ChEA3

ChEA3 performs transcription factor enrichment analysis to identify transcription factors associated with input gene sets and to elucidate regulatory influences on gene expression.

Key Features:

• Integrated gene set libraries: Uses TF-gene co-expression data from RNA-seq, TF-target associations from ChIP-seq, and TF-gene co-occurrence from crowd-sourced gene lists as background libraries.
• Enrichment analysis: Computes enrichment of input gene sets against multiple gene-set libraries to score TF associations.
• Composite ranking system: Integrates enrichment results from varied sources to produce a composite rank for candidate TFs.
• Benchmarking: Has been evaluated against existing transcription factor prediction tools and reported improved performance.
• Functional inference: Provides information on general TF properties such as activator or repressor roles using its integrated libraries.

Scientific Applications:

• Gene regulatory network analysis: Identification of transcription factors driving observed changes in gene expression for reconstruction or interpretation of regulatory networks.
• Biological process and disease investigation: Prioritization of key TFs involved in specific biological processes or disease states based on enriched associations.
• Functional characterization of TF activity: Exploration of activation versus repression roles of TFs inferred from integrated evidence across omics-derived libraries.

Methodology:

Utilizes gene-set libraries derived from RNA-seq co-expression, ChIP-seq TF-target associations, and crowd-sourced gene lists; computes enrichment for each library and integrates those enrichment results into a composite TF ranking.