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[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
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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
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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
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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
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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
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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 ...
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[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 ...
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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
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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 ...
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Brain pH has a significant impact on human postmortem
hippocampal gene expression profiles - all 3 versions »
User
Name: Password: Remember me on this computer, Forgotten password? ...
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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,
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 ...
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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
80
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.
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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. ...
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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 ...
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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 ...
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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 ...
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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. ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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. ...
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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 ...
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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 ...
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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 ...
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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 Peripheral‐Blood 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,
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 ...
Cited by 16 - Related Articles - Web Search - Full-Text Plus! - BL Direct
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,
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 ...
Cited by 2 - Related Articles - Web Search - Full-Text Plus! - BL Direct
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). ...
Related Articles - Web Search - Full-Text Plus!
[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
...
Related Articles - Web Search
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 ...
Related Articles - Web Search
[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,
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.
...
Related Articles - Web Search
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 版, 2007 - 维普资讯
... P〞value≒0ㄝ001 and the false discovery rate≒0ㄝ1ㄛcalculated by BRB
Array〞Tools(httpㄩㄞㄞlinusㄝnciㄝnihㄝgovㄞBRB〞ArrayToolsㄝhtm1)ㄝ1 ...
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