peak-motifs ING

Sequence composition (test sequences)

Nb of peaks: 648
Total seq. size: 566 kb
Min length: 414 bp
Mean length: 873.218 bp
Max length: 1000 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_mkv3_m1

k-mer sig=57.76; evalue=1.7e-58

hamcaAAACCCTAayyy

RRRTTAGGGTTTTGKTD

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 248 (38.27%)
Max nb of predicted sites per peak: 9
(5:5245369-5246641(.))
Mean nb of predicted sites per peak: 2.29

[ view in genome browser :

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

Motif 2 oligos_6nt_mkv3_m2

k-mer sig=41.05; evalue=8.9e-42

wwaGGCCCAwtwaw

WTWAWTGGGCCTWW

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 157 (24.23%)
Max nb of predicted sites per peak: 18
(1:29898025-29899123(.))
Mean nb of predicted sites per peak: 3.38

[ view in genome browser :

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

Motif 3 oligos_6nt_mkv3_m3

k-mer sig=32.81; evalue=1.5e-33

sgggtCGGGTCGgg

CCCGACCCGACCCS

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 106 (16.36%)
Max nb of predicted sites per peak: 27
(5:23056369-23057730(.))
Mean nb of predicted sites per peak: 3.73

[ view in genome browser :

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

Motif 4 oligos_6nt_mkv3_m4

k-mer sig=22.11; evalue=7.8e-23

ccgCCGCCGCcg

CGGCGGCGGCGG

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 228 (35.19%)
Max nb of predicted sites per peak: 30
(1:2620378-2621593(.))
Mean nb of predicted sites per peak: 4.11

[ view in genome browser :

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

Motif 5 oligos_6nt_mkv3_m5

k-mer sig=17.76; evalue=1.7e-18

cwCCaCCaCCGtcr

YGACGGTGGTGGWG

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 225 (34.72%)
Max nb of predicted sites per peak: 18
(1:2620378-2621593(.))
Mean nb of predicted sites per peak: 3.08

[ view in genome browser :

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

Motif 6 positions_6nt_m1

k-mer sig=0.81; evalue=0.15

tkCTTCTCyk

MRGAGAAGMA

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 268 (41.36%)
Max nb of predicted sites per peak: 16
(4:2587002-2588351(.))
Mean nb of predicted sites per peak: 2.88

[ view in genome browser :

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

Motif 7 positions_6nt_m2

k-mer sig=0.75; evalue=0.18

ygaCGGCGgc

GCCGCCGTCR

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 252 (38.89%)
Max nb of predicted sites per peak: 27
(1:2620378-2621593(.))
Mean nb of predicted sites per peak: 3.38

[ view in genome browser :

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

Motif 8 positions_6nt_m3

k-mer sig=0.69; evalue=0.2

maATCAAAac

GTTTTGATTK

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 150 (23.15%)
Max nb of predicted sites per peak: 9
(4:14495218-14496431(.))
Mean nb of predicted sites per peak: 1.97

[ view in genome browser :

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

Motif 9 positions_6nt_m4

k-mer sig=0.64; evalue=0.23

twTATGaAyh

DRTTCATAWA

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 135 (20.83%)
Max nb of predicted sites per peak: 12
(5:792595-794445(.))
Mean nb of predicted sites per peak: 2.01

[ view in genome browser :

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

Motif 10 positions_6nt_m5

k-mer sig=0.55; evalue=0.28

kwTGGAAAcr

YGTTTCCAWM

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 105 (16.20%)
Max nb of predicted sites per peak: 6
(4:10469201-10470103(.))
Mean nb of predicted sites per peak: 1.97

[ view in genome browser :

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

Motif 11 oligos_7nt_mkv4_m1

k-mer sig=35.42; evalue=3.8e-36

cmaaAACCCTAahy

RDTTAGGGTTTTKG

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 247 (38.12%)
Max nb of predicted sites per peak: 9
(5:5245369-5246641(.))
Mean nb of predicted sites per peak: 2.35

[ view in genome browser :

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

Motif 12 oligos_7nt_mkv4_m2

k-mer sig=21.29; evalue=5.1e-22

mraCCCGACCCGahy

RDTCGGGTCGGGTYK

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 114 (17.59%)
Max nb of predicted sites per peak: 21
(5:23056369-23057730(.))
Mean nb of predicted sites per peak: 3.20

[ view in genome browser :

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

Motif 13 oligos_7nt_mkv4_m3

k-mer sig=8.40; evalue=4e-09

cyCACGCGCyky

RMRGCGCGTGRG

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 73 (11.27%)
Max nb of predicted sites per peak: 10
(2:19593465-19596299(.))
Mean nb of predicted sites per peak: 2.23

[ view in genome browser :

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

Motif 14 oligos_7nt_mkv4_m4

k-mer sig=7.33; evalue=4.7e-08

yttaGGCCCAttwww

WWWAATGGGCCTAAR

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 142 (21.91%)
Max nb of predicted sites per peak: 16
(3:19304278-19305376(.))
Mean nb of predicted sites per peak: 3.42

[ view in genome browser :

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

Motif 15 oligos_7nt_mkv4_m5

k-mer sig=35.42; evalue=3.8e-36

cmaAAACCCTArmyy

RRKYTAGGGTTTTKG

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 241 (37.19%)
Max nb of predicted sites per peak: 12
(5:5245369-5246641(.))
Mean nb of predicted sites per peak: 2.34

[ 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) ]

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: ING (07/04/2025 19:24)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results