peak-motifs 1

Sequence composition (test sequences)

Nb of peaks: 306
Total seq. size: 323 kb
Min length: 500 bp
Mean length: 1055.08 bp
Max length: 7928 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) ]

Sequence composition (ctrl sequences)

Nb of peaks: 306
Total seq. size: 323 kb
Min length: 500 bp
Mean length: 1055.08 bp
Max length: 7928 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_test_vs_ctrl_m1

k-mer sig=12.44; evalue=3.6e-13

gmvGaaGaaGaGaaaGwag

CTWCTTTCTCTTCTTCBKC

[ 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: 95 (31.05%)
Max nb of predicted sites per peak: 13
(CM028435.1:10881102-10885073)
Mean nb of predicted sites per peak: 2.03

[ view in genome browser :

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=12.44; evalue=3.6e-13

carCtaaGaGaaaGtmv

BKACTTTCTCTTAGYTG

[ 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: 49 (16.01%)
Max nb of predicted sites per peak: 3
(CM028434.1:9866421-9872436)
Mean nb of predicted sites per peak: 1.20

[ view in genome browser :

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=6.70; evalue=2e-07

yvGaaatCga

TCGATTTCBR

[ 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: 55 (17.97%)
Max nb of predicted sites per peak: 3
(CM028435.1:34250266-34251202)
Mean nb of predicted sites per peak: 1.20

[ view in genome browser :

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=6.64; evalue=2.3e-07

crCaaGattCtaCttyg

CRAAGTAGAATCTTGYG

[ 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: 66 (21.57%)
Max nb of predicted sites per peak: 3
(CM028435.1:34360541-34361564)
Mean nb of predicted sites per peak: 1.12

[ view in genome browser :

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=6.08; evalue=8.3e-07

ymGaaCCabm

KVTGGTTCKR

[ 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: 67 (21.90%)
Max nb of predicted sites per peak: 5
(CM028433.1:3546201-3549497)
Mean nb of predicted sites per peak: 1.36

[ view in genome browser :

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

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=7.25; evalue=5.6e-08

rrtaGaaGaGaatrm

KYATTCTCTTCTAYY

[ 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: 55 (17.97%)
Max nb of predicted sites per peak: 4
(CM028433.1:36664747-36668520)
Mean nb of predicted sites per peak: 1.24

[ view in genome browser :

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

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=7.25; evalue=5.6e-08

twGataaGaGaatra

TYATTCTCTTATCWA

[ 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: 35 (11.44%)
Max nb of predicted sites per peak: 2
(CM028435.1:350896-351813)
Mean nb of predicted sites per peak: 1.20

[ view in genome browser :

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

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=6.21; evalue=6.2e-07

wkCtaCtaGcw

WGCTAGTAGMW

[ 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: 24 (7.84%)
Max nb of predicted sites per peak: 2
(CM028432.1:7604822-7606200)
Mean nb of predicted sites per peak: 1.12

[ view in genome browser :

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

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=5.59; evalue=2.6e-06

smaCtCtaCGCys

SRGCGTAGAGTKS

[ 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: 49 (16.01%)
Max nb of predicted sites per peak: 3
(CM028435.1:30807868-30808545)
Mean nb of predicted sites per peak: 1.24

[ view in genome browser :

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

Motif 10 oligos_7nt_test_vs_ctrl_m5

k-mer sig=5.59; evalue=2.6e-06

wkatGGttCarv

BYTGAACCATMW

[ 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: 40 (13.07%)
Max nb of predicted sites per peak: 3
(CM028433.1:28351700-28358426)
Mean nb of predicted sites per peak: 1.12

[ view in genome browser :

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

Motif 11 dyads_test_vs_ctrl_m1

k-mer sig=19.59; evalue=2.6e-20

gaaGarRatGaaGaa

TTCTTCATYYTCTTC

[ 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: 100 (32.68%)
Max nb of predicted sites per peak: 8
(CM028435.1:10881102-10885073)
Mean nb of predicted sites per peak: 2.13

[ view in genome browser :

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

Motif 12 dyads_test_vs_ctrl_m2

k-mer sig=19.59; evalue=2.6e-20

gyaGassssSvssssGaagm

KCTTCSSSSBSSSSSTCTRC

[ 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: 77 (25.16%)
Max nb of predicted sites per peak: 5
(CM028434.1:40673405-40674431)
Mean nb of predicted sites per peak: 1.44

[ view in genome browser :

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

Motif 13 dyads_test_vs_ctrl_m3

k-mer sig=16.56; evalue=2.8e-17

rwGCtsssssssaGarb

VYTCTSSSSSSSAGCWY

[ 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: 49 (16.01%)
Max nb of predicted sites per peak: 3
(CM028433.1:215448-218047)
Mean nb of predicted sites per peak: 1.18

[ view in genome browser :

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

Motif 14 dyads_test_vs_ctrl_m4

k-mer sig=19.59; evalue=2.6e-20

gsaGasssbSswsssrvsysyssraGagg

CCTCTYSSRSRSBYSSSWSSVSSSTCTSC

[ 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: 46 (15.03%)
Max nb of predicted sites per peak: 4
(CM028434.1:40271168-40279096)
Mean nb of predicted sites per peak: 1.20

[ view in genome browser :

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

Motif 15 dyads_test_vs_ctrl_m5

k-mer sig=19.59; evalue=2.6e-20

kyCttSsscKssgmrrssssssdMGaagr

YCTTCKHSSSSSSYYKCSSMGSSSAAGRM

[ 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: 38 (12.42%)
Max nb of predicted sites per peak: 6
(CM028433.1:28351700-28358426)
Mean nb of predicted sites per peak: 1.53

[ 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: 1 (13/01/2025 04:33)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results