T-profiler

T-profiler quantifies changes in the average activity of predefined gene groups from microarray gene expression data using t-tests to relate expression patterns to transcriptional programs and cellular states in Saccharomyces cerevisiae and Candida albicans.

Key Features:

• Gene Group Definition: Defines gene groups based on Gene Ontology categorization, chromatin immunoprecipitation followed by microarray (ChIP-chip) experiments, upstream matches to consensus transcription factor binding motifs, and genes co-located on the same chromosome.
• Statistical Analysis: Applies t-tests to score changes in the average activity of predefined gene groups from microarray data, enabling statistical assessment without requiring parameter selection or data combination.
• Iterative Optimization: Provides an optional iterative procedure to select an optimal representative from overlapping gene groups.
• Organism Focus: Targets analysis of gene expression in the yeast species Saccharomyces cerevisiae and Candida albicans.

Scientific Applications:

• Transcriptional Program Interpretation: Interpreting complex gene expression datasets in relation to transcriptional programs and cellular states.
• Group-Level Differential Activity Detection: Identifying significant changes in gene-group activity associated with specific biological processes or experimental conditions.
• Regulatory Network Exploration: Exploring regulatory relationships involving transcription factors and chromosomal context.

Methodology:

Gene groups are defined from Gene Ontology, ChIP-chip data, upstream consensus transcription factor binding motif matches, and chromosomal co-location; t-tests are applied to group-average expression values, with an optional iterative procedure to choose representatives from overlapping groups.