| Name |
Description |
URL |
| ABS |
Database of Annotated regulatory Binding Sites from orthologous promoters |
http://genome.imim.es/datasets/abs2005/downloads.html |
| AGRIS AtcisDB and AtTFDB |
Arabidopsis thaliana cis-regulatory db and transcription factor db |
http://arabidopsis.med.ohio-state.edu/ |
| AtProbe |
Arabidopsis thaliana promoter binding element database |
http://rulai.cshl.edu/cgi-bin/atprobe/atprobe.pl |
| AthaMap |
Genome-wide map of potential transcription factor binding sites in Arabidopsis thaliana |
http://www.athamap.de/ |
| BOND |
The Biomolecular Object Network Databank (BOND) is a resource to perform cross-database
searches of available sequence, interaction, complex and pathway information. |
http://bond.unleashedinformatics.com/Action? |
| CEPDB |
C. elegans Promoter Db |
http://rulai.cshl.edu/cgi-bin/CEPDB/home.cgi |
| cisreg.ca |
Contains musle and liver data sets |
http://www.cisreg.ca/tjkwon/ |
| Compel |
Composite regulatory elements: structure, function and classification |
http://compel.bionet.nsc.ru/new/compel/compel.html |
| DATF |
The Database of Arabidopsis Transcription Factors (DATF) |
http://datf.cbi.pku.edu.cn/ |
| DBTSS |
Database of Transcriptional Start Sites |
http://dbtss.hgc.jp/ |
| DoOP |
Orthologous clusters of promoters |
http://doop.abc.hu/ |
| DBSD |
Drosophila Binding Site Database |
http://rulai.cshl.org/dbsd/index.html
*Note that this website is not yet functional but will be soon. |
| Drosophila DNase I Footprint Database |
Webpage providing access to results of the systematic
curation and genome annotation of 1,365 DNase I footprints for the fruitfly
D. melanogaster |
http://www.flyreg.org/ |
| DRTF |
Database of Rice Transcription Factors |
http://drtf.cbi.pku.edu.cn/ |
| ECRBase |
Database of Evolutionary Conserved Regions (ECRs), Promoters, and
Transcription Factor Binding Sites in Vertebrate Genomes created using
ECR Browser alignments |
http://ecrbase.dcode.org/ |
| EDGEdb |
PDI, PPI and gene expression data
generated by the Walhout laboratory and others are made available to
the community through EDGEdb (elegans differential gene expression data) |
http://edgedb.umassmed.edu/IndexAction.do |
| EPD |
Eukaryotic Promoter Database |
http://www.epd.isb-sib.ch/ |
| ERTargetDB |
ERTargetDB integrates information from ongoing
Chip-on-chip experiments and promoter sequence conservation
from the OMGProm database. |
http://bioinformatics.med.ohio-state.edu/ERTargetDB/ |
| Globin Gene Server |
Experimental data on the regulation of the globin gene cluster |
http://globin.cse.psu.edu/ |
| Harbison Lab |
Datasets useful in comparative genomics and in erythroid gene regulation |
http://www.bx.psu.edu/~ross/dataset/DatasetHome.html |
| HemoPDB |
Hematopoiesis Promoter Db |
http://bioinformatics.med.ohio-state.edu/HemoPDB/ |
| JASPAR |
high-quality transcription factor binding profile database. |
http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl |
| LSPD |
The Liver Specific Gene Promoter Database |
http://rulai.cshl.edu/LSPD/ |
| MPD |
Mammalian Promoter Db (human, mouse and rat) |
http://rulai.cshl.edu/CSHLmpd2 |
| MPromDb |
Mammalian Promoter Db with experimentally supported annotations |
http://bioinformatics.med.ohio-state.edu/MPromDb/ |
| MTIR |
Muscle-specific regulation of transcription |
http://www.cbil.upenn.edu/MTIR/HomePage.html |
| OMGProm |
Orthologous Mammalian Gene Promoters |
http://bioinformatics.med.ohio-state.edu/OMGProm/ |
| ooTFD |
object-oriented Transcription Factors Db |
ttp://www.ifti.org/ootfd/ |
| OPD |
Osteo-Promoter Db (promoters of genes in the osteogenic pathway) |
http://www.opd.tau.ac.il/ |
| Oreganno |
Open regulatory annotation database |
http://oreganno.org |
| PLACE |
Plant Cis-acting Regulatory DNA Elements |
http://www.dna.affrc.go.jp/PLACE/ |
| Plant CARE |
Cis-Acting regulatory element.database |
http://intra.psb.ugent.be:8080/PlantCARE/
*Note: This database does not appear to currently be online. |
| Plant Prom DB |
Plant Promoter Sequences |
http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom |
| RARTF |
RIKEN Arabidopsis Transcription Factor db |
http://rarge.gsc.riken.jp/rartf/ |
| REDfly |
Regulatory Element Database for Drosophila |
http://redfly.ccr.buffalo.edu/?content=/search.php |
| RiceTFDB |
Rice genes involved in transcriptional control |
http://ricetfdb.bio.uni-potsdam.de/v2.1/ |
| RIKEN TFdb |
Mouse Transcription Factor Db |
http://genome.gsc.riken.jp/TFdb/ |
| rSNP |
Influence of single nucleotide mutations in regulatory gene regions |
http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ |
| SCPD |
S. cerevisiae Promoter Db |
http://rulai.cshl.edu/SCPD/ |
| Stanford Encode Project |
ENCyclopedia Of DNA Elements |
http://www-shgc.stanford.edu/genetics/encode.html |
| transcription factors dd |
transcription factors of humans and other organisms |
http://www.proteinlounge.com/trans_home.asp
*Note: a subscription is required to view search results |
| TRANSFAC |
eukaryotic transcription factors and their binding profiles |
http://www.gene-regulation.de/
*Note: Downloads from the public version are not available |
| TRED |
Transcriptional Regulatory Element Database |
http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home |
| TRRD |
Transcription Regulatory Regions Db |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/ |
| VISTA Enhancer Browser |
A database of tissue-specific human enhancers. |
http://enhancer.lbl.gov |
