peak-motifs MEthistle1

peak-motifs  -v 1 -title MEthistle1 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.030430_2025-05-21.030430_b90O2g/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.030430_2025-05-21.030430_b90O2g/peak-motifscontrol_seq -markov auto -disco oligos,dyads,positions -nmotifs 10 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -offset 200 -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.030430_2025-05-21.030430_b90O2g

Sequence composition (test sequences)

Nb of peaks: 49
Total seq. size: 33 kb
Min length: 202 bp
Mean length: 666.633 bp
Max length: 701 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: 27124 kb
Min length: 201 bp
Mean length: 655.805 bp
Max length: 701 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

oligos_6nt_test_vs_ctrl

oligos_6nt_test_vs_ctrl_m1	assembly: ccgaca (sig=0.52; e-value=0.3)	RC: tgtcgg
oligos_6nt_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

oligos_7nt_test_vs_ctrl

oligos_7nt_test_vs_ctrl_m1	assembly: agttgtc (sig=0.20; e-value=0.63)	RC: gacaact
oligos_7nt_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

oligos_8nt_test_vs_ctrl

Not a single significant pattern

[oligos_8nt_test_vs_ctrl]

dyads_test_vs_ctrl

Not a single significant pattern

[dyads_test_vs_ctrl]

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

k-mer sig=0.52; evalue=0.3

srCCGaCAmy

RKTGTCGGYS

[ 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 srCCGaCAmy

ARF2:MA1206.1:JASPAR ARF2/MA1206.1/JASPAR D 10 1.0000 0.889 0.889 NA NA

ATCBF3:M0031_1.02:CISBP ATCBF3/M0031_1.02/CISBP R 10 1.0000 0.880 0.880 NA NA

ARF8:M0147_1.02:CISBP ARF8/M0147_1.02/CISBP R 9 0.9000 0.957 0.862 NA NA

Total matches= 195 (192 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: 10 (20.41%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr14g0367981)
Mean nb of predicted sites per peak: 1.30

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

Motif 2 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.20; evalue=0.63

kwaGTTGtCkk

MMGACAACTWM

[ 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 kwaGTTGtCkk

AT2G40620:M0262_1.02:CISBP AT2G40620/M0262_1.02/CISBP R 10 0.9091 0.751 0.682 NA NA

BZIP30:MA1744.1:JASPAR BZIP30/MA1744.1/JASPAR R 10 0.9091 0.706 0.642 NA NA

AT2G21230:M0260_1.02:CISBP AT2G21230/M0260_1.02/CISBP R 10 0.9091 0.706 0.642 NA NA

Total matches= 126 (123 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: 9 (18.37%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr25g0286571)
Mean nb of predicted sites per peak: 1.22

[ 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: MEthistle1 (21/05/2025 03:18)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results