peak-motifs gene

Sequence composition (test sequences)

Nb of peaks: 865
Total seq. size: 1772 kb
Min length: 160 bp
Mean length: 2048.02 bp
Max length: 4000 bp [ 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: 865
Total seq. size: 1772 kb
Min length: 160 bp
Mean length: 2048.02 bp
Max length: 4000 bp [ 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=60.34; evalue=4.6e-61

aaaCaaaCaaamaaam

KTTTKTTTGTTTGTTT

[ 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: 518 (59.88%)
Max nb of predicted sites per peak: 25
(chr_022_119_634752_638420)
Mean nb of predicted sites per peak: 3.12

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=60.34; evalue=4.6e-61

kwttktttGattGattg

CAATCAATCAAAMAAWM

[ 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: 482 (55.72%)
Max nb of predicted sites per peak: 19
(chr_105_468_1978037_1981835)
Mean nb of predicted sites per peak: 2.95

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=60.34; evalue=4.6e-61

caaGCaaGCaaaaaarm

KYTTTTTTGCTTGCTTG

[ 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: 445 (51.45%)
Max nb of predicted sites per peak: 12
(chr_105_468_1978037_1981835)
Mean nb of predicted sites per peak: 2.70

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=60.34; evalue=4.6e-61

attCattCaaaaaawm

KWTTTTTTGAATGAAT

[ 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: 308 (35.61%)
Max nb of predicted sites per peak: 5
(chr_128_631_228348_232333)
Mean nb of predicted sites per peak: 1.37

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=25.99; evalue=1e-26

ataGataGatag

CTATCTATCTAT

[ 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: 365 (42.20%)
Max nb of predicted sites per peak: 14
(chr_135_669_1351717_1355314)
Mean nb of predicted sites per peak: 2.14

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=77.47; evalue=3.4e-78

aaaCaaaCaaaCam

KTGTTTGTTTGTTT

[ 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: 501 (57.92%)
Max nb of predicted sites per peak: 35
(chr_099_420_540385_543020)
Mean nb of predicted sites per peak: 3.49

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=77.47; evalue=3.4e-78

caaaCaaaCaaamaaasaa

TTSTTTKTTTGTTTGTTTG

[ 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: 497 (57.46%)
Max nb of predicted sites per peak: 33
(chr_022_119_634752_638420)
Mean nb of predicted sites per peak: 4.01

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=46.49; evalue=3.2e-47

awmaatCaatCaaamaaasaa

TTSTTTKTTTGATTGATTKWT

[ 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: 478 (55.26%)
Max nb of predicted sites per peak: 26
(chr_105_468_1978037_1981835)
Mean nb of predicted sites per peak: 3.33

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=46.49; evalue=3.2e-47

armaaGCaaGCaaamaaaSaa

TTSTTTKTTTGCTTGCTTKYT

[ 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: 464 (53.64%)
Max nb of predicted sites per peak: 21
(chr_105_468_1978037_1981835)
Mean nb of predicted sites per peak: 3.37

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 10 oligos_7nt_test_vs_ctrl_m5

k-mer sig=28.79; evalue=1.6e-29

agataGataGatag

CTATCTATCTATCT

[ 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: 462 (53.41%)
Max nb of predicted sites per peak: 16
(chr_135_669_1351717_1355314)
Mean nb of predicted sites per peak: 2.92

[ sites: text ]
[ 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: gene_down (18/05/2026 12:58)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results