T-profiler: scoring the activity of predefined groups of genes using gene expression data
- 1 July 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (Web Server) , W592-W595
- https://doi.org/10.1093/nar/gki484
Abstract
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 .Keywords
This publication has 27 references indexed in Scilit:
- NCBI GEO: mining millions of expression profiles--database and toolsNucleic Acids Research, 2004
- Transcriptional regulatory code of a eukaryotic genomeNature, 2004
- ArrayExpress--a public repository for microarray gene expression data at the EBINucleic Acids Research, 2003
- Transcriptional Regulatory Networks in Saccharomyces cerevisiaeScience, 2002
- Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotationBioinformatics, 2000
- CLICK: a clustering algorithm with applications to gene expression analysis.2000
- Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiationProceedings of the National Academy of Sciences, 1999
- Cluster analysis and display of genome-wide expression patternsProceedings of the National Academy of Sciences, 1998
- Expression monitoring by hybridization to high-density oligonucleotide arraysNature Biotechnology, 1996
- Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA MicroarrayScience, 1995