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Jose Carbonell, 01/15/2010 01:12 pm

Functional profiling documentation

Single enrichment analysis


FatiGO takes two lists of genes (ideally a group of interest and the rest of the genes in the experiment, although any two groups, formed in any way, can be tested against each other) and convert them into two lists of GO terms using the corresponding gene-GO association table. Then a Fisher's exact test for 2×2 contingency tables is used to check for significant over-representation of GO terms in one of the sets with respect to the other one. Multiple test correction to account for the multiple hypothesis tested (one for each GO term) is applied as previously described.

Tutorial - WEB form


Extracts blocks of related genes from an ordered list of genes by an associated value to the Marmite tool.

Tutorial - WEB form

Set enrichment analysis

Gene set analysis

Implements a segmentation test which checks for asymmetrical distributions of biological labels.

Tutorial - WEB form


Resource for Gene Set Enrichment Analysis.

Tutorial - WEB form


Resource for extracting relevant information from a list of sorted human genes analysing precomputed gene-bioentity co-occurrences obtained by a text-mining software.

Tutorial - WEB form


Resource to check for pathway (or GO terms) associations to diseases (or any other trait) in genome-wide association analysis (GWAS) with SNPs or CNVs.

Tutorial - WEB form

Module enrichment analysis


Tutorial - WEB form

Tissue phenotype based profiling


Give additional information about the general phenotype transcriptional profiling of the genes selected from two steps functional enrichment analysis. For Affymetrix chips.

Tutorial - WEB form


Technique that allow serial analysis of gene expression.

Tutorial - WEB form


Tool for functional annotation of (novel) sequences and the analysis of annotation data.

Tutorial - WEB form


Tool for the statistical analysis of protein-protein interaction networks.

Tutorial - WEB form