Data Analysis
The core will provide a basic analysis of RNA expression data free of charge. We will perform pair-wise comparisons of sample groups and provide the user with lists of genes that are differentially expressed between the groups using VAMPIRE. These genes will be mapped to GO and KEGG pathways to aid in biological interpretation. In order for us to provide this service, users are requested to submit the Data Analysis Form listing the samples and pair-wise comparisons that they wish to perform.
For more sophisticated analyses, including different normalization options, analysis techniques, clustering, pathway mapping etc., the core can provide assistance for $90 per hour, or on an occasional collaborative basis.
The Core has software allowing users to perform their own analyses. This includes the GeneChip® Operating Software (GCOS) which enables researchers to perform gene expression, SNP mapping and resequencing analysis. With the GCOS platform, data can be extracted from individual chips, or between two chips using probe-level, pair-wise comparisons. Data can be transferred to other Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip® DNA Analysis Software (GDAS) to establish biological relevance of the data.
The Core has two floating licenses to Agilent/Silicon Genetics GeneSpring. This software provides very useful statistical, filtering and visualization tools for microarray data that is MIAME compliant. The statistical tests include t-tests, 2-way ANOVA tests and 1-way post-hoc tests for identifying differentially expressed genes. GeneSpring also contains class prediction tools to identify genes capable of discriminating between one or more experimental parameters or sample phenotypes. Clustering options inlcude: gene trees (hierarchical clustering), experiment trees, self-organizing maps, k-means, Principal Components Analysis (PCA) and QT clustering. The software allows 3D Data Visualization with in-depth and interactive representations of highly complex data. Sixteen transformations are available for flexible normalization options. These normalization steps can be applied in virtually any order and include operations such as dye swapping experiments and median polishing. In the Pathway Viewer, genes and their expression patterns can be visually characterized based on their location within a cellular pathway using either custom pathway diagrams or publicly available pathway maps.
The Core also has a single floating license to Genego.MetaCore. MetaCore is a comprehensive suite for data analysis solutions for Microarrays. This software integrates interactive data visualization, mapping and exchange and multiple networking algorithms. It is compatible with Affymetrix GeneChip system for gene expression analysis and designed to analyze large volumes of high dimensional data.
Please note: Users of MetaCore need to contact the Core at the following email address to set up a new account.
Email: genechip@vapop.ucsd.edu
Other Options:
A number of other commercial software products are available. These tend to be expensive, highly-polished software packages for data analysis. For information on these, users should contact the company directly.
For expression analysis: J-Express, GeneSifter, GenePilot, SAS Microarray, ArrayAssist, Rosetta Resolver, Vector Xpression , ArrayMiner
For pathway mapping: BIOSExplorer , PathwayAssist, MetaCore, Ingenuity, TRANSFAC, NetAffx
For genetic analysis: Helix-Tree , Exemplar, Varia
Academic software packages are also available. Most address one aspect of microarray analysis rather than provide a complete data analysis solution. They are generally free to the academic community, but features are more limited and documentation and support are usually weak. Some are downloadable programs whereas others are server-based and require data upload to the web-site. A number of useful programs are available.
Array normalization: dChip , CORGON, RMAExpress
Statistical Analysis: SAM , PAM, q-value, VAMPIRE, RankProducts, Cyber-T, sig_terms, BioConductor
Clustering: HCE , Cluster & TreeView
Pathway/network mapping: GenMAPP , GOby, GOstat, cytoscape, Onto-Express, GO-SCAN
Promoter analysis: PAINT , MEME, CompareProspector, CONREAL
Annotation: MatchMiner , ChiliBot
