Tag: Enrichment Analysis

miRHiC 1.2 – Enrichment Analysis of miRNA Targets in Hierarchical Gene Co-expression Signatures

miRHiC 1.2

:: DESCRIPTION

miRHiC is a new method to infer the perturbed miRNA regulatory networks by using the hierarchical co-expression signatures in large-scale cancer gene expression datasets.

::DEVELOPER

Bioinformatics & Intelligent Information Processing Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Perl

:: DOWNLOAD

 miRHiC

 :: MORE INFORMATION

Citation

PLoS One. 2013 Nov 20;8(11):e81032. doi: 10.1371/journal.pone.0081032. eCollection 2013.
Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures.
Gu J, Xuan Z.

PhenoFam – Gene Set Enrichment Analysis in the Protein Domain Context

PhenoFam

:: DESCRIPTION

PhenoFam performs gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. The tool is designed to analyse complete sets of results from quantitative high-throughput studies (gene expression microarrays, functional RNAi screens, etc.) without prior pre-filtering or hits-selection steps.

::DEVELOPER

Frank Buchholz , Max Planck Institute of Molecular Cell Biology and Genetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 PhenoFam

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 May 17;11:254. doi: 10.1186/1471-2105-11-254.
PhenoFam – gene set enrichment analysis through protein structural information.
Paszkowski-Rogacz M, Slabicki M, Pisabarro MT, Buchholz F.

GENECODIS 3 – Modular and Singular Enrichment Analysis for Functional Genomics

GENECODIS 3

:: DESCRIPTION

GeneCodis is a web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology.

::DEVELOPER

the Bioinformatics initiative – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Tabas-Madrid D, Nogales-Cadenas R, Pascual-Montano A
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics.
Nucleic Acids Research 2012; doi: 10.1093/nar/gks402