Neuroinformatics Tools

INIA-West

 

Colorado Neuroinformatics Tools
URL: http://phenogen.ucdenver.edu

To see complete descriptions of the tools available from the Colorado INIA-West website, click here.

A large number of normalization, statistics, QTL and informatics tools are available to registered INIA users for various analytical purposes.  All registered members will have access to all of the tools.  The actual data uploaded and analyzed by any individual user will be accessible ONLY by that user and to specific individuals authorized by that user.  Currently, this INIA website has 977 fully annotated arrays available to authorized users.

Number of annotated arrays available at Colorado Gene Array/Informatics site:

Organism	Number of arrays
Drosophila	28
Human	4
Mouse	688
Rat	266

description:     
                  • Upload raw microarray data using the INIA copy of MIAMExpress
                  • Upload gene lists
                  • Share data with other INIA investigators
                  • Search literature
                  • Gene annotations using multiple databases
                  • Utilizing expression- and phenotypic-QTL data
                  • Oligonucleotide microarray quality control analysis
                  • Oligonucleotide microarray data normalization
                  • Data filtering (noise filtering)
                  • Statistical analyses, including most common statistical tests and permutations
                  • Promoter analysis (analysis of transcription factor binding sites)
                  • Upstream sequence extraction

A manual is available at the Colorado Gene Array/Informatics site for details regarding the use of these tools.

            For more information contact:            Boris Tabakoff:  Boris.Tabakoff@uchsc.edu

Indiana Microarray Data Portal
URL: http://cmg.iupui.edu/mdp/ (password protected)
description:  

• analyzes Affymetrix data
• filters out genes not detectably expressed
• performs t test on signal or log-transformed signal, calculates FDR
• performs ANOVA (1 and 2-way)
• performs various clusterings (e.g. hierarchical), SVD
• maps data onto KEGG pathways
• maps data into Gene Ontology categories
• provides links to public bioinformatics sites

For more information, contact:       Howard Edenberg:  edenberg@iupui.edu

            To request use of this resource, click here.

INIA Texas Gene Expression Database
URL: http://inia.icmb.utexas.edu
description:           
                  The INIA Texas Gene Expression Database (IT-GED) contains extended lists of differentially expressed genes (nominal P<0.05) from genomic studies >>focusing on models of excessive alcohol consumption. IT-GED provides support for 1) easy search for genes associated with >>high alcohol drinking, 2) comparing results across genomic studies in forms of significant gene overlaps and downloadable gene lists, 3) integrating results across studies in forms of networks of co-regulated genes, 4) generating novel hypotheses.

            To request use of this resource, click here.

 

 

 

 

Other Links

 GeneNetwork / WebQTL
URL: http://www.genenetwork.org

            description:           
                                    • consists of set of linked resources for systems genetics
                                    • designed for multiscale integration of networks of genes, transcripts, and traits
                                    • combines data generated with full genome sequence and deep transcriptome data sets
                                    • has been optimized for online analysis of traits controlled by combinations of allelic variants and environmental factors
                                    • exploits several permanent mouse and rat genetic reference populations
                                    • includes genetic correlations between transcripts
                                    • includes genetic correlations between transcript abundance values and alcohol traits

            This site is self-explanatory and available to the general public.

 

Mouse Neuronal Expression Database
URL: http://mouse.bio.brandeis.edu

            description:           
                                    • describes transcriptomes of 12 neuronal populations obtained from cerebral cortex, amygdala, hippocampus, and thalamus
                                    • see Sugino et al., Nat Neurosci 2006
                                    • can be used to classify transcripts detected by microarrays into cellular categories

            This site is self-explanatory and available to the general public.

 Allen Brain Atlas
URL: http://www.brain-map.org

            description:           
                                    • project of Allen Institute of Brain Science
                                    • uses non-isotopic in situ hybridization and high resolution imaging to map mRNA expression of known mouse genes
                                    • can be used to classify transcripts detected by microarrays into cellular categories

            This site is self-explanatory and available to the general public.

 

 

 WebGestalt
URL: http://genereg.ornl.gov/webgestalt

            description:           
                                    • WEB-based GEne SeT AnaLysis Toolkit
                                    • incorporates information from different public resources
                                    • allows simple manipulation of integrated information to detect patters that otherwise are not easily detectable
                                    • includes functional group annotation and functional group over representation analysis

            This site is self-explanatory and available to the general public.