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Here is a list of some of the software and tools that are available and in use at the University of Otago. The Otago Genomics Facility is constantly reviewing software and analysis methods, so users should contact the facility for current information.

Genetraffic (commercial software) www.iobion.com
Access: Server based analysis software that the Otago Genomics Facility makes available to its users.
Used for: Data normalization. Extraction of data subsets up and down regulated genes. Clustering, spot flagging. MIAME compliant database.

GenePIX Pro4.0 (commercial software) http://www.axon.com
Used for: Imaging software used for extraction of raw data from scanned images.

SNOMAD (interactive website) http://pevsnerlab.kennedykrieger.org/snomad.htm
Access: Free software which has some tools which are not available in Genetraffic.
Used for: SNOMAD is a program for the standardization and normalization of gene expression datasets. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed across the range of microarray element signal intensities: local mean normalization and local variance correction (Z-score generation using a locally calculated standard deviation).

Cluster and Tree view (free software download) http://rana.lbl.gov/
Used for: Clustering Microarray data from Eisen Lab. This software has different algorithms than Genetraffic.

MIDAS/MEV (free software download) www.tigr.org/tdb/microarray

TIGR Microarray Data Analysis System (MIDAS)
Used for: Data filtering to reduce the quantity of uninformative data used for final analysis. Replicate analysis and the use of a variety of sophisticated data normalization algorithms. Statistical data analysis. Clustering SOMs etc.

Dragon microarray (interactive website) http://pevsnerlab.kennedykrieger.org/dragon.htm
Used for: Manipulating microarray data, for example converting accession numbers from microarray data from different sources to a single common accession number so they can be directly compared. Other tools including gene ontology also available.

BRB Array Tools (free software download) http://linus.nci.nih.gov/BRB-ArrayTools.html
BRB ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The array tools package utilizes an Excel front end. Scientists are familiar with Excel and utilizing Excel as the front end makes the system portable and not tied to any database. The input data is assumed to be in the form of Excel spreadsheets describing the expression values and a spreadsheet providing user-specified phenotypes for the samples arrayed. The analytic and visualization tools are integrated into Excel as an add-in. The analytic and visualization tools themselves are developed in the powerful R statistical system, in C and Fortran programs and in Java applications. Visual Basic for Applications is the glue that integrates the components and hides the complexity of the analytic methods from the user. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis.

The PubGeneTM Webtools (interactive website) http://proteomicssurf.com/PubGene/tools/Network/Browser
Literature and Sequence Networks, Network Browser , text based search tools used to find genes commonly associate in the literature with your genes of interest.

David (interactive website) http://www.david.niaid.nih.gov
David is used for Ontology searching with gene list with a tabular output.

PubMatrix (interactive website) http://pubmatrix.grc.nia.nih.gov/
PubMatrix is a simple way to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table. Lists of terms can be anything for example gene names.

Pathway Assist (commercial software package) http://www.iobion.com/
Pathway assist used for investigating interactions between genes within the literature with a good graphical display. Used for the construction of pathway and gene networks.

Genomatx Promoter analysis (interactive website) http://www.genomatix.de/cgi-bin/matinspector/matinspector.pl
(Limited free Academic access) Used for promoter analysis. A set of tools which allow users to look for common regulatory elements transcription factor binding sites within a set of genes.

Traser (interactive website) http://genome-www6.stanford.edu/cgi-bin/Traser/traser
Used for the extraction of promoter sequences for promoter analysis.

OTFBS (interactive website) http://www.bioinfo.tsinghua.edu.cn/~zhengjsh/OTFBS
Used for identification of over represented transcription factor binding sites in microarray data sets.

The Source at Stanford (interactive website) http://genome-www5.stanford.edu/cgi-bin/source/sourceSearch
Used for: Batch searches of accession numbers. You can get gene name, function sub cell localization, enzyme function, chromosome location etc. Very useful.

BioRag (interactive website) http://www.biorag.org/
Arizona Cancer Institute tools for microarray. Very good for pathways.

GSCope (free software download) http://gscope.gsc.riken.go.jp/index.htm
Information from different sources has been integrated into a set of free tools for mouse pathway analysis and gene ontology from the RIKEN (The Institute of Physcial and Chemical Research)

GO stat (interactive website) http://gostat.wehi.edu.au/
The Gene-Ontology database provides a useful tool to annotate and analyze the function of large numbers of genes. .Find statistically overrepresented GO terms within a group of genes.

ONTO-express (interactive website) http://vortex.cs.wayne.edu/projects.htm
Free gene ontology tools for array analysis. Finds statistically overrepresented GO terms results in a different format than GO stat but can be a bit prone to crashing. Worth looking at.

CGAP (interactive website) http:// cgap.nci.nih.gov/
The Cancer Genome Anatomy Project (CGAP)
Used for: A good reference site for gene expression. Can look at gene expression tissue by tissue has useful pathway tools for both BioCata and KEGG