||The ABC4DE web-interface allows for the analysis of sets of variants within a region of interest. For a given variant, the tool reports: 1) if it falls within a predicted regulatory region; 2) the predicted role for that region (promoter/enhancer); and 3) if the variant will alter a potential TFBSs.
||The webtool allows for the motif enrichment analysis of CAGE-derived transcription start sites (TSSs): http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/
||Deep learning for identifying cis-regulatory elements and other applications.
|Deep Learning Package in Python Based on The Deep Learning Tutorials and Theano
||This deep learning package is an extension of the Deep Learning Tutorials (www.deeplearning.net/tutorial/).
|Gene Characerization Index
||A bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described: http://www.cisreg.ca/gci/
||Using Medical Subject Heading Overrepresentation Profiles (MeSHOPs), an entity of interest can be robustly summarized, quantitatively identifying associated biomedical terms and suggesting indirect associations: http://meshop.oicr.on.ca/meshop/index.html
||Algorithm that detects clusters of transcription factor binding sites in genomic sequences: http://www.cisreg.ca/cgi-bin/mscan/MSCAN
||A computational predictor of nuclear hormone receptor binding sites: http://www.cisreg.ca/cgi-bin/NHR-scan/nhr_scan.cgi
||A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences: http://opossum.cisreg.ca/oPOSSUM3/
||Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite): http://cisreg.cmmt.ubc.ca/cgi-bin/ORCAtk/orca
||An open-access system for the collection and dissemination of regulatory sequence annotation: http://www.pazar.info/
||An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes: http://www.cisreg.ca/cgi-bin/tfe/home.pl
||Transcription factor binding site detection using phylogenetic footprinting. Note that this is an older tool which is hosted remotely. You may also be interested in our ORCAtk tool which is maintained locally and performs similar functionality: http://consite.genereg.net/
||Multiple Tissue Northern Blot Comparison Tool: http://www.cisreg.ca/cgi-bin/dbmtn/index.pl
|Gene Set Builder
||A tool for collation, curation and distribution of sets of genes: http://www.cisreg.ca/gsb/
||A portal to the human genome. This tool was developed to fulfill a need for easily accessible gene information at a particular point in time. Having fulfilled its purpose, this tool has been retired. Current tools are available to provide similar services.
||Functional Investigation of Gene Datasets: http://genome.crg.es/GOToolBox/
||The 2014 version of the JASPAR database was publicly released on November 2013 with the incorporation of new and updated transcription factor binding profiles. Beyond the transcription factor binding profiles, we provide the ChIP-seq derived sequences that have been used to construct the profiles.
||A bioinformatics tool created to accelerate characterization of gene families sharing uncharacterized protein domains
|oPOSSUM2 v2 (2008)
||Web-based analysis of over-represented transcription factor binding sites: http://burgundy.cmmt.ubc.ca/oPOSSUM/
||Alignment of DNA sequences: http://www.cisreg.ca/cgi-bin/orthoseq/index.pl
||Developed by the Wasserman Laboratory at UBC, PFOND is a web-based service to promote the sharing of information about research, treatment, and resources for rare genetic disorders: http://pfond.cmmt.ubc.ca/
||Regulatory analysis of Variation in ENhancers: http://burgundy.cmmt.ubc.ca/cgi-bin/RAVEN/a?rm=home
||A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome: http://burgundy.cmmt.ubc.ca/SAGE2Splice/
||Protein Interactions Conserved Across Evolution: http://www.cisreg.ca:8080/ulysses/