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Links for Exploring Networks of Genes and Phenotypes 
GeneNetwork and WebQTL have integrated links to the following resources
Resources for Analysis of Single Genes, mRNAs, and Proteins
Harvester retrieves summary data on any one of 57,000 proteins from several bioinformatic resources.
[Added Dec 22, 2004; last site review July 16, 2005 by RWW.]
Human Protein Reference DB a manually curated resource with data on 20,000 proteins. Very effective interface and rich data.
[Added Oct 30, 2005; last site review Oct 30, 2005 by RWW.]
iHOP retrieves PubMed sentences that report interactions between a reference gene and associate genes and proteins. It allows the assembly of complex graphs that plot the literature interactions of genes. Effective interface for humans and machines.
[Added Dec 25, 2004; last site review Aug 7, 2005 by RWW.]
AceView and the Alternate Transcript Diversity DB provide excellent resources for systematic information about the many alternative transcripts produced from single genes.
[Added Jan 1, 2005; last site review Sept 28, 2005 by RWW.]
MGI and RGD are reference sites for mouse and rat genetics, respectively.
[Added Dec 22, 2004; last site review Dec 25, 2004 by RWW.]
GenAtlas provides summary data for approximately 19300 human genes and has a useful link that will fetch 10 Kb of upstream sequence for promoter analysis.
[Added Jan 9, 2005; last site review July 15, 2005 by RWW.]
PromoLign aligns homologous regions of mouse and human promoters and highlights SNPs and transcription factor binding sites. Check the quick tutorial to see how to extract key data.
[Added May 10, 2005; last site review July 16, 2005 by RWW.]
CONSITE's Gene Pair tool retrieves matched mouse and human sequences and performs highy customizable searches for common transcription factor binding sites along with lovely sequence conservation graphs and position weight matrix displays. Any part of the pair of genes can be analyzed, including the 3' UTR. [Added Jan 28, 2005; last site review July 16, 2005 by RWW.]
SCL Mouse Protein database provides images of the subcellular distribution of ~1000 proteins. Good interface to information on domains and supporting data.
[Added Dec 31, 2004; last site review July 16, 2005 by RWW.]
CGAP SNP Viewer allows users to view SNPs in the context of transcripts, ORFs and protein motifs for either human or mouse genes. Try the Ahr gene in mouse as an example.
[Added April 10, 2006; last site review April 10, 2006 by RWW.]
Synapse Database (SynDB) is a comprehensive database of genes and proteins associated with the neuronal or neuromuscular synapse. Many Trait Data and Analysis pages provide links to SynDB.
[Added May 29, 2005; last site review April 8, 2006 by RWW.]
Dragon Genome Explorer provides a suite of tools for sequence analysis.
[Added Dec 22, 2004; last site review July 16, 2005 by RWW.]
MutDB and SNPs3D provide great data on functional SNPs in human genes. To analyze the functional impact of non-synonymous SNPs you will also find SNP Analyzer useful because it evaluates SNP impact in terms of the whole protein structural context.
[Added Dec 22, 2004; sites review July 29, 2005 by RWW.]
Alternative Splicing Project provide great summaries and output graphs on splice variants in human, mouse, and Drosophila.
[Added Nov 8, 2005; sites review Nov 8, 2005 by RWW.]
Resources for the Spatial Analysis of Gene and Protein Expression
Several excellent resources can be used to explore patterns of gene expression primarily in C57BL/6J mice. This strain is one of the parents of the BXD, AXB/BXA, BXH, and CXB genetic reference populations that are key resources in the Gene Network and its companion site, the Mouse Brain Library.
- BGEM and GENSAT provide images of gene expression in brains of embryos, neonates, and adult mice (roughly 2008 genes as of July 2005).
- GenePaint and GeneAtlas are companion sites that also provide expression data in embryos, neonates, and adults at high spatial resolution. GeneAtlas has excellent but slow image searching and matching capabilities.
- Allen Brain Atlas has expression data for ~12000 transcripts (adult males in the sagittal plane).
- EMAP (Edinburgh Mouse Atlas Project) provides data on expression of ~800 genes during development (in situ, immunohistochemistry, and reporter knock-in expression patterns). Most data are from wholemounts between Theiler stages 11 and 20 (embryonic days E7 to E13). EMAP can be used as a Java WebStart application.
- Mouse Atlas of Gene Expression is a massive SAGE library. The Atlas has quantified the normal state for many tissues by determining the number and identity of genes expressed throughout development. The scope of the project encompasses multiple stages of development of C57BL/6J mouse, from the single cell zygote to the adult, and includes an extensive initial collection of 200 tissues. DiscoverySpace is a WebStart application for use with The Mouse Atlas of Gene Expression.
- Mahoney Center maintains a rich image collection for ~1000 transcription factors expressed in brain (developmental stages, coronal plane).
[Added Dec 22, 2004; sites reviewed last on Sept 26, 2005 by RWW.]
Resources for the Analysis of Sets of Transcripts, Genes, and Proteins
GenomeNet is a terrific site for the analysis of molecular networks. Download the very effective KegArray 0.2.6beta package (May 2005) for exploratory data analysis of microarray data set. This package is as good as most commerical software and includes with built-in linkage to the KEGG databases. Versions are available for Mac OS X and Windows.
[Added Jan 3, 2005; last site review Aug 5, 2005 by RWW.]
GenMAPP 2.0 (2004), the Gene Map Annotation and Pathway Prolifer, is a free Windows application (simple registration required) with which you can visualize expression and other genomic data sets on maps of biological pathways. Very flexible suite of programs that you can also use to make custom gene annotation maps (and more).
[Added Aug 5, 2005; last site review Aug 5, 2005 by RWW.]
BIND and STRING and IntAct are great sites that provide access to well curated data on protein-protein interactions. BIND and IntAct focus on experimentally verified interactions whereas STRING and preBIND incorporate inferred interaction based on other data types, including gene expression. Links to BIND and STRING have been added to the Trait Data and Analysis forms on the GeneNetwork BETA site.
[Added Aug 21, 2005; last site reviews Aug 27, 2005 by RWW.]
Microarray Module Maps is a great site that databases a large number of coexpression modules defined using many cancer array studies.
[Added Aug 26, 2005; last site review Aug 26, 2005 by RWW.]
The Gene Ontology Consortium maintains a well annotated list of open resources for the analysis of large expression data sets and gene ontologies. Note that there are several different lists, each with valuable links.
[Added July 15, 2005; last site review July 15, 2005 by RWW.]
QSB: QSB is a stand-alone JAVA program with a sophisticated GUI developed for genetical genomics or systems genetics, an emerging field that combines quantitative genetics and genomics. QSB stands for QTL mapping, Sequence polymorphism analysis (or SNP analysis) and Bayesian network analysis. QSB takes marker and array data from a segregating population as input and identifies significant QTLs and then evaluated networks of candidate genes associated with these QTLs.
[Added July 29, 2005; last site review Jan 7, 2006 by RWW.]
eQTL Explorer is a Java WebStart application that has also been designed for the calculation and display of QTL maps for large rat data sets, particuarly those generated using the HXB strains. Locations of QTLs for both mRNA traits and conventional physiological traits are displayed on chromosome ideograms. High precision QTL maps can also be generated. A password is required to gain access to the primary data files.
[Added January 7, 2006; last site review Jan 7, 2006 by RWW.]
Clique-GO Analysis is a novel tool for extracting cliques of coregulated transcripts. The current data requires Affymetrix U74Av2 probe set IDs as input. Try "103370_at" (the gene Lin7c) as an example.
[Added Jan 4, 2005; last site review Jan 4, 2005 by RWW.]
ErmineJ is a stand-alone program for gene ontology analysis using expression data sets.
[Added Jan 4, 2005; last site review Jan 5, 2005 by RWW.]
Cytoscape is one of several SBML-compatible open source programs for visualizing molecular interaction networks and overlaying these networks with gene expression profiles and other data sets to generate and test specific hypotheses.
[Added Jan 5, 2005; last site review Jan 5, 2005 by RWW.]
Pathway Searcher provides fast access to gene/protein interaction pathways. An intuitive interface.
[Added Dec 30, 2004; last site review Dec 30, 2004 by RWW.]
Gene Sorter is a tool for generating and sorting sets of genes using a wide variety of information integrated into UCSC's Genome Brower.
[Added Dec 31, 2004; last site review Dec 31, 2004 by RWW.]
Genomica 1.0 is a free JAVA program for the analysis and visualization of genomic data. It can integrate gene expression data, DNA sequence data, and gene and experiment annotation. Last software release, Jan 2004.
[Added Mar 18, 2005; last site review Mar 18, 2005 by RWW.]
oPPOSUM is a tool for finding over-represented transcription factor binding sites in lists of mouse and human genes. It handles about 100 out of greater than 600 TFBSs.
[Added Jan 27, 2005; last site review Nov 21, 2005 by RWW.]
MOTIF and PAINT search for motifs in submitted sequences or lists of genes. Paint makes use of the TRANSFAC Pro database.
[Added Dec 22, 2004; last site review Dec 25, 2004 by RWW.]
Arrowsmith provides a fast way to evaluate known interactions or common mechanisms between two genes or proteins. It carries out a sophisticated comparison of the current PubMed database.
[Added Dec 22, 2004; last site review Dec 25, 2004 by RWW.]
Chilibot applies natural-language processing to the PubMed database to hunt for directed relationships among genes, proteins, and keywords. [Added Dec 30, 2004; last site review Dec 5, 2005 by RWW.]
Resources for the Analysis of Phenotypes in Genetic Reference Populations
MBL is a extensive image database of brain sections from genetic reference populations of mice, including the BXD, AXB, CXB, BXH strains included in WebQTL. The MBL is a companion database of WebQTL.
[Added Dec 22, 2004; last site review Aug 6, 2005 by RWW.]
Phenome Project provides access to a wide variety of phenotype data many common and wild inbred strains of mice.
[Added Dec 22, 2004; last site review Dec 25, 2004 by RWW.]
QTL Mapping Resources
QTL Reaper is software, written in C and compiled as a Python module, for rapidly scanning microarray expression data for QTLs. It is essentially the batch-oriented version of WebQTL. It requires, as input, expression data from members of a set of recombinant inbred lines and genotype information for the same lines. It searches for an association between each expression trait and all genotypes and evaluates that association by a permutation test. For the permutation test, it performs only as many permutations as are necessary to define the empirical P-value to a reasonable precision. It also performs bootstrap resampling to estimate the confidence region for the location of a putative QTL.
[Added Jan 27, 2005; last site review Jan 27, 2005 by KFM.]
MouseHapMap project genotypes from Mark Daly and colleagues. Approximately 140,000 SNPs across 49 strains. Updated Feb 2006.used to explore the Oxford Wellcome Heterogeneous stock QTL mapping project population. It currently includes mapping data for 100+ phenotypes typed across 2000 animals and 13,000 SNPs.
[Added May 10, 2006; last site review May 10, 2006 by RWW.]
A valuable list of Software for QTL Data Analysis and Gene Expression Microarray Software is managed by Brian Yandell at University of Wisconsin.
[Added May 16, 2006; last site review May 16, 2006 by RWW.]
GSCAN DB is a browser used to explore the Oxford Wellcome Heterogeneous stock QTL mapping project population. It currently includes mapping data for 100+ phenotypes typed across 2000 animals and 13,000 SNPs.
[Added May 10, 2006; last site review May 10, 2006 by RWW.]
The Wellcome Trust-CTC SNP Data Set consists of high density SNP data for approximately 490 strains of mice at 13,377 SNPs. These data fiels were processed slightly to generate many of the mouse mapping files used in WebQTL.
[Added Sept 27, 2005; last site review Sept 27, 2005 by RWW.]
The NIEHS-Perlegen Mouse Strain Resequencing Project provides links to SNP data for up to 15 strains of mice. Very high density data for many chromosomes. These data are integrated to some extent in the GeneNetwork.
[Added Sept 25, 2005; last site review Sept 25, 2005 by RWW.]
Affymetrix Array Annotation Resources
Affy MOE430A and MOE430B Annotation files are explained more clearly that Affymetrix has ever done by Earl F Glynn at the Stowers Institute. ([email protected]).
[Added July 17, 2006; last site review July 17, 2005 by RWW.]
Information about this HTML page:
This text originally generated by RWW, Dec 21, 2004. Updated by EJC, Feb 27, 2005; by RWW, July 15, Sept 25.
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