peak-motifs PTEN

Sequence composition (test sequences)

Nb of peaks: 6
Total seq. size: 12 kb
Min length: 1999 bp
Mean length: 1999 bp
Max length: 1999 bp [ view peaks in genome browser : ]
[ coordinates: UCSC BED track ]
[ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Motif discovery

Motif 1 oligos_6nt_mkv2_m1

k-mer sig=0.50; evalue=0.32

ysCCAGCCyb

VRGGCTGGSR

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ENCODE

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ysCCAGCCyb

SP1_known1 SP1_known1 R 10 1.0000 0.748 0.748 NA NA

CACBP_1 CACBP_1 R 9 0.9000 0.824 0.741 NA NA

TCF12_known1 TCF12_known1 D 8 0.8000 0.703 0.562 NA NA

Total matches= 10 (7 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 5 (83.33%)
Max nb of predicted sites per peak: 4
(chromosome_GRCh38_10_1_133797422_1:88272000-88274000())
Mean nb of predicted sites per peak: 3.00

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 2 oligos_6nt_mkv2_m2

k-mer sig=0.34; evalue=0.46

rrAATTAAam

KTTTAATTYY

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ENCODE

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor rrAATTAAam

HOXD9_2 HOXD9_2 D 10 1.0000 0.827 0.827 NA NA

HOXC10_3 HOXC10_3 D 10 1.0000 0.768 0.768 NA NA

HMX1_2 HMX1_2 D 10 0.9091 0.842 0.765 NA NA

Total matches= 234 (231 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 6 (100.00%)
Max nb of predicted sites per peak: 5
(chromosome_GRCh38_10_1_133797422_1:88388000-88390000())
Mean nb of predicted sites per peak: 2.83

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 3 oligos_7nt_mkv2_m1

k-mer sig=1.06; evalue=0.087

raAATTAAAcy

RGTTTAATTTY

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ENCODE

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor raAATTAAAcy

HOXD9_2 HOXD9_2 D 10 0.9091 0.836 0.760 NA NA

HOXC10_6 HOXC10_6 D 10 0.9091 0.790 0.718 NA NA

HOXC10_3 HOXC10_3 D 10 0.9091 0.782 0.711 NA NA

Total matches= 208 (205 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 6 (100.00%)
Max nb of predicted sites per peak: 4
(chromosome_GRCh38_10_1_133797422_1:88388000-88390000())
Mean nb of predicted sites per peak: 2.50

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 4 dyads_m1

k-mer sig=1.17; evalue=0.068

rcCCCAGCCmb

VKGGCTGGGGY

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ENCODE

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor rcCCCAGCCmb

CACBP_1 CACBP_1 R 9 0.8182 0.847 0.693 NA NA

CCNT2_disc2 CCNT2_disc2 D 10 0.9091 0.747 0.679 NA NA

SP1_known1 SP1_known1 R 10 0.9091 0.743 0.675 NA NA

Total matches= 12 (9 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 5 (83.33%)
Max nb of predicted sites per peak: 4
(chromosome_GRCh38_10_1_133797422_1:88272000-88274000())
Mean nb of predicted sites per peak: 2.40

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 5 dyads_m2

k-mer sig=0.48; evalue=0.33

gyCCCmgsCTCms

SKGAGSCKGGGRC

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ENCODE

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor gyCCCmgsCTCms

SP1_known7 SP1_known7 D 10 0.7692 0.754 0.580 NA NA

CCNT2_disc2 CCNT2_disc2 D 10 0.7692 0.736 0.566 NA NA

SP1_disc3 SP1_disc3 R 12 0.7500 0.719 0.539 NA NA

Total matches= 12 (9 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 6 (100.00%)
Max nb of predicted sites per peak: 5
(chromosome_GRCh38_10_1_133797422_1:88066000-88068000())
Mean nb of predicted sites per peak: 2.83

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 6 dyads_m3

k-mer sig=0.10; evalue=0.79

wmACCtcmwrcwcmrGACra

TYGTCYKGWGYWKGAGGTKW

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ENCODE

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor wmACCtcmwrcwcmrGACra

SMAD3_2 SMAD3_2 D 13 0.5417 0.795 0.431 NA NA

Total matches= 1

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 5 (83.33%)
Max nb of predicted sites per peak: 4
(chromosome_GRCh38_10_1_133797422_1:88066000-88068000())
Mean nb of predicted sites per peak: 2.80

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Predicted sites on test peaks (all motifs)

[tab]
[bed]

Word significance table
Word comparisons		[tab] [html] [heatmap]
Comparisons between discovered motifs
Discovered motifs versus discovered motifs		[ Discovered motif(s): tf ] [ table: html txt ] [ alignments (logo): html text ] [ clustering: html ] [ graph: gml (for CytoScape) ]
Discovered motifs versus transcription factor databases
Motifs versus ENCODE database		[ table: html txt ] [ alignments (logo): html text ] [ graph: gml (for CytoScape) ]

Log files
Parameters and files		[txt] [html]
Time log		[time table] [time log] [html]

Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31.
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568.

RSAT - peak-motifs result

Analysis: PTEN_PE (29/03/2026 19:52)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

ENCODE

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor wmACCtcmwrcwcmrGACra

SMAD3_2 SMAD3_2 D 13 0.5417 0.795 0.431 NA NA

Total matches= 1

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: PTEN_PE (29/03/2026 19:52)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor wmACCtcmwrcwcmrGACra SMAD3_2 SMAD3_2 D 13 0.5417 0.795 0.431 NA NA Total matches= 1

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

ENCODE

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor wmACCtcmwrcwcmrGACra

SMAD3_2 SMAD3_2 D 13 0.5417 0.795 0.431 NA NA

Total matches= 1