software. ...
Cited by 11 - Related Articles - Web Search

 

210

FGF is essential for both condensation and mesenchymal–epithelial transition stages of pronephric … - all 3 versions »
AE Urban, X Zhou, JM Ungos, DW Raible, CR Altmann, … - Developmental Biology, 2006 - Elsevier
... Analysis of responses was performed using BRB ArrayTools developed by Richard Simon
and Amy Peng (http://www.linus.nci.nih.gov/BRB-ArrayTools.html). ...
Cited by 7 - Related Articles - Web Search - Full-Text Plus!

BRB-ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing …
Y Zhao, R Simon - Cancer Informatics - doaj.org
... Title: BRB-ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and
Efficient Data Sharing Resource. Author: Yingdong Zhao ; Richard Simon. ...
Cached - Web Search

Molecular signatures of eight thyroid tumor types
NB Prasad, Y Wang, CB Umbricht, SK Libutti, MA … - Proceedings of the American Association for Cancer Research, 2006 - aacrmeetingabstracts.org
... MO 63141) and BRB Array Tools, a statistical package developed by Biometric Research
Branch, NCI/NIH (http://linus.nci.nih.gov/BRB-ArrayTools.html).ANOVA test ...
Web Search

[PDF] A bioinformatic workbench for the analysis of microarray data based on open source software and …
M Mutarelli, G Colonna, A Facchiano - crisceb.unina2.it
... tigr.org/software) - the BRB Array Tools package from the Biometric Research Branch
(BRB) of the NCI (http://linus.nci.nih.gov/BRB-ArrayTools.html) - GenMAPP ...
Related Articles - View as HTML - Web Search

Comparison of longitudinal leukocyte gene expression after burn injury or trauma-hemorrhage in mice - all 3 versions »
JA Lederer, BH Brownstein, MC Lopez, S MacMillan, … - Physiological Genomics, 2008 - Am Physiological Soc
... tools and the time series algorithms implemented in BRB Array Tools developed by
Richard Simon and Amy Peng Lam (http://linus.nci.nih.gov/BRB-ArrayTools). ...
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[PDF] Heterogeneous gene expression changes in colorectal cancer cells share the WNT pathway in response …
B Humar - dovepress.com
... A low stringency data analysis approach using BRB array tools coupled with QPCR ... bythe
Kegg and Biocarta pathway data bases), BRB-ArrayTools’ ‘path- way ...
View as HTML - Web Search

Identification of Candidate KLF4 Target Genes Reveals the Molecular Basis of the Diverse Regulatory …
S Swamynathan, J Davis, J Piatigorsky - Investigative Ophthalmology & Visual Science, 2008 - ARVO
... Methods: Expression of more than 22,000 genes in 10 WT and Klf4CN corneas was compared
by microarrays, analyzed using BRB ArrayTools and validated by Q-RT-PCR. ...
Web Search

 

220

[CITATION] Comprehensive expression profiling yields some clues as to the cell of origin of osteosarcoma- …
GE Mason, R Yang, R Sowers, JH Healey, AG Huvos, … - AACRMTG, 2006 - American Association for Cancer Research
Web Search

Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller …
B Wan - SAR and QSAR in Environmental Research, 2008 - informaworld.com
... ArrayTools (Version 3.5.0; available at: http://linus.nci.nih.gov/BRB-ArrayTools.
html). O S CH 3 CH 3 N 1-MA ... [18] and class comparison (BRB-ArrayTools). ...
Web Search - BL Direct

A Review of:“Design and Analysis of DNA Microarray Investigations”
J Hardin - Journal of Biopharmaceutical Statistics, 2005 - informaworld.com
... Appendix C gives an introduction to the software (BRB-ArrayTools) used by the
authors to analyze microarray data. Many of the techniques ...
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Finding Fibrosis Genes - all 2 versions »
LH Burch, DA Schwartz - Fibrosis Research: Methods And Protocols, 2005 - Springer
... download. BRB ArrayTools are compatible with an Excel format, which is convenient
for most users. 1.5. Perform Your Own Microarray Study ...
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[CITATION] Comparison of Different Microarray Affymetrix Data Pre-Processing Methods
M Gedil, H Ressom
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[CITATION] Metastatic gastric adenocarcinomas do not exhibit previously reported metastasis-specific gene …
L Paon, KR Cummins, N Rainov, L Pazmany, PG … - AACRMTG, 2004 - American Association for Cancer Research
Web Search

[CITATION] Molecular determinants for transfection efficiency of siRNA lipofection
M Takeda, T Arao, H Kimura, T Shimoyama, N Hayama, … - AACRMTG, 2005 - American Association for Cancer Research
Web Search

Elevated levels of the 64-kDa cleavage stimulatory factor (CstF-64) in LPS-stimulated macrophages … - all 2 versions »
SA Shell, C Hesse, SM Morris Jr, C Milcarek - Journal of Biological Chemistry - ASBMB
... by BRB-ArrayTools v3.02 (http://linus.nci.nih.gov/BRB- ArrayTools.html ... random variance
for each calculation (Class Comparison feature of BRB Array Tools), and 3 ...
Related Articles - Web Search

Differential gene expression in cumulus cells as a prognostic indicator of embryo viability: a … - all 3 versions »
A van Montfoort, JPM Geraedts, J Dumoulin, APM … - Molecular Human Reproduction, 2008 - Oxford Univ Press
... over- or underexpression of the remaining probe sets in one of the two groups was
analysed using the class comparison method in BRB ArrayTools software package ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus!

 

230

BIOINFORMATICS - all 2 versions »
LM McShane, MD Radmacher, B Freidlin, R Yu, MC Li, … - Bioinformatics, 2002 - Oxford Univ Press
... specimens. Availability: Software to implement these methods is contained in
BRB ArrayTools microarray analysis package available Page 3. ...
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Interaction of cellular-localized signature modules in response to prostate cancer
Z Jing, G Zheng, Z Min, Y Da, W Jang, W Chenguang -
自然 科学 进展: 英文 , 2007 - 维普资讯
... P
value0001 and the false discovery rate01calculated by BRB
Array
Tools(httpㄩㄞㄞlinusncinihgovBRBArrayToolshtm1)1 ...
Web Search

Cytoprotection of human endothelial cells from menadione cytotoxicity by caffeic acid phenethyl …
X Wang, S Stavchansky, B Zhao, JA Bynum, SM Kerwin … - European Journal of Pharmacology, 2008 - Elsevier
... treatment groups was performed using BRB Array Tools (Biometric Research Branch,
National Cancer Institute, USA, http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Web Search

[CITATION] Gene expression and cell cycle arrest in a rat keratinocyte line exposed to 56Fe ions
FJ Burns, F Wu, R Zhang, A Uddin - AACRMTG, 2006 - American Association for Cancer Research
Web
Search

 

BIOINFORMATICS
GW Wright, RM Simon - Bioinformatics, 2003 - Oxford Univ Press
... positives.
Availability: This method is incorporated into BRB-ArrayTools
version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). ...
Related Articles - Web Search

Microarray Data Analysis and Management in Colorectal Cancer
O Garcıa-Hernandez, G Lopez-Campos, JP Sanchez, R … - Springer
... of colorectal cancer patients is done using BRB-Array Tools from NCI [8 ... a group of
filters are applied using Agilent’s Feature Extraction and BRB-ArrayTools. ...
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Different modulation of cellular transcription by adenovirus 5, ΔE1/E3 adenovirus and helper- … - all 2 versions »
Y Martina, D Avitabile, S Piersanti, G Cherubini, … - Virus Research, 2007 - Elsevier
... normalization (Bolstad et al., 2003) and BRB Array Tools for class comparisons
(http://linus.nci.nih.gov/BRB-ArrayTools.html). The BRB Array Tools used for ...
Web Search - Full-Text Plus!

[PDF] BMC Genomics
M Steinau, DR Lee, MS Rajeevan, SD Vernon, MT … - BMC Genomics, 2005 - bmc.ub.uni-potsdam.de
... (1) BRB Array Tools 3.2 http://linus.nci.nih.gov/BRB- ArrayTools: Log 2 transformed
sARM values were normal- ized over the median of each array and subjected
...
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Bromodomain 4 activation predicts breast cancer survival
NPS Crawford, J Alsarraj, L Lukes, RC Walker, JS … - Proceedings of the National Academy of Sciences, 2008 - National Acad Sciences
... 5.0.0.03 [EC] 2. Normalization was performed with the BRB-Array Tools software
(27 ... expression from breast cancer datasets was performed by using BRB ArrayTools. ...
Web Search - BL Direct

[PDF] Statistically Sound Distribution Plots in Excel - all 2 versions »
G Vidmar - mf.uni-lj.si
... 7 eg, commercial Miner3D TM (http://www.miner3d.com) and freeware VisuLab
(http://www.inf.ethz.ch/personal/hinterbe/Visulab) 8 eg,
BRB ArrayTools (http:// ...
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240

Selective deficits in the expression of striatal-enriched mRNAs in Huntington’s disease
SR Head, JG Sutcliffe, EA Thomas - Journal of Neurochemistry, 2006 - ingentaconnect.com
... the ‘Present list’ and their respective RMA expression signal values, hierarchical
clustering by sample was performed with BRB-ArrayTools software (http ...
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A Novel Ensemble Decision Tree Approach for Mining Genes Coding Ion Channels for Cardiopathy Subtype - all 2 versions »
J Zhang, X Li, W Jiang, Y Wang, C Li, Q Wang, S … - LECTURE NOTES IN COMPUTER SCIENCE, 2005 - Springer
... The selected data set including measures for all the genes is standardized using
the BRB-ArrayTools Version 3.0.1(Dr. Richard Simon, Biometrics Research Branch ...
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TOXICOLOGY INFORMATION/LINKS TOXNET http://toxnet. nlm. nih. gov/index. html
HK Hamadeh, RP Amin - doi.wiley.com
... BRB ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools.html BRB ArrayTools is
an integrated package for the visualization and statistical ...
Web Search

A Genetic Switch, Phage Lambda Revisited. M. Ptashne. Cold Spring Harbor Laboratory Press. 2004. 154 …
GW BLAKELY - Genetics Research, 2005 - Cambridge Univ Press
... authors (Appendix C). A great asset of this book is that all the example data are
freely available for analysis, along with the BRB-ArrayTools software (http ...
Web Search

Chronic treatment with aripiprazole induces differential gene expression in the rat frontal cortex - all 3 versions »
MC Cheng, DL Liao, CA Hsiung, CY Chen, YC Liao, CH … - The International Journal of Neuropsychopharmacology, 2007 - Cambridge Univ Press
... The signal data were subjected to further analysis using BRB-ArrayTools v3.4, which
was developed by Dr Richard Simon and Amy Peng Lam (available from http ...
Cited by 1 - Related Articles - Web Search - Full-Text Plus! - BL Direct

Identifying disease feature genes based on cellular localized gene functional modules and regulation … - all 6 versions »
M Zhang, J Zhu, Z Guo, X Li, D Yang, L Wang, S Rao - Chinese Science Bulletin, 2006 - Springer
... Each microarray is standardized to zero median across the measured genes using BRB
ArrayTools software (http://linus.nci.nih.gov/BRB-ArrayTools.html), and then ...
Cited by 1 - Related Articles - Web Search - BL Direct

[PDF] Gene expression profiling in a rat model of flow-associated pulmonary hypertension: effects of … - all 2 versions »
ME van Albada, B Bartelds, H Wijnberg, S Mohaupt, … - Pulmonary arterial hypertension - dissertations.ub.rug.nl
... Analyses were performed using BRB ArrayTools developed by Dr. Richard Simon and
Amy Peng Lam (http:// linus. nci. nih. gov/
BRB-ArrayTools. html). ...
Related Articles - View as HTML - Web Search

Molecular analysis of colonic transformation in the ileum after total colectomy in rats - all 3 versions »
K Fukushima, S Haneda, KI Takahashi, H Ogawa, K … - Surgery, 2006 - Elsevier
... microarray analysis. Data also were analyzed with the use of BRB ArrayTools.
Quantitative reverse transcriptase-polymerase chain reaction. ...
Related Articles - Web Search - Full-Text Plus!

Classifying Breast Cancer Models - all 3 versions »
SIS BELIEVING, O SIGNATURES - The Scientist, 2002 - the-scientist.com
... transcription.
Free Software Find BRB ArrayTools and technical reports
on microarray analysis online at linus.nci.nih.gov/~brb. ...
Related Articles - Cached - Web Search

Annual Review of Pathology: Mechanisms of Disease - all 2 versions »
MCU Cheang, M van de Rijn, TO Nielsen - Annual Reviews
... software freely available for academic users includes dChip (DNA-Chip Analyzer,
http://biosun1.harvard.edu/complab/dchip/) and BRB ArrayTools (http://linus.nci ...
Web Search

 

250

Identifying disease feature genes based on cellular localized gene functional modules and regulation … - all 6 versions »
M Zhang, J Zhu, Z Guo, X Li, D Yang, L Wang, S Rao - Chinese Science Bulletin, 2006 - Springer
... Each microarray is standardized to zero median across the measured genes using BRB
ArrayTools software (http://linus.nci.nih.gov/BRB-ArrayTools.html), and then ...
Cited by 1 - Related Articles - Web Search - BL Direct

[PDF] Gene expression profiling in a rat model of flow-associated pulmonary hypertension: effects of … - all 2 versions »
ME van Albada, B Bartelds, H Wijnberg, S Mohaupt, … - Pulmonary arterial hypertension - dissertations.ub.rug.nl
... Analyses were performed using BRB ArrayTools developed by Dr. Richard Simon and
Amy Peng Lam (http:// linus. nci. nih. gov/
BRB-ArrayTools. html). ...
Related Articles - View as HTML - Web Search

Molecular analysis of colonic transformation in the ileum after total colectomy in rats - all 3 versions »
K Fukushima, S Haneda, KI Takahashi, H Ogawa, K … - Surgery, 2006 - Elsevier
... microarray analysis. Data also were analyzed with the use of BRB ArrayTools.
Quantitative reverse transcriptase-polymerase chain reaction. ...
Related Articles - Web Search - Full-Text Plus!

Classifying Breast Cancer Models - all 3 versions »
SIS BELIEVING, O SIGNATURES - The Scientist, 2002 - the-scientist.com
... transcription.
Free Software Find BRB ArrayTools and technical reports
on microarray analysis online at linus.nci.nih.gov/~brb. ...
Related Articles - Cached - Web Search

Annual Review of Pathology: Mechanisms of Disease - all 2 versions »
MCU Cheang, M van de Rijn, TO Nielsen - Annual Reviews
... software freely available for academic users includes dChip (DNA-Chip Analyzer,
http://biosun1.harvard.edu/complab/dchip/) and BRB ArrayTools (http://linus.nci ...
Web Search

Microarray-based expression profiling and informatics - all 3 versions »
R Simon - Current Opinion in Biotechnology, 2007 - Elsevier
... The BRB-ArrayTools software contains the statistical methods we have found most
appropriate and effective for the analysis of such studies [2]. The software is ...
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[PDF] ANALYZING DNA MICROARRAYS WITH UNDERGRADUATE STATISTICIANS - all 2 versions »
J Hardin, L Hoopes, R Murphy - stat.auckland.ac.nz
... The computer lab activities will be done using BRB ArrayTools (written by Richard
Simon and Amy Peng Lam, http://linus.nci.nih.gov/
BRB-ArrayTools.html), a ...
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Forum Original Research Communication
SCCVIITC Grown - Signal - liebertonline.com
... after radiation at which mRNA was col- lected were 0, 1, 3, 6, 12, and 24 h. Analyses
were performed by using BRB ArrayTools, developed by Dr. Richard Simon ...
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