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Breast Cancer
Classification and Prognosis Based on Gene Expression Profiles from a
Population-Based - Full-Text
Plus! - all
7 versions
C Sotiriou, SY Neo, LM McShane, EL Korn, PM Long, … -
Proceedings of the National Academy of Sciences of the …, 2003 - National
Acad Sciences
... Hierarchical agglomerative clustering using the statis- tical
package BRB - ARRAYTOOLS
software (available at http: linus.nci.nih.gov BRB-ArrayTools.html)
was ...
Cited
by 339 - Related
Articles - Web
Search
Methods
for assessing reproducibility of clustering patterns observed in analyses of
microarray data
- Full-Text
Plus! - 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 96 - Related
Articles - Web
Search
Molecular
Classification of Tamoxifen-Resistant Breast Carcinomas by Gene Expression
Profiling - Full-Text
Plus! - all
5 versions
MPHM Jansen, JA Foekens, IL van Staveren, MM … - Journal of
Clinical Oncology, 2005 - jco.ascopubs.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 81 - Related
Articles - Web
Search
De
Novo Kidney Transplantation Without Use of Calcineurin Inhibitors Preserves
Renal Structure and … - Full-Text
Plus! - all
9 versions
SM Flechner, SM Kurian, K Solez, DJ Cook, JT Burke … - American
Journal of Transplantation, 2004 - pt.wkhealth.com
... 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 101 - Related
Articles - Web
Search
Laser
Capture Microdissection and Microarray Expression Analysis of Lung
Adenocarcinoma Reveals … - Full-Text
Plus! - 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 79 - Related
Articles - Web
Search
Kidney
Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and
Peripheral Blood … - Full-Text
Plus! - all
6 versions
SM Flechner, SM Kurian, SR Head, SM Sharp, TC … - American
Journal of Transplantation, 2004 - pt.wkhealth.com
... 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 49 - Related
Articles - Web
Search
Expression
Profiling of Serous Low Malignant Potential, Low-Grade, and High-Grade Tumors
of the … - Full-Text
Plus! - 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 30 - Related
Articles - Web
Search
Gene expression patterns for doxorubicin
(Adriamycin) and cyclophosphamide (Cytoxan)(AC) response … - Full-Text Plus! - 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 15 - Related Articles - Web Search
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 32 - Related Articles - Web Search
Analysis of gene expression in cancer cell lines
identifies candidate markers for pancreatic … - Full-Text Plus! - 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 32 - Related Articles - Web Search
The p53 Tumor Suppressor Network Is a Key Responder
to Microenvironmental Components of Chronic … - all 4 versions
F Staib, AI Robles, L Varticovski, XW Wang, BR … - Cancer
Research, 1714 - 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 16 - Related Articles - Web Search - Full-Text Plus!
[PDF] Gene microarray analysis of peripheral blood cells
in pulmonary arterial hypertension. - Full-Text Plus! - all 7 versions
TM Bull, CD Coldren, M Moore, SM Sotto-Santiago, … - American
Journal of Respiratory and Critical Care Medicine, 2004 - 171.66.122.149
... 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 28 - Related Articles - View as HTML - Web Search
Cancer-associated molecular signature in the tissue
samples of patients with cirrhosis - Full-Text Plus! - 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 26 - Related Articles - Web Search
Evaluation of a linear amplification method for
small samples used on high-density oligonucleotide … - Full-Text Plus! - 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 19 - Related Articles - Web Search
Condensin binding at distinct and specific
chromosomal sites in the Saccharomyces cerevisiae genome - Full-Text Plus! - 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 16 - Related Articles - Web Search
Expression Profiles of Osteosarcoma That Can
Predict Response to Chemotherapy - all 3 versions
TK Man, M Chintagumpala, J Visvanathan, J Shen, L … - Cancer
Research, 985 - 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 15 - Related Articles - Web Search - Full-Text Plus!
Transcript profiling of human platelets using
microarray and serial analysis of gene expression - Full-Text Plus! - all 5 versions
DV Gnatenko, JJ Dunn, SR McCorkle, D Weissmann, PL … - Blood,
2003 - bloodjournal.hematologylibrary.org
... Microarray data were visualized and analyzed using BRB-ArrayTools
software (Version
2.1), kindly developed and provided by Dr Richard Simon and Amy Peng (linus ...
Cited by 236 - Related Articles - Web Search
Identification by Real-time PCR of 13 mature
microRNAs differentially expressed in colorectal cancer … - Full-Text Plus! - all 9 versions
E Bandrés, E Cubedo, X Agirre, R Malumbres, R … - Molecular
Cancer, 2006 - pubmedcentral.nih.gov
... samples, two multivariate permutation test provided in BRB-ArrayTools
were performed ...
attempted to use the class prediction tool (BRB-Array tools)
that creates a ...
Cited by 29 - Related Articles - Web Search
Cryptococcus neoformans Gene Expression during
Murine Macrophage Infection - Full-Text Plus! - 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 16 - Related Articles - Web Search
Analysis of Orthologous Gene Expression between
Human Pulmonary Adenocarcinoma and a Carcinogen- … - Full-Text Plus! - 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 14 - Related Articles - Web Search
20
Gene Expression Profiling of Microsatellite
Unstable and Microsatellite Stable Endometrial Cancers … - all 3 versions
JI Risinger, GL Maxwell, GVR Chandramouli, O … - Cancer
Research, 850 - 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 11 - Related Articles - Web Search - Full-Text Plus!
Signatures of differentially regulated interferon
gene expression and vasculotrophism in the … - Full-Text Plus! - 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 16 - Related Articles - Web Search - BL Direct
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 11 - Related Articles - Web Search - Full-Text Plus! - BL Direct
Lung Adenocarcinoma Global Profiling Identifies Type
II Transforming Growth Factor-{beta} Receptor … - Full-Text Plus! - 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 10 - Related Articles - Web Search
Molecular mechanisms of West Nile virus pathogenesis
in brain cell - Full-Text Plus! - 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 8 - Related Articles - Cached - Web Search
[PDF] Gene Expression Profiles in Paraffin-Embedded Core
Biopsy Tissue Predict Response to Chemotherapy in … - Full-Text Plus! - all 9 versions
L Gianni, M Zambetti, K Clark, J Baker, M Cronin, … - Journal
of Clinical Oncology, 2005 - jco.ascopubs.org
... Statistical analysis was per- formed by using the BRB-Arraytools
software package
(http:// linus.nci.nih.gov/BRB-ArrayTools.html). RESULTS ...
Cited by 97 - Related Articles - View as HTML - Web Search
Differential gene expression profiles in stage I
primary biliary cirrhosis - Full-Text Plus! - all 3 versions
M Honda, H Kawai, Y Shirota, T Yamashita, S Kaneko - Am J
Gastroenterol, 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 8 - Related Articles - Web Search
Alterations in the expression of DEAD-box and other
RNA binding proteins during HIV-1 replication - all 10 versions
V Krishnan, SL Zeichner - feedback, 2005 - retrovirology.com
... Using BRB -ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools,
the data were subjected
to statistical analyses using univariate parametric and multivariate ...
Cited by 11 - Related Articles - Cached - Web Search
Gene expression profile of cervical tissue compared
to exfoliated cells: Impact on biomarker … - all 4 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 9 - Related Articles - Cached - Web Search
Differential gene alteration among hepatoma cell
lines demonstrated by cDNA microarray-based … - Full-Text Plus! - all 3 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 7 - Related Articles - Web Search
Distinct Transcriptional Changes in Donor Kidneys
upon Brain Death Induction in Rats: Insights in … - Full-Text Plus! - all 4 versions
TA Schuurs, F Gerbens, JAB van der Hoeven, PJ … - American
Journal of Transplantation, 2004 - pt.wkhealth.com
... 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 13 - Related Articles - Web Search
[CITATION] Independent
Validation of Prognostic Relevance of a Previously Reported Gene-Expression
Signature in … - Full-Text Plus!
G Marcucci, MD Radmacher, AS Ruppert, K Mrozek, JE … - Blood,
2005 - 2005, The American Society of Hematology
Cited by 9 - Related Articles - Web Search
Unique microRNA molecular profiles in lung cancer
diagnosis and prognosis - Full-Text Plus! - all 13 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 114 - Related Articles - Web Search
The role of microRNA genes in papillary thyroid
carcinoma - all 5 versions
H He, K Jazdzewski, W Li, S Liyanarachchi, R Nagy, … - Proc
Natl Acad Sci US A, 2005 - pubmedcentral.nih.gov
... Raw data from miRNA chips were assembled by using BRB ArrayTools
(Richard Simon
and Amy Peng Lam, National Cancer Institute, Bethesda). ...
Cited by 86 - Related Articles - Web Search
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 22 - Related Articles - Web Search - Full-Text Plus!
A Paradigm for Class Prediction Using Gene
Expression Pro les - Full-Text Plus! - all 7 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 106 - Related Articles - Web Search
Downregulation in components of the mitochondrial
electron transport chain in the postmortem frontal … - Full-Text Plus! - all 5 versions
X Sun, JF Wang, M Tseng, LT Young - J Psychiatry Neurosci, 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 9 - Related Articles - Web Search - BL Direct
Elevated Levels of the 64-kDa Cleavage Stimulatory
Factor (CstF-64) in Lipopolysaccharide-stimulated … - Full-Text Plus! - all 2 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 12 - Related Articles - Web Search
A two-gene expression ratio predicts clinical
outcome in breast cancer patients treated with … - Full-Text Plus! - all 17 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 180 - Related Articles - Web Search
Human immunodeficiency virus type 1 Vpr-dependent
cell cycle arrest through a mitogen-activated … - Full-Text Plus! - all 4 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 9 - Related Articles - Web Search
40
Hepatocellular carcinoma in HCV-infected patients
awaiting liver transplantation: Genes involved in … - Full-Text Plus! - 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 9 - Related Articles - Web Search
Laparoscopic donor nephrectomy gene expression
profiling reveals upregulation of stress and ischemia … - Full-Text Plus! - all 4 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 6 - Related Articles - Web Search
Molecular profiling of malignant peritoneal
mesothelioma identifies the ubiquitin–proteasome … - Full-Text Plus! - 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 6 - |
