Downloads

Data:

Complete release data including the original motifs are available at Zenodo.
Harmonized list of human transcription factors and respective mouse orthologs based on the TFClass classification: tf_masterlist.tsv.

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

Technical questions and suggestions should be addressed to Ilya Vorontsov and Ivan Kulakovskiy.
General questions should be addressed to Ivan Kulakovskiy, Yulia Medvedeva or Vsevolod Makeev.

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 (MOUSE subset: 1161)	1443 (MOUSE subset: 1161)	1427 (MOUSE subset: 1145)	1443 (MOUSE subset: 1161)
Complete model annotation (including gene id mapping)	All motifs	H12CORE_annotation.jsonl	H12INVIVO_annotation.jsonl	H12INVITRO_annotation.jsonl	H12RSNP_annotation.jsonl
Complete model annotation (including gene id mapping)	MOUSE subset	H12CORE-MOUSE_annotation.jsonl	H12INVIVO-MOUSE_annotation.jsonl	H12INVITRO-MOUSE_annotation.jsonl	H12RSNP-MOUSE_annotation.jsonl
PWM	One file per matrix	H12CORE_pwm.tar.gz	H12INVIVO_pwm.tar.gz	H12INVITRO_pwm.tar.gz	H12RSNP_pwm.tar.gz
PWM	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
PCM	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
PFM	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