Forms and Links

Secondary Analysis Software Links:

Free software:

Cyber-T home page (Institute for Genomics and Bioinformatics, UC Irvine; a statistics program with a web interface that can be conveniently used on high-dimensional array data for the identification of statistically significant differentially expressed genes; the program also contains a computational method [PPDE] for estimating experiment-wide false positive and negative levels based on the modeling of p-value distributions)

Bioconductor (Bioconductor Project; an open source set of software modules for bioinformatics designed for the analysis and comprehension of genomic data, focused primarily on DNA microarray data analysis, though many of the software tools can be used broadly for the analysis of genomic data, such as sequence or SNP data; requires the installation of R programming language)

GR’s Microarray Software Suite TM4 (A suite of open source tools consisting of four major applications designed primarily for spotted two-color arrays but can be adapted for single color; designed to capture, manage, and analyze effectively data from DNA microarray experiments)

Affymetrix Tools and Software (Affymetrix, Inc. and others; a listing of software resources to assist you in establish biological relevance through data analysis, mining, and management solutions)

Commercial software:

GeneSpringGX (Agilent Technologies; commercial software visualization and analysis program designed for use with expression data; free trial version available at website) The UCI DNA & Protein MicroArray Facility currently has a copy for use on a recharge basis.

JMP Microarray (JMP, a Division of SAS; designed for discovering meaningful patterns in array data in a statistically rigorous (SAS) manner with built-in import routines for a variety of microarray data formats)

ArrayAssist Expression Software (Stratagene; allows for typical Affymetrix workflow and primary analysis including: current probe-level analysis methods, QC reports and transformations)

Pathway Architect Software (Stratagene; allows for construction of Biological Interaction Networks for genes and proteins of interest; text mining of related literature or find pathways and GO groups enriched for in a given list of interesting genes) The UCI DNA & Protein MicroArray Facility currently has a copy for use on a recharge basis.