Data Analysis Software
There are a number of software packages and online databases that are helpful when analyzing microarray data. We present here a summary of the software we use in the core, along with some of our favorite online tools.
Analysis Software
This software is available for use by GSR Microarrays customers in our computer lab for an hourly fee. Investigators can contact GSR Microarrays microarray@vanderbilt.edu to arrange an appointment to use the software in the computer lab.
Please contact the Computational Genomics Core, CHGR if you are not familiar with the software and would like to arrange an appointment for training..
- Partek Genomics Suite - an advanced microarray analysis package for expression and genotyping
Pathway and Functional Classification Tools
- DAVID - aids in functional classification and analysis of your gene list.
- PANTHER Gene Expression Data Analysis - allows classification of genes by pathway, molecular function, or biological process. Allows pathways to be viewed in pictorial form with genes of interest highlighted. Accepts Entrez Gene IDs, Gene Symbols, RefSeq transcript and protein accession numbers, and Applied Biosystems 1700 IDs.
- WebGestalt - a web-based integrated data mining system. Can organize gene lists by Gene Ontology, tissue expression pattern, chromosome distribution, metabolic and signaling pathways, protein domain information and publications. Accepts most common identifiers, including Affymetrix IDs.
- Ingenuity Pathways Analysis - Identifies relationships, mechanisms, functions, and pathways of relevance in data. It also has resources to easily search scientific literature for genes or pathways of interest. A demo account is offered through their website which provides the fully functional software for a limited time. A per-user license may be purchased through GSR Microarrays with access available for the fiscal year (July 1-June 30).
- Acumenta Literature Lab - A text mining application that enriches gene lists by identifying significant biological and chemical terms associated with the genes as a set. This enrichment is performed in 18 biological dimensions that include diseases, pathways, chemical substances, cell lines, metabolism and cell biology. Analysis of a dataset by Literature Lab can be performed by GSR Microarrays for a fee.
Online Databases and Tools
- NCBI - the US National Center for Biotechnology Information. Home of the Entrez Gene, UniGene, and PubMed databases, among others. A useful starting point is the Cross-database search.
- EnsEMBL - provided by the European Molecular Biology Laboratory and the Sanger Institute, Ensembl provides over two dozen annotated eukaryotic genomes. The BioMART interface allows for complex online queries, and convenient programming tools are also available.
- UCSC - the University of California, Santa Cruz Genome site. Includes annotations for more than 30 genomes, as well as a BLAST-like alignment tool and a Genome Browser.
- SOURCE - at Stanford University. A unification tool - draws information from several public databases to present as complete a picture of each gene as possible. Also has a Batch interface for large-scale annotation.
- NetAffx - the Affymetrix database, includes information on every GeneChip on the market. A free login is required.
- Mouse Genome Informatics - the Jackson Laboratory's database of all things mouse.
- FatiGO or FatiGO+ - provided by the Centro de Investigacion Principe Felipe in Valencia, Spain. Finds differential distribution of ontology terms between gene lists. FatiGO is restricted solely to GO terms, while FatiGO+ includes KEGG Pathways, SwissProt keywords, and several other data sources.
- miRBase - at the Sanger Institute. miRBase is the source for micro RNA information - includes databases of sequences and predicted targets, as well as an official name registry for new miRNA genes.