Gene function analysis in complex data sets using ErmineJ

Gillis, J., Mistry, M., Pavlidis, P. (2010) Gene function analysis in complex data sets using ErmineJ. Nature Protocols, 5 (6). pp. 1148-1159. ISSN 17502799 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/20539290
DOI: 10.1038/nprot.2010.78

Abstract

ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allows users to assess whether microarray data or other gene lists are enriched for a particular pathway or gene class. This protocol provides steps on how to format data files, determine analysis type, create custom gene sets and perform specific analyses-including overrepresentation analysis, genes score resampling and correlation resampling. ErmineJ differs from other methods in providing a rapid, simple and customizable analysis, including high-level visualization through its graphical user interface and scripting tools through its command-line interface, as well as custom gene sets and a variety of statistical methods. The protocol should take approximately 1 h, including (one-time) installation and setup.

Item Type: Paper
Uncontrolled Keywords: animal article biology computer interface computer program DNA microarray gene expression profiling genetic database genomics human information processing methodology statistics Animals Automatic Data Processing Computational Biology Databases, Genetic Humans Oligonucleotide Array Sequence Analysis Software User-Computer Interface
Subjects: bioinformatics > genomics and proteomics > computers
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
CSHL Authors:
Communities: CSHL labs > Gillis Lab
Depositing User: Matt Covey
Date Deposited: 04 Apr 2013 13:41
Last Modified: 04 Apr 2013 13:41
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28078

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