peak-motifs p300_heart_versus_limb

Sequence composition (test sequences)

Nb of peaks: 1000
Total seq. size: 815 kb
Min length: 283 bp
Mean length: 814.943 bp
Max length: 2636 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: 1000
Total seq. size: 680 kb
Min length: 276 bp
Mean length: 679.55 bp
Max length: 2301 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=87.40; evalue=4e-88

tyCTTATCTCtgacy

RGTCAGAGATAAGRA

[ 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: 253 (25.30%)
Max nb of predicted sites per peak: 4
(mm9_chr4_13192038_13193491_+)
Mean nb of predicted sites per peak: 1.16

[ 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=87.40; evalue=4e-88

rhcCTGATAAGra

TYCTTATCAGGDY

[ 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: 200 (20.00%)
Max nb of predicted sites per peak: 3
(mm9_chr6_50840518_50841477_+)
Mean nb of predicted sites per peak: 1.14

[ 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=35.83; evalue=1.5e-36

gkcTGGGTGACAGtsd

HSACTGTCACCCAGMC

[ 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: 166 (16.60%)
Max nb of predicted sites per peak: 3
(mm9_chr6_87532831_87533981_+)
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 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=40.18; evalue=6.6e-41

kstcAGAGATAGGrr

YYCCTATCTCTGASM

[ 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: 175 (17.50%)
Max nb of predicted sites per peak: 4
(mm9_chr1_187295885_187297742_+)
Mean nb of predicted sites per peak: 1.17

[ 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=35.83; evalue=1.5e-36

rsaCTgTCCTGTCACCcagkc

GMCTGGGTGACAGGACAGTSY

[ 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: 160 (16.00%)
Max nb of predicted sites per peak: 3
(mm9_chr13_73435821_73437168_+)
Mean nb of predicted sites per peak: 1.09

[ 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=65.50; evalue=3.2e-66

rsAGAGATAAGGma

TKCCTTATCTCTSY

[ 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: 252 (25.20%)
Max nb of predicted sites per peak: 4
(mm9_chr3_101234265_101235240_+)
Mean nb of predicted sites per peak: 1.14

[ 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=47.72; evalue=1.9e-48

ttCCTTATCAGtgh

DCACTGATAAGGAA

[ 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: 193 (19.30%)
Max nb of predicted sites per peak: 3
(mm9_chr8_28199211_28199982_+)
Mean nb of predicted sites per peak: 1.21

[ 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=27.78; evalue=1.7e-28

ghaaCTGTCACCAsr

YSTGGTGACAGTTDC

[ 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: 195 (19.50%)
Max nb of predicted sites per peak: 3
(mm9_chr8_122817058_122818100_+)
Mean nb of predicted sites per peak: 1.16

[ 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=65.50; evalue=3.2e-66

rragggacAGATAAGGma

TKCCTTATCTGTCCCTYY

[ 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: 215 (21.50%)
Max nb of predicted sites per peak: 3
(mm9_chr6_30571555_30572999_+)
Mean nb of predicted sites per peak: 1.19

[ 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=65.50; evalue=3.2e-66

rsAGAGATAAGArw

WYTCTTATCTCTSY

[ 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: 274 (27.40%)
Max nb of predicted sites per peak: 4
(mm9_chr6_30571555_30572999_+)
Mean nb of predicted sites per peak: 1.15

[ 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: p300_heart_versus_limb_Blow2010 (17/01/2025 06:55)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results