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Other Resources
Transcription Factor Binding Sites |
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| TRANSFAC | Eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles |
| Drosophila DNase I Footprint Database | DNase I footprints for the fruitfly D. melanogaster |
| Transcription Regulatory Regions Database (TRRD) | Structural and functional organization of transcription regulatory regions of eukaryotic genes. |
| Transcriptional Regulatory Element Database (TRED) | Curated repository for both cis- and trans- regulatory elements in mammals (promoters and transcription factor binding sites) |
| Riken Transcription Factor Database (TFdb) | Database containing mouse transcription factor genes and their related genes. It is intended to select transcription factor genes nonredundantly from the entire Mouse genome. |
| plantCARE | Cis-acting regulatory element database for plants |
| Arabidopsis thaliana Promoter Binding Element Database (AtProbe) | Arabidopsis thaliana promoter binding element database |
| The Arabidopsis cis-regulatory element database (AtcisDB) | a searchable relational database, which includes many different datatypes, such as transcription factor binding site information, promoter sequence and related annotations |
Regulatory Regions |
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| Hematopoiesis Promoter Database (HemoPDB) | Experimentally defined regulatory information, including TFs, cis-regulatory elements, their target gene promoters and corresponding annotations for transcriptional regulation in hematopoiesis |
| MPromDb | Database for gene promoters with experimentally supported annotation of transcription start sites (TSS), cis-regulatory elements, CpG islands and ChIP-chip experimental results with intuitively visualized presentation |
| Mammalian Promoter Database | Collection of promoter databases for human, mouse and rat. |
| Osteo - Promoter Database (OPD) | Database that analyzes promoters of genes which differentiate along with the osteogenic pathway |
| Orthologous Mammalian Gene Promoter datababse (OMGProm) | an integrated resource of mammalian gene promoters |
| Arabidopsis transcription factor database (AtTFDB) | public Arabidopsis transcription factor database |
| Eukaryotic Promoter Database (EPD) | an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally |
| PlantProm DB | an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species |
| Promoter Database of Saccharomyces cerevisiae (SCPD) | Yeast Promoter Database |
| C. elegans promoter database (CEPDB) | C. elegans Promoter Database |
| The Liver Specific Gene Promoter Database | promoter regions responsible for liver specific transcriptions, experimentally verified regulatory regions and elements. |
Regulatory Polymorphisms |
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| rSNP_Guide | System of databases documenting the influence of mutations in regulatory gene regions onto DNA interaction with nuclear proteins. |
| Human Gene Mutation Database (HGMD) | published gene lesions responsible for human inherited disease (including regulatory mutations) |
| dbQSNP | Accumulates and presents experimental data of sequences and allele frequencies of SNPs in the promoter regions |
| PromoLign | Promolign provides graphical presentation for SNPs and transcription factor binding sites in the promoter region of genes in the context of human-mouse orthologous sequence alignment |
Regulatory Haplotypes |
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| NA | NA |
Questions or comments to oreganno@bcgsc.ca. (Archived here)
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