-Zlab Gene Regulation Tools-

This webpage collects links related to bioinformatics of gene regulation (mostly transcriptional regulation). At the top you can find resources developed locally by members of the Zlab, and below that we have organized external resources by category. On Sept 13th,2005, we fixed several broken links due to a recent server migration. Please contact us if you notice any glitches. Thank you!

Local Resources (Zlab)
Promoser - human, mouse and rat promoter extraction service Possum - simple matrix-based motif search CARRIE - Generate transcriptional regulatory networks from microarray and promoter sequence data CisML - An XML format for Sequence Motif Detection Programs HuGE Index - database of gene expression in normal human tissues Cis-element information - count matrices and background info for some cis-elements site2genome - locate sites in the human, mouse and rat genomes REPFIND - find clustered, exact repeats in nucleotide sequences ICSF - identifies conserved structural features at sequentially degenerate locations in transcription factor binding sites		Tools to find motif clusters in DNA sequences Cluster-Buster (newest method - our favorite!) Comet (includes statistical significance estimates) Cister (our original method) Tools to find diagnostic motifs in a set of regulatory (e.g. promoter) sequences GLAM - gapless local alignment of multiple sequences (motif discovery) Clover - find overrepresented motifs in DNA sequences ROVER - find relatively overrepresented motifs in DNA sequences. New Java Version Available MotifViz - Integration of tools for detecting overrepresented motifs SeqVISTA - a viewer of sequences and their annotations; now with a Motif module for integrating transcriptional regulation analysis tools.

External Resources
Promoter Databases EPD - Eukaryotic Promoter Database DBTSS - DataBase of Transcriptional Start Sites (human) SCPD - Saccharomyces cerevisiae promoter database DCPD - Drosophila core promoter database PlantProm DB Davuluri Lab databases PromEC - E. coli promoters Promoter Prediction DoOP - Database of Orthologous Promoters First Exon Finder, CorePromoter and CpGpromoter CpGProD - CpG island promoter detection CONPRO McPromoter PromoterInspector DRAGON Promoter / Gene Start Finder Promoter 2.0 PromFD NNPP FunSiteP Gene Expression Databases Gene Expression Omnibus ArrayExpress Stanford Microarray Database ExpressDB SAGE Genie Microarray Analysis Software VERA and SAM Wong Lab software SAM: Significance Analysis of Microarrays GeneCluster and GeneCruiser Eisen Lab software Bioconductor Phylogenetic Footprinting TraFaC PipMaker VISTA LAGAN Toolkit SeqComp and FamilyRelations Bayesian Phylogenetic Footprint ConSite FootPrinter CpG Islands CpG Island Searcher Repeat Detection RepeatMasker nseg dust Tandem Repeats Finder Sequence and Annotation Visualization Apollo Alfresco Artemis Ensembl UCSC Genome Browser NCBI Map Viewer		Transcription Factor, Binding Site & Motif Databases & Analysis Tools JASPAR TRANSFAC - public GeneExpress / TRRD RegulonDB Cis-regulatory Modules from Drosophila Muscle-Specific Regulation of Transcription DBTBS - A Database of Bacillus Subtilis Promoters and Transcription Factors PRODORIC - A Database of prokaryotic gene regulation Motif Search Patser MATCH - public BindGene TFbind MatInspector and ConsInspector TESS TFSEARCH PROMO MDscan - uses ChIP-on-chip data Motif Cluster Search MSCAN Cis-analyst Fly enhancer ModelGenerator and ModelInspector Transcription Factor Binding Site Clusters in the Human Genome Ab-initio Motif Discovery Gibbs Motif Sampler AlignACE BioProspector Motif Sampler SeSiMCMC Consensus and Co-Bind ANN-Spec MEME YEBIS YMF MultiProfiler MITRA cis-Site Seeker CoreSearch MACAW - Multiple Alignment Construction & Analysis Workbench Melina Motif Overrepresentation OTFBS PRIMA Pipelined Analysis Programs Regulatory Sequence Analysis Tools Toucan INCLUSive

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