Downloads
Data: Complete release data including the original motifs are available at Zenodo.
Tools:
  • MoLoTool - web interface for motif finding.
  • SPRY-SARUS tool for motif finding (Java): jar, readme
  • MACRO-APE tool for motif comparison, P-value and threshold estimation: jar, manual, website
  • PERFECTOS-APE tool for functional annotation of sequence variants overlappint TFBS: jar, manual, website
Contacts
Citation:
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Ruslan N. Sharipov; Alla D. Fedorova; Eugene I. Rumynskiy; Yulia A. Medvedeva; Arturo Magana-Mora; Vladimir B. Bajic; Dmitry A. Papatsenko; Fedor A. Kolpakov; Vsevolod J. Makeev
Nucl. Acids Res., Database issue, gkx1106 (11 November 2017)
doi: 10.1093/nar/gkx1106
License: HOCOMOCO motif collection is distributed under WTFPL. If you prefer more standard licenses, feel free to treat WTFPL as CC-BY.

HOCOMOCO v12 subcollections

H12CORE H12INVIVO H12INVITRO H12RSNP
Number of motifs 1443 1443 1427 1443
Complete model annotation (including gene id mapping) H12CORE_annotation.jsonl H12INVIVO_annotation.jsonl H12INVITRO_annotation.jsonl H12RSNP_annotation.jsonl
PWM One file per matrix
H12CORE_pwm.tar.gz H12INVIVO_pwm.tar.gz H12INVITRO_pwm.tar.gz H12RSNP_pwm.tar.gz
Flat file H12CORE_pwms.txt H12INVIVO_pwms.txt H12INVITRO_pwms.txt H12RSNP_pwms.txt
PCM One file per matrix
H12CORE_pcm.tar.gz H12INVIVO_pcm.tar.gz H12INVITRO_pcm.tar.gz H12RSNP_pcm.tar.gz
Flat file H12CORE_pcms.txt H12INVIVO_pcms.txt H12INVITRO_pcms.txt H12RSNP_pcms.txt
PFM One file per matrix
H12CORE_pfm.tar.gz H12INVIVO_pfm.tar.gz H12INVITRO_pfm.tar.gz H12RSNP_pfm.tar.gz
Flat file H12CORE_pfms.txt H12INVIVO_pfms.txt H12INVITRO_pfms.txt H12RSNP_pfms.txt
Alignments H12CORE_words.tar.gz H12INVIVO_words.tar.gz H12INVITRO_words.tar.gz H12RSNP_words.tar.gz
Threshold to P-value map
H12CORE_thresholds.tar.gz H12INVIVO_thresholds.tar.gz H12INVITRO_thresholds.tar.gz H12RSNP_thresholds.tar.gz
Matrices in other formats JASPAR H12CORE_jaspar_format.txt H12INVIVO_jaspar_format.txt H12INVITRO_jaspar_format.txt H12RSNP_jaspar_format.txt
MEME H12CORE_meme_format.meme H12INVIVO_meme_format.meme H12INVITRO_meme_format.meme H12RSNP_meme_format.meme
TRANSFAC H12CORE_transfac_format.txt H12INVIVO_transfac_format.txt H12INVITRO_transfac_format.txt H12RSNP_transfac_format.txt
HOMER
P-value 0.001
P-value 0.0005
P-value 0.0001
P-value 0.001
P-value 0.0005
P-value 0.0001
P-value 0.001
P-value 0.0005
P-value 0.0001
P-value 0.001
P-value 0.0005
P-value 0.0001