` Transcriptomics Analysis Tools
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Analysis Tools

Gene Annotation

Database for Annotation, Visualization and Integrated Discovery, NIAID
This set of tools provides integrated annotation and analysis of lists of GenBank Accession numbers and Affymetrix, Locus Link, or Unigene Identifiers. It also provides links to Gene ontology tools, and KEGG charts. (Web interface)

NCI Genomics and Bioinformatics Group

This tool performs extensive annotations of gene lists including also Affymetrix identifiers. (Web interface)

Gene Ontology Tools

EASE - Expression Analysis Systematic Explorer, NIAID
Gives GO annotations of gene lists with statistics adjusted for multiple comparisons to identify significantly over-represented biological functions. (Web interface and Windows)

NCI Genomics and Bioinformatics Group
GO annotations displayed in tree view or as a Directed Acyclic Graph. Statistical analysis of GO categories and integration to public databases including PubMed, Bio Carta, CGAP, GeneCards, etc. (Windows and Mac OSX)

High Throughput GoMiner, NCI Genomics and Bioinformatics Group

This is similar to GoMiner, but integrates GO information across multiple microarrays. Results can be displayed in “heatmap” or cluster format, and include statistical analyses. (Web interface or UNIX systems including OSX)

Panther Classification System

SRI International

Provides tools for protein classification and alignments, maps genes to biological processes and molecular functions. Can use gene expression levels in addition to gene lists, and overlay results on pathways. (Web interface)

Data Analysis Tools

BRB Array Tools, NCI Biometric Research Branch
This is a package for visualization and statistical analysis of DNA microarray gene expression data. Identifies genes differentially expressed in groups of experiments, builds and tests multivariate predictors for sample classification by gene expression profiles. Incorporates PCA and clustering visualization tools. (Windows – Excel Add-in)

The Cytoscape Consortium
This is a standalone platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles. Additional modules are available to provide added functionality. This can also be used as a module in geWorkBench. (Windows and Mac OSX)

SAM - Significance Analysis of Mircoarrays, Stanford University
This is a tool for statistical assessment of differential gene expression, giving false discovery rates. It is prone to miss significant changes across experiments when there are large changes, and consequently large biological variability. (Windows – Excel Add-in)

PAM - Prediction Analysis of Microarrays, Stanford University
This tool performs sample classification from gene expression data using nearest shrunken centroids. It produces lists of genes that characterize defined classes, and provides cross-validation testing and false discovery rates. (Windows – Excel Add-in)

Sample Size and Power Calculations for Microarray Studies, Mei-Ling Ting Lee
This tool may be useful for planning new array experiments based on the parameters of prior experiments with the same or similar systems. (Web interface)

Public Databases of Microarray Data

ArrayExpress, EMBL-EBI European Bioinformatics Institute




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