peak-motifs MEnavajowhite2_Up2

Sequence composition (test sequences)

Nb of peaks: 283
Total seq. size: 365 kb
Min length: 2 bp
Mean length: 1288.15 bp
Max length: 1501 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: 41359
Total seq. size: 50495 kb
Min length: 1 bp
Mean length: 1220.9 bp
Max length: 1501 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=1.03; evalue=0.093

scAaCGGCgm

KCGCCGTTGS

[ 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 scAaCGGCgm

PC-MYB1:MA2352.1:JASPAR PC-MYB1/MA2352.1/JASPAR R 9 0.9000 0.889 0.800 NA NA

MYB56:MA1174.2:JASPAR MYB56/MA1174.2/JASPAR D 10 1.0000 0.789 0.789 NA NA

MYB70:MA1393.2:JASPAR MYB70/MA1393.2/JASPAR R 10 0.9091 0.809 0.735 NA NA

Total matches= 89 (86 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: 31 (10.95%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr16g0376851)
Mean nb of predicted sites per peak: 1.10

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=0.33; evalue=0.47

csCatGCGss

SSCGCATGSG

[ 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 csCatGCGss

LEC2:MA0581.1:JASPAR LEC2/MA0581.1/JASPAR D 10 0.9091 0.852 0.775 NA NA

FUS3:MA0565.1:JASPAR FUS3/MA0565.1/JASPAR D 9 0.9000 0.851 0.766 NA NA

AtLEC2:AtLEC2:Athamap AtLEC2/AtLEC2/Athamap D 10 1.0000 0.707 0.707 NA NA

Total matches= 23 (20 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: 46 (16.25%)
Max nb of predicted sites per peak: 5
(gene-Lalb_Chr15g0083521)
Mean nb of predicted sites per peak: 1.30

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=0.31; evalue=0.49

syCaCtTCsc

GSGAAGTGRS

[ 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 syCaCtTCsc

LEC1-A:UN0423.1:JASPAR LEC1-A/UN0423.1/JASPAR R 10 1.0000 0.734 0.734 NA NA

bZIP60:bZIP60_2:ArabidopsisPBM bZIP60/bZIP60_2/ArabidopsisPBM D 10 1.0000 0.713 0.713 NA NA

0300010311:M0363_1.02:CISBP 0300010311/M0363_1.02/CISBP R 10 0.9091 0.713 0.648 NA NA

Total matches= 40 (37 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: 96 (33.92%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr24g0399051)
Mean nb of predicted sites per peak: 1.38

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=0.11; evalue=0.78

rkAAAGCAyr

YRTGCTTTMY

[ 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 rkAAAGCAyr

NAC007:UN0370.1:JASPAR NAC007/UN0370.1/JASPAR D 10 0.9091 0.799 0.726 NA NA

SMB:UN0380.1:JASPAR SMB/UN0380.1/JASPAR D 10 0.9091 0.792 0.720 NA NA

NAC101:UN0377.1:JASPAR NAC101/UN0377.1/JASPAR D 10 0.9091 0.792 0.720 NA NA

Total matches= 85 (82 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: 121 (42.76%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr14g0372811)
Mean nb of predicted sites per peak: 1.36

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

Motif 5 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.15; evalue=0.71

rrtaaaGCawa

TWTGCTTTAYY

[ 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 rrtaaaGCawa

e_gw1.170.52.1:M0659_1.02:CISBP e_gw1.170.52.1/M0659_1.02/CISBP D 10 0.9091 0.744 0.676 NA NA

PHYPADRAFT_140773:MA0987.1:JASPAR PHYPADRAFT_140773/MA0987.1/JASPAR D 10 0.9091 0.744 0.676 NA NA

AT1G64620:M0647_1.02:CISBP AT1G64620/M0647_1.02/CISBP D 10 0.9091 0.743 0.675 NA NA

Total matches= 60 (57 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: 56 (19.79%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr11g0069781)
Mean nb of predicted sites per peak: 1.14

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

Motif 6 dyads_test_vs_ctrl_m1

k-mer sig=0.53; evalue=0.3

scAaCGGCgm

KCGCCGTTGS

[ 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 scAaCGGCgm

PC-MYB1:MA2352.1:JASPAR PC-MYB1/MA2352.1/JASPAR R 9 0.9000 0.889 0.800 NA NA

MYB56:MA1174.2:JASPAR MYB56/MA1174.2/JASPAR D 10 1.0000 0.789 0.789 NA NA

MYB70:MA1393.2:JASPAR MYB70/MA1393.2/JASPAR R 10 0.9091 0.809 0.735 NA NA

Total matches= 89 (86 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: 31 (10.95%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr16g0376851)
Mean nb of predicted sites per peak: 1.10

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

Motif 7 dyads_test_vs_ctrl_m2

k-mer sig=0.53; evalue=0.3

yvaaaSSSSttyrrvbctaasy

RSTTAGVBYYRAASSSSTTTBR

[ 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 yvaaaSSSSttyrrvbctaasy

ANAC062.DAP:M0684:AthalianaCistrome ANAC062.DAP/M0684/AthalianaCistrome D 14 0.6087 0.751 0.457 NA NA

ANAC062.ampDAP:M0672:AthalianaCistrome ANAC062.ampDAP/M0672/AthalianaCistrome D 14 0.5385 0.763 0.411 NA NA

Total matches= 2

[ 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: 33 (11.66%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr20g0123591)
Mean nb of predicted sites per peak: 1.15

[ 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: MEnavajowhite2_Up2_W2 (26/05/2025 03:44)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results