Contacts

Tools

Sequence data

Collection preparation

Citation:
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

TFBS models (Technical notes)

CORE COLLECTION: primary binding models of ABC quality

Human Mouse
Mononucleotide Dinucleotide Mononucleotide Dinucleotide
Complete model annotation (including gene id mapping) annotation_HUMAN_mono.tsv annotation_HUMAN_di.tsv annotation_MOUSE_mono.tsv annotation_MOUSE_di.tsv
PWM
One file per matrix
pwm_HUMAN_mono.tar.gz pwm_HUMAN_di.tar.gz pwm_MOUSE_mono.tar.gz pwm_MOUSE_di.tar.gz
Flat file pwms_HUMAN_mono.txt pwms_HUMAN_di.txt pwms_MOUSE_mono.txt pwms_MOUSE_di.txt
PCM One file per matrix
pcm_HUMAN_mono.tar.gz pcm_HUMAN_di.tar.gz pcm_MOUSE_mono.tar.gz pcm_MOUSE_di.tar.gz
Flat file pcms_HUMAN_mono.txt pcms_HUMAN_di.txt pcms_MOUSE_mono.txt pcms_MOUSE_di.txt
Alignments words_HUMAN_mono.tar.gz words_HUMAN_di.tar.gz words_MOUSE_mono.tar.gz words_MOUSE_di.tar.gz
Standard thresholds standard_thresholds_HUMAN_mono.txt standard_thresholds_HUMAN_di.txt standard_thresholds_MOUSE_mono.txt standard_thresholds_MOUSE_di.txt
Threshold to P-value map
thresholds_HUMAN_mono.tar.gz thresholds_HUMAN_di.tar.gz thresholds_MOUSE_mono.tar.gz thresholds_MOUSE_di.tar.gz
Sequence LOGOs logo_HUMAN_mono.tar.gz logo_HUMAN_di.tar.gz logo_MOUSE_mono.tar.gz logo_MOUSE_di.tar.gz
Matrices in other formats JASPAR H11_HUMAN_mono_jaspar_format.txt H11_MOUSE_mono_jaspar_format.txt
MEME H11_HUMAN_mono_meme_format.meme H11_MOUSE_mono_meme_format.meme
TRANSFAC H11_HUMAN_mono_transfac_format.txt H11_MOUSE_mono_transfac_format.txt
HOMER

FULL COLLECTION: primary and alternative binding models

Human Mouse
Mononucleotide Dinucleotide Mononucleotide Dinucleotide
Complete model annotation (including gene id mapping) annotation_HUMAN_mono.tsv annotation_HUMAN_di.tsv annotation_MOUSE_mono.tsv annotation_MOUSE_di.tsv
PWM
One file per matrix
pwm_HUMAN_mono.tar.gz pwm_HUMAN_di.tar.gz pwm_MOUSE_mono.tar.gz pwm_MOUSE_di.tar.gz
Flat file pwms_HUMAN_mono.txt pwms_HUMAN_di.txt pwms_MOUSE_mono.txt pwms_MOUSE_di.txt
PCM One file per matrix
pcm_HUMAN_mono.tar.gz pcm_HUMAN_di.tar.gz pcm_MOUSE_mono.tar.gz pcm_MOUSE_di.tar.gz
Flat file pcms_HUMAN_mono.txt pcms_HUMAN_di.txt pcms_MOUSE_mono.txt pcms_MOUSE_di.txt
Alignments words_HUMAN_mono.tar.gz words_HUMAN_di.tar.gz words_MOUSE_mono.tar.gz words_MOUSE_di.tar.gz
Standard thresholds standard_thresholds_HUMAN_mono.txt standard_thresholds_HUMAN_di.txt standard_thresholds_MOUSE_mono.txt standard_thresholds_MOUSE_di.txt
Threshold to P-value map
thresholds_HUMAN_mono.tar.gz thresholds_HUMAN_di.tar.gz thresholds_MOUSE_mono.tar.gz thresholds_MOUSE_di.tar.gz
Sequence LOGOs logo_HUMAN_mono.tar.gz logo_HUMAN_di.tar.gz logo_MOUSE_mono.tar.gz logo_MOUSE_di.tar.gz
Matrices in other formats JASPAR H11_HUMAN_mono_jaspar_format.txt H11_MOUSE_mono_jaspar_format.txt
MEME H11_HUMAN_mono_meme_format.meme H11_MOUSE_mono_meme_format.meme
TRANSFAC H11_HUMAN_mono_transfac_format.txt H11_MOUSE_mono_transfac_format.txt
HOMER