T-profiler: scoring the activity of predefined groups of genes using gene expression data

被引:150
作者
Boorsma, A
Foat, BC
Vis, D
Klis, F
Bussemaker, HJ
机构
[1] Univ Amsterdam, Swammerdam Inst Life Sci Microbiol, Bioctr Amsterdam, NL-1018 WV Amsterdam, Netherlands
[2] Columbia Univ, Dept Biol Sci, New York, NY 10027 USA
[3] Columbia Univ, Ctr Computat Biol & Bioinformat, New York, NY 10032 USA
关键词
D O I
10.1093/nar/gki484
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. Here we describe T-profiler, a tool that uses the t-test to score changes in the average activity of predefined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif or location on the same chromosome. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can upload their microarray data for analysis on the web at http://www.t-profiler.org.
引用
收藏
页码:W592 / W595
页数:4
相关论文
共 28 条
[21]   FunSpec: a web-based cluster interpreter for yeast [J].
Robinson, MD ;
Grigull, J ;
Mohammad, N ;
Hughes, TR .
BMC BIOINFORMATICS, 2002, 3 (1)
[22]   REDUCE:: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data [J].
Roven, C ;
Bussemaker, HJ .
NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3487-3490
[23]   QUANTITATIVE MONITORING OF GENE-EXPRESSION PATTERNS WITH A COMPLEMENTARY-DNA MICROARRAY [J].
SCHENA, M ;
SHALON, D ;
DAVIS, RW ;
BROWN, PO .
SCIENCE, 1995, 270 (5235) :467-470
[24]  
Sharan R, 2000, Proc Int Conf Intell Syst Mol Biol, V8, P307
[25]   Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation [J].
Tamayo, P ;
Slonim, D ;
Mesirov, J ;
Zhu, Q ;
Kitareewan, S ;
Dmitrovsky, E ;
Lander, ES ;
Golub, TR .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (06) :2907-2912
[26]  
Van Helden J, 2000, YEAST, V16, P177, DOI 10.1002/(SICI)1097-0061(20000130)16:2<177::AID-YEA516>3.0.CO
[27]  
2-9
[28]   GOAL: automated Gene Ontology analysis of expression profiles [J].
Volinia, S ;
Evangelisti, R ;
Francioso, F ;
Arcelli, D ;
Carella, M ;
Gasparini, P .
NUCLEIC ACIDS RESEARCH, 2004, 32 :W492-W499