Targetfinder.org

TargetFinder.org identifies genes with expression patterns similar to a user-defined seed to prioritize candidate transcription factor targets.

Key Features:

• Expression compendium: Leverages a gene expression compendium encompassing over 1,200 experiments and more than 13,000 genes.
• Gene expression pattern matching: Generates a ranked list of genes based on the similarity of their expression patterns to those of the seed genes.
• Recovery/cross-validation test: Assesses consistency between the provided seed and the quality of the resulting gene ranking.
• Transcription factor affinity analysis: Analyzes transcription factor affinities to promoter regions of top-ranked genes to aid candidate selection.

Scientific Applications:

• Transcription factor target identification: Expand and prioritize lists of known or putative transcription factor targets based on co-expression and promoter affinity.
• Gene regulatory network exploration: Detect genes with co-expression patterns indicative of shared regulatory mechanisms or network membership.
• Experimental candidate prioritization: Select top-ranked genes for downstream experimental validation using combined expression ranking and promoter TF affinity data.

Methodology:

Leverages a gene expression compendium (>1,200 experiments, >13,000 genes); computes similarity of expression patterns between a user-defined seed and other genes to produce a ranked list; performs a recovery/cross-validation test to assess ranking consistency; and computes transcription factor affinities to promoter regions of top-ranked genes.