Functional

Tools for the functional interpretation of the genomic data:

• [Single Enrichment](Single Enrichment). Also known as FatiGO. This is the conventional enrichment test where we compare two lists of genes, usually a group of genes which are significant in a given test that are compared to the rest of the genes in the experiment, although any two groups formed in any way can be tested against each other. This approach detects significant over-representation of functional annotations (Gene Ontology terms, Interpro...) in one gene set respect to the other one. For further information on the tool please visit Single Enrichment.

• [Gene Set Enrichment](Gene Set Enrichment). Also known as FatiScan or LogisticModel. Gene set methods are much more sensitive than single enrichment methods in detecting gene sets (defined as sets of genes with a common annotation) with a collective behavior in a genomic experiment. This method very efficiently detects gene sets (functional annotations) that are consistently associated to high or low values in a ranked list of genes. For further information about these topics see Gene Set Enrichment.

• Network Enrichment. Also known as SNOW. The tool is like the conventional enrichment test where a group of genes or proteins (such as a group of gene that are differentially expressed when compared in a case/control study), is analysed to see if they represent any biological process. Network Enrichment tool (also known as SNOW) extracts and evaluates the cooperative behavior of a list of selected proteins/genes using the interactome as scaffold. The difference is that here we introduce the protein-protein interaction data into the functional profiling of genomic data. For more information see Network Enrichment.

• [Gene Set Network Enrichment](Gene Set Network Enrichment (Network Miner)). Also known as NetworkMiner. As the previous tool, this one introduces protein-protein interaction data in the functional profiling of high-throughput experiments results. The method detects gene sets (forming a protein-protein interaction subnetwork) that are consistently associated to high or low values in a ranked list of genes. For more information see Gene Set Network Enrichment .