peak-motifs test

Sequence composition (test sequences)

Nb of peaks: 839
Total seq. size: 380 kb
Min length: 201 bp
Mean length: 452.95 bp
Max length: 1000 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_6-8nt_m1

k-mer sig=6.58; evalue=2.6e-07

kgCGTGCCrs

SYGGCACGCM

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

footprintDB-plants

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

columns aligned correlation cor kgCGTGCCrs

ABF3:MA0930.2:JASPAR ABF3/MA0930.2/JASPAR D 10 1.0000 0.766 0.766 NA NA

GLYMA-08G357600:UN0420.1:JASPAR GLYMA-08G357600/UN0420.1/JASPAR D 10 1.0000 0.755 0.755 NA NA

MYC3:M0165_1.02:CISBP MYC3/M0165_1.02/CISBP D 10 1.0000 0.704 0.704 NA NA

Total matches= 103 (100 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: 242 (28.84%)
Max nb of predicted sites per peak: 5
(CHLRE_12g546600v5)
Mean nb of predicted sites per peak: 1.41

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

Motif 2 oligos_6-8nt_m2

k-mer sig=5.96; evalue=1.1e-06

rwTACcGTAtww

WWATACGGTAWY

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

footprintDB-plants

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

columns aligned correlation cor rwTACcGTAtww

PK22320.1:M1560_1.02:CISBP PK22320.1/M1560_1.02/CISBP R 10 0.8333 0.762 0.635 NA NA

SPL5:M1565_1.02:CISBP SPL5/M1565_1.02/CISBP R 9 0.7500 0.825 0.619 NA NA

SPL5:MA1059.1:JASPAR SPL5/MA1059.1/JASPAR R 9 0.7500 0.823 0.617 NA NA

Total matches= 43 (40 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: 98 (11.68%)
Max nb of predicted sites per peak: 6
(CHLRE_02g141846v5)
Mean nb of predicted sites per peak: 1.96

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

Motif 3 oligos_6-8nt_m3

k-mer sig=4.87; evalue=1.3e-05

cccCCCTCCCccc

GGGGGGAGGGGGG

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

footprintDB-plants

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

columns aligned correlation cor cccCCCTCCCccc

ODO1motif1B:EEAD0088:EEADannot ODO1motif1B/EEAD0088/EEADannot D 9 0.6923 0.712 0.493 NA NA

TB1:MA1430.2:JASPAR TB1/MA1430.2/JASPAR D 8 0.5714 0.720 0.411 NA NA

TB1:MA1430.1:JASPAR TB1/MA1430.1/JASPAR D 8 0.5333 0.759 0.405 NA NA

Total matches= 3

[ 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: 150 (17.88%)
Max nb of predicted sites per peak: 13
(CHLRE_08g382545v5)
Mean nb of predicted sites per peak: 2.69

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

Motif 4 oligos_6-8nt_m4

k-mer sig=4.01; evalue=9.8e-05

wwwTACAGTAww

WWTACTGTAWWW

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

footprintDB-plants

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

columns aligned correlation cor wwwTACAGTAww

ALOG:EEAD0170:EEADannot ALOG/EEAD0170/EEADannot R 11 0.9167 0.758 0.695 NA NA

AtMYB104_I:AtMYB104_I:AthaMYB AtMYB104_I/AtMYB104_I/AthaMYB R 8 0.6667 0.743 0.496 NA NA

SPL14:M1561_1.02:CISBP SPL14/M1561_1.02/CISBP D 8 0.6154 0.762 0.469 NA NA

Total matches= 7 (4 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: 90 (10.73%)
Max nb of predicted sites per peak: 4
(CHLRE_17g698750v5)
Mean nb of predicted sites per peak: 1.52

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

Motif 5 oligos_6-8nt_m5

k-mer sig=3.57; evalue=0.00027

trTAgATAyw

WRTATCTAYA

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

footprintDB-plants

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

columns aligned correlation cor trTAgATAyw

PK27213.1:M1312_1.02:CISBP PK27213.1/M1312_1.02/CISBP D 10 1.0000 0.709 0.709 NA NA

PK00738.1:M1302_1.02:CISBP PK00738.1/M1302_1.02/CISBP D 10 1.0000 0.704 0.704 NA NA

AT1G19000:M1318_1.02:CISBP AT1G19000/M1318_1.02/CISBP D 10 1.0000 0.703 0.703 NA NA

Total matches= 75 (72 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: 119 (14.18%)
Max nb of predicted sites per peak: 5
(CHLRE_17g698150v5)
Mean nb of predicted sites per peak: 1.37

[ 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) ]
Discovered motifs versus transcription factor databases
Motifs versus footprintDB-plants 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: test (19/06/2025 08:52)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results