Downloads (HOCOMOCO-14)

Data:

Complete release data is available at Zenodo.
Harmonized list of human transcription factors and respective mouse orthologs based on the TFClass classification (Extended with Codebook TFs for v14): 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 in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors

Ilya E Vorontsov, Irina A Eliseeva, Arsenii Zinkevich, Mikhail Nikonov, Sergey Abramov, Alexandr Boytsov, Vasily Kamenets, Alexandra Kasianova, Semyon Kolmykov, Ivan S Yevshin, Alexander Favorov, Yulia A Medvedeva, Arttu Jolma, Fedor Kolpakov, Vsevolod J Makeev, Ivan V Kulakovskiy

Nucleic Acids Research, gkad1077 (16 November 2023)

doi: 10.1093/nar/gkad1077

License: HOCOMOCO motif collection is distributed under WTFPL. If you prefer more standard licenses, feel free to treat WTFPL as CC-BY.

HOCOMOCO v14 subcollections

		H14CORE	H14INVIVO	H14INVITRO	H14RSNP
Number of TFs		1107 (MOUSE subset: 809)	1107 (MOUSE subset: 809)	1107 (MOUSE subset: 809)	1107 (MOUSE subset: 809)
Number of motifs		1595 (MOUSE subset: 1245)	1595 (MOUSE subset: 1245)	1579 (MOUSE subset: 1229)	1595 (MOUSE subset: 1245)
Complete model annotation (including gene id mapping)	All motifs	H14CORE_annotation.jsonl	H14INVIVO_annotation.jsonl	H14INVITRO_annotation.jsonl	H14RSNP_annotation.jsonl
Complete model annotation (including gene id mapping)	MOUSE subset	H14CORE-MOUSE_annotation.jsonl	H14INVIVO-MOUSE_annotation.jsonl	H14INVITRO-MOUSE_annotation.jsonl	H14RSNP-MOUSE_annotation.jsonl
PWM	One file per matrix	H14CORE_pwm.tar.gz	H14INVIVO_pwm.tar.gz	H14INVITRO_pwm.tar.gz	H14RSNP_pwm.tar.gz
PWM	Flat file	H14CORE_pwms.txt	H14INVIVO_pwms.txt	H14INVITRO_pwms.txt	H14RSNP_pwms.txt
PCM	One file per matrix	H14CORE_pcm.tar.gz	H14INVIVO_pcm.tar.gz	H14INVITRO_pcm.tar.gz	H14RSNP_pcm.tar.gz
PCM	Flat file	H14CORE_pcms.txt	H14INVIVO_pcms.txt	H14INVITRO_pcms.txt	H14RSNP_pcms.txt
PFM	One file per matrix	H14CORE_pfm.tar.gz	H14INVIVO_pfm.tar.gz	H14INVITRO_pfm.tar.gz	H14RSNP_pfm.tar.gz
PFM	Flat file	H14CORE_pfms.txt	H14INVIVO_pfms.txt	H14INVITRO_pfms.txt	H14RSNP_pfms.txt
Threshold to P-value map		H14CORE_thresholds.tar.gz	H14INVIVO_thresholds.tar.gz	H14INVITRO_thresholds.tar.gz	H14RSNP_thresholds.tar.gz
Matrices in other formats	JASPAR	H14CORE_jaspar_format.txt	H14INVIVO_jaspar_format.txt	H14INVITRO_jaspar_format.txt	H14RSNP_jaspar_format.txt
	MEME	H14CORE_meme_format.meme	H14INVIVO_meme_format.meme	H14INVITRO_meme_format.meme	H14RSNP_meme_format.meme
	TRANSFAC	H14CORE_transfac_format.txt	H14INVIVO_transfac_format.txt	H14INVITRO_transfac_format.txt	H14RSNP_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

Non-redundant motif subset

	H14CORE-CLUSTERED
Number of motif clusters	648
Clusters annotation	cluster_list.tsv
Representative motifs annotation	H14CORE-CLUSTERED_annotation.jsonl
PWM	H14CORE-CLUSTERED_pwm.tar.gz
PCM	H14CORE-CLUSTERED_pcm.tar.gz
PFM	H14CORE-CLUSTERED_pfm.tar.gz
Threshold to P-value map	H14CORE-CLUSTERED_thresholds.tar.gz
Cluster logos	H14CORE-CLUSTERED_cluster_logos.tar.gz