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Stefan Goetz, 05/28/2010 04:55 pm


Functional profiling documentation

Single enrichment analysis

FatiGO

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.

Methods - Input form - Output results

Tutorial

Marmite

Marmite stands for My Accurate Resource for MIning TExt and its aim is to provide to the research community an easy and accurate way to analyse the association between gene lists and the terms that have been found to be anyway related to their genes in PubMed documents.

Methods - Input form - Output results

Set enrichment analysis

Gene set analysis

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

Tutorial - WEB form

MarmiteScan

MarmiteScan comes out as the application of a threshold free method (FatiScan) that extracts blocks of related genes from an ordered list of genes by an associated value to the Marmite tool, a tool that finds differential distributions of bioentities extracted from PubMed between two groups of genes.

Tutorial - WEB form

GeSBAP

This is a novel web-based 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

Genecodis

Tutorial - WEB form

Tissue phenotype based profiling

Resource to extract differences between the distributions of the expression values of two groups of genes in a set of tissues. In order to improve the posibilities of your analysis and to cover most of the scope of the possible experiments users are interested in, we provide data from two type of platforms, SAGE Tags and Microarray (Affymetrix) expression data.

SAGE

Tissue phenotype profiling based on SAGE Tags.

Tutorial - WEB form

Affymetrix

Tissue phenotype profiling based on Microarray Affymetrix expression data.

Tutorial - WEB form

Blast2GO

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

Methods - Input form - Output results

SNOW

SNOW is a web-based tool that introduces protein-protein interaction data into the functional profiling of genome-scale experiments. It extracts from a list of pre-selected proteins or genes the minimal connected network (smallest network that connects all the elements of the list) that they conform in terms of physical interactions and then it evaluates its topological parameters comparing them versus same-size networks generated from random lists of genes/proteins.
Methods - Input form - Output results