ChIPSummitDB |
http://summit.med.unideb.hu/summitdb/index.php |
ChIP-seq-based data of transcription factor binding sites and the topological arrangements of the proteins |
Yes |
Online |
CREME |
https://creme.dcode.org/ |
Cis-regulatory module explorer for the human genome |
Yes |
Online |
CRUNCH |
http://crunch.unibas.ch/crunch/ |
ChIP-seq data analysis |
Yes |
Online |
FirstEF |
http://rulai.cshl.org/tools/FirstEF/ |
First Exon Finder (FirstEF) is a 5’ terminal exon and promoter prediction program |
Yes |
Online |
GlycoViewer |
http://www.glycoviewer.babs.unsw.edu.au/ |
Visualisation tool for representing a set of glycan structures |
Yes |
Online |
HERVd |
https://herv.img.cas.cz/ |
Human endogenous retroviruses database |
No |
Online |
HumCFS |
https://webs.iiitd.edu.in/raghava/humcfs/index.html |
Human chromosomal fragile sites data |
No |
Online |
Interferome* |
http://interferome.its.monash.edu.au/interferome/home.jspx |
Contains type I, II and III interferon (IFN) regulated genes |
No |
Online |
JASPAR |
http://jaspar.genereg.net/ |
The high-quality transcription factor binding profile database |
Yes |
Online |
MANTA |
http://manta.cmmt.ubc.ca/manta2/upload |
Maps of transcription factor binding sites |
Yes |
Online |
MAPPER |
http://genome.ufl.edu/mapperdb |
Multi-genome analysis of positions and patterns of elements of regulation |
No |
Offline |
MEME Suite |
http://meme-suite.org/ |
DNA motifs, transcription factor binding sites or protein domain |
Yes |
Online |
MET |
http://veda.cs.uiuc.edu/MET/ |
The motif enrichment tool identifies significantly associated sets of genes that share a regulatory motif |
Yes |
Online |
microDoR |
http://reprod.njmu.edu.cn/cgi-bin/microdor/index.py |
Predict Human miRNA-mediated gene silencing |
Yes |
Online |
OsteoporosAtlas |
http://biokb.ncpsb.org/osteoporosis/index.php |
Regulatory sequences in osteoporosis-related genes |
Yes |
Online |
PReMod |
http://genomequebec.mcgill.ca/PReMod |
Predict transcriptional regulatory modules of human genome |
Yes |
Online |
pseudoMap |
http://pseudomap.mbc.nctu.edu.tw/php/index.php |
Gathers information about transcribed pseudogenes |
No |
Offline |
SM-TF |
http://zoulab.dalton.missouri.edu/SM-TF/ |
Database of small molecule-transcription factor complexes |
Yes |
Online |
SNP@lincTFBS |
http://210.46.85.180:8080/SNP_linc_tfbs/ |
SNPs in potential TFBSs of human Large intergenic non-coding RNAs (lincRNAs) |
Yes |
Offline |
TcoF-DB |
https://tools.sschmeier.com/tcof/home/ |
Human transcription co-factors and transcription factor interacting proteins |
No |
Online |
TFBSbank |
http://tfbsbank.co.uk/ |
Chip-seq data of 585 transcription factors in 5 species |
Yes |
Online |
TFCat |
http://www.tfcat.ca/ |
Curated catalog of mouse and human transcription factors |
No |
Offline |
TFClass |
http://tfclass.bioinf.med.uni-goettingen.de/ |
Eukaryotic TFs according to their DNA-binding domains |
No |
Online |
TFCONES |
http://tfcones.fugu-sg.org/ |
Transcription factor genes and conserved noncoding elements |
Yes |
Online |
TFM-Explorer |
https://bioinfo.lifl.fr/TFM/ |
Putative TFBS within a set of upstream regulatory sequences for a given set of genes |
Yes |
Online |
TMREC |
http://www.jianglab.cn/TMREC/ |
TF and miRNA regulatorY cascades in human diseases |
Yes |
Online |
TRANSFAC |
http://genexplain.com/transfac/ |
Eukaryotic TF, their experimentally-proven binding sites, consensus binding sequences and regulated genes |
No |
Online |
TTSMI database* |
http://ttsmi.bii.a-star.edu.sg/ |
Triplex target DNA site mapping and integration database |
No |
Online |