GeneTerm Linker – Functional Analysis beyond Enrichment

GeneTerm Linker

:: DESCRIPTION

GeneTerm Linker is a new algorithm for functional annotation of a list of genes that provides a set of functional metagroups in a single output. GeneTerm Linker filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations.

::DEVELOPER

GeneTerm Linker team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Fontanillo C, Nogales-Cadenas R, Pascual-Montano A, De Las Rivas J (2011)
Functional Analysis beyond Enrichment: Non-Redundant Reciprocal Linkage of Genes and Biological Terms.
PLoS ONE 6(9): e24289. doi:10.1371/journal.pone.0024289

FunCluster 1.07 – Functional Analysis of Gene Expression data

FunCluster 1.07

:: DESCRIPTION

FunCluster is a genomic data analysis tool designed to perform a functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis allows to detect co-regulated biological processes (i.e. represented by annotating genomic themes) through a specifically designed co-clustering procedure involving biological annotations and gene expression data. FunCluster’s functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo sapiens, Mus musculus and Saccharomyces cerevisiae.

::DEVELOPER

Corneliu Henegar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R package

:: DOWNLOAD

FunCluster

:: MORE INFORMATION

Citation

Clustering biological annotations and gene expression data to identify putatively co-regulated biological processes
Henegar C, Cancello R, Rome S, Vidal H, Clement K, Zucker JD
J Bioinform Comput Biol. 2006 Aug;4(4):833-52.

GOFFA – Gene Ontology for Functional Analysis

GOFFA

:: DESCRIPTION

GOFFA is a tool developed for ArrayTrack that takes a list of genes and identifies terms in Gene Ontology (GO) associated with those genes.

::DEVELOPER

the National Center for Toxicological Research (NCTR).

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows/MacOsX
Java

:: DOWNLOAD

GOFFA

:: MORE INFORMATION

Citation

Sun, H., Fang, H., Chen, T., Perkings, R., and Tong, W.,
“GOFFA: Gene Ontology For Functional Analysis – Software for gene ontology-based functional analysis of genomic and proteomic data.”
BMC Bioinformatics, 7(Suppl 2):S23, 2006.