> Gene Expression/Data Mining1, 2
Spotfire DecisionSite
Spotfire is a data mining and visualization software with microarray and high-throughput screening analysis capabilities. (server based client application, solaris box)
MDAP (Microarray Data Analysis Pipeline)
The Hartwell Center Microarray Data Analysis Pipeline (MDAP) is a web-based tool that provides an automated standard analysis of gene expression for two color and Affymetrix arrays. MDAP guides the user with a data input wizard and is suitable for beginners. The pipeline performs the most common statistical analysis for gene expression and emails the results back to the user in Excel format. MDAP provides log ratios, p values, and p values adjusted to minimize false discoveries. MDAP also tests data quality and provides a Quality Control (QC) report that includes diagnostic graphics, statistical tests, explanations, and recommendations. MDAP can access user data from network drives or local folders.
MDAP is recommended for analysis of two-sample control versus treated experiments as well as experiments with multiple treatments, doses or time points. For more complex analysis or if you have any general questions please contact David Finkelstein at david.finkelstein@stjude.org or Perdeep Mehta at perdeep.mehta@stjude.org for further assistance.
Users can log into MDAP with their St. Jude user name and password (the same username and password used to log into Windows, Outlook, and Enterprise system). Each user can access only their own microarray data for analysis and can store results for up to 30 days.
NetAffx
NetAffx provides the scientific community with unprecedented access to array content, including target and probe sequences, and gene annotations. (web)
HCNetDat version 2.2
HCNetDat is a DNA microarray gene annotation database. The queriable database was developed to provide St. Jude investigators with the most current gene annotation possible for genes present on commonly used Affymetrix GeneChips ™ and spotted cDNA arrays designed and produced in the Hartwell Center. HCNetDat also contains most current and validated Human-Mouse ortholog information, physical location and a Map Viewer for visual display of genes on chromosomes (currently only available for human genes) has also been added. (web)
1Please contact your Local Support Provider (LSPs) to have any of these applications installed on your system. Click on the link below for a complete listing of the LSPs and their contact information: http://www.hartwellcenter.org/bio_rescom/clientSer/contactlsp.php
2To establish an account on a computer system, please fill out the Account Request Form and return to Bioinformatics (room D1010, first floor DTRT).
