Bioinformatics Tools

Text-mining tools

Semantic Gene Organizer
Gene-set Cohesion Analysis Tool
GeneIndexer
Chilibot
ArrowSmith
GoPubMed
iHOP
String

Gene Expression tools

GeneSpring
GeneMaths
WebGestalt

Free Microarray Analysis Tools

BioConductor
By BioConductor Team
It is Primarily based on the R programming language. It aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data. Analysis packages are available for: pre-processing Affymetrix and cDNA array data.

Cleaver 1.0
By Stanford Biomedical Informatics
Classification (discriminant analysis), K-means clustering, PCA

Cluster Identification Tool (CIT)
By Van Andel Research Institute
Statistical discrimination metric and permutation analysis to identify clusters of genes or individual genes that best differentiate experimental groups.

Gene Cluster 2.0
By Whitehead Institute Centre for genome research
filter and preprocess data in a variety of ways; Self-Organizing Map; unsupervised classification by weighted voting (WV) and k-nearest neighbors (KNN) algorithms, gene selection and permutation test methods

PAM (Prediction Analysis for Microarrays)
By Tibshirani Lab; Department of Statistics, Stanford University
Performs sample classification from gene expression data, Estimates prediction error via cross-validation, Provides a list of significant genes whose expression characterizes each diagnostic class

SAM (Significance Analysis of Microarrays)
By Tibshirani Lab; Department of Statistics, Stanford University
Correlates gene expression data to a wide variety of clinical parameters including  treatment, diagnosis categories, survival time and time trends; Provides estimate of False Discovery Rate for multiple testing.