Cis-BP

CisBP Links


Other TF DNA binding motif databases
FactorBook - Human Motifs derived from ENCODE ChIP-seq experiments
Fly Factor Survey - Fly TF motifs derived from Bacterial one-hybrid (B1H) experiments
hmCHIP - Human and Mouse motifs derived from ChIP-seq experiments
HOCOMOCO - Human motifs collected and curated from various sources
JASPAR - Motifs collected and curated from various sources
Transfac - Motifs collected and curated from various sources
UniProbe - PBM motifs and data


Publications from which data was taken (First author/Year/PMID/Description):
Badis et al., 2008 (PMID: 19111667): Yeast TFs (PBMs)
Badis et al., 2009 (PMID: 19443739): Mouse TFs (PBMs)
Barazandeh et al., 2018 (PMID: 29146583): Many human KRAB C2H2 zinc fingers (ChIP-seq/ChIP-exo + modeling)
Barrera et al., 2016 (PMID: 27013732): >100 human TFs with common genetic variants in their DBDs (PBMs)
Berger et al., 2006 (PMID: 16998473): Original universal PBM study (PBMs)
Berger et al., 2008 (PMID: 18585359): Mouse Homeodomains (PBMs)
Busser et al., 2012a (PMID: 22296846): Drosophila homeodomain TFs (PBMs)
Busser et al., 2012b (PMID: 23184988): Drosophila Lmd TF (PBMs)
Campbell et al., 2010 (PMID: 21060817): Plasmodium falciparum AP2 family TFs (PBMs)
Chang et al., 2013 (PMID: 23795294): Arabidopsis thaliana and Physcomitrella patens TFs (PBMs)
Cheatle-Jarvela et al., 2014 (PMID: 25016582): Tbrain TF in two species of echinoderms (PBMs)
Chen et al., 2011 (PMID: 21450710): hmCHIP database (ChIP-seq)
Contrino et al., 2012 (PMID: 22080565): Motifs from modENCODE (ChIP-seq)
DeBoer et al., 2011 (PMID: 22102575): S. cerevisiae TF database (various)
DelBianco et al., 2010 (PMID: 21124806): RBPJ/CSL binding in the presence/absence of its co-factors (PBMs)
DeMasi et al., 2011 (PMID: 21335608): bHLH TFs and mutant TFs (PBMs)
DeSilva et al., 2008 (PMID: 18541913): Protist AP2 family TFs (PBMs)
Franco-Zorrilla et al., 2014 (PMID: 24477691): 63 Arabidopsis TFs (PBMs)
Gabut et al., 2011 (PMID: 21924763): FOXP1 TF splicing variants (PBMs)
Gerstein et al., 2012 (PMID: 22955619): ENCODE consortium human TFs (ChIP-seq)
Gordan et al., 2011 (PMID: 22189060): 26 yeast TFs (PBMs)
Grove et al., 2009 (PMID: 19632181): Worm bHLH TFs (PBMs)
Guo et al., 2014 (PMID: 25287278): MYC and MAX TFs (PBMs)
Hallikas et al., 2006 (PMID: 16413481): Six eukaryotic TFS (HT-SELEX)
Heinz et al., 2010 (PMID: 20513432): Large collection of motifs in the HOMER library (ChIP-seq)
Isakova et al., 2017 (PMID: 28092692): 58 human, mouse, and Drosophila TFs (SMiLE-seq)
Jolma et al., 2010 (PMID: 20378718): 14 different classes of human TFs (HT-SELEX)
Jolma et al., 2013 (PMID: 23332764): Many human and mouse TFs (HT-SELEX)
Kulakovskiy et al., 2009 (PMID: 20067172): 39 Drosophila TFs (various)
Kulakovskiy et al., 2013 (PMID: 23175603): HOCOMOCO database (various)
Lambert et al., 2019 (In press): 340 eukaryotic TFs (PBMs)
Lam et al., 2011 (PMID: 21321018): C2H2 zinc finger constructs (PBMs)
LehtiShiu et al., 2015 (PMID: 26103993): Arabidopsis AP2 TFs (PBMs)
Lesch et al., 2009 (PMID: 19204119): nsy-7 C. elegans TF (PBM)
Li et al., 2017 (PMID: 28869966): Two Polycomb-like human proteins (PBMs)
Lindemose et al., 2014 (PMID: 24914054): 14 Arabidopsis TFs (PBMs)
Liu et al., 2018 (PMID: 29606353): BCL11A and B, with mutants (PBMs)
Mann et al., 2013 (PMID: 23590861): Mouse bZIP TFs (PBMs)
Mathelier et al., 2014 (PMID: 24194598): JASPAR database (various)
Matys et al., 2006 (PMID: 16381825): Transfac database (various)
Ming et al., 2013 (PMID: 24418439): Drosophila peb TF (SELEX)
Najafabadi et al., 2015a (PMID: 25690854): 43 diverse eukaryotic C2H2 Zinc Fingers (PBMs)
Najafabadi et al., 2015b (PMID: 25690854): 39 human C2H2 Zinc Fingers (ChIP-seq)
Nakagawa et al., 2013 (PMID: 23836653): 20 diverse eukaryotic Forkhead family TFs (PBMs)
Narasimhan et al., 2015 (PMID: 25905672): 129 C. elegans TFs (PBM)
Nitta et al., 2015 (PMID: 25779349): 248 Drosophila TFs (HT-SELEX)
OMalley et al., 2016 (PMID: 27203113): 534 Arabidopsis TFs (Dap-seq)
Peterson et al., 2012 (PMID: 23249739): GLI family C2H2 ZFs in mouse (PBMs)
Radke et al., 2013 (PMID: 23572590): Toxoplasma AP2 family TF (PBMs)
Rhee et al., 2011 (PMID: 22153082): One human and four yeast TFs (ChIP-exo)
Rodriguez-Martinez et al., 2017 (PMID: 28186491)
Scharer et al., 2009 (PMID: 19147588): SOX4 human TF (PBM)
Schmitges et al., 2016 (PMID: 27852650): 131 human C2H2 Zinc Finger TFs (ChIP-seq)
SebePedros et al., 2013 (PMID: 24043797): T-box family TFs (PBM)
Siggers et al., 2014 (PMID: 25042805): Diverse yeast C2H2 Zinc Finger TFs (PBMs)
Soruco et al., 2013 (PMID: 23873939): Drosophila Clamp TF (PBMs)
Sullivan et al., 2014 (PMID: 25220462): 43 Arabidopsis TFs (PBMs)
Tillo et al., 2017 (PMID: 29072898): Epstein-Barr Virus Zta TF binding to chemically modified DNA (PBMs)
Wei et al., 2010 (PMID: 20517297): Ets family TFs (human and mouse) (PBMs)
Weirauch et al., 2013 (PMID: 23354101): DREAM challenge paper (82 mouse TFs) (PBMs)
Weirauch et al., 2014 (PMID: 25215497): 1,000+ TFs across eukaryotes (PBMs)
Yin et al., 2017b (PMID: 28473536): 8 human TFs with and without DNA methylation (PBMs)
Yin et al., 2017 (PMID: 28473536): 542 TFs with and without DNA methylation (HT-SELEX)
Zhu et al., 2009 (PMID: 19158363): Yeast TFs (PBMs)
Zhu et al., 2011 (PMID: 21097781): Fly TFs (B1H)