peak-motifs STAT1_motif

Sequence composition (test sequences)

Nb of peaks: 2400
Total seq. size: 482 kb
Min length: 201 bp
Mean length: 201 bp
Max length: 201 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_7nt_mkv4_m1

srTTTCCwGGAAay

RTTTCCWGGAAAYS

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor srTTTCCwGGAAay

STAT1 MA0137.2 D 14 0.9333 0.967 0.903 srTTTCCwGGAAay cayTTCChrGAAry.

Stat3 MA0144.1 D 10 0.7143 0.948 0.677 ...TTCCwGGAAa. TTCCaGGAAr

NFATC2 MA0152.1 D 7 0.5000 0.913 0.456 .rTTTCCw...... TTTTCCA

Total maches= 6 (3 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: 1208 (50.33%)
Max nb of predicted sites per peak: 5
(EP_1460)
Mean nb of predicted sites per peak: 1.67

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

Motif 2 oligos_7nt_mkv4_m2

rwrTGAsTCATky

RMATGASTCAYWY

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor rwrTGAsTCATky

AP1 MA0099.2 R 7 0.5385 0.951 0.512 ...TGAsTCA... TGAKTCA

NFE2L1::MafG MA0089.1 R 6 0.4615 0.942 0.435 ......sTCATt. GTCATS

Pax2 MA0067.1 R 8 0.6154 0.767 0.472 rwrTGAsT..... VMRTGACW

Total maches= 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: 492 (20.50%)
Max nb of predicted sites per peak: 4
(EP_809)
Mean nb of predicted sites per peak: 1.73

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

Motif 3 oligos_7nt_mkv4_m3

ryTTCCmrGAAry

RYTTCYKGGAARY

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor ryTTCCmrGAAry

STAT1 MA0137.2 D 13 0.8667 0.972 0.842 ryTTCCmrGAAry .ayTTCChrGAAry.

Stat3 MA0144.1 R 10 0.7692 0.922 0.709 .yTTCCmrGAA.. YTTCCTGGAA

NFATC2 MA0152.1 D 7 0.5385 0.875 0.471 ryTTCCm...... TTTTCCA

Total maches= 8 (5 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: 1119 (46.62%)
Max nb of predicted sites per peak: 4
(EP_2382)
Mean nb of predicted sites per peak: 1.12

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

Motif 4 local_words_7nt_m1

wbwCATTTcCygkAAATGtat

ATACATTTMCRGGAAATGWVW

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor wbwCATTTcCygkAAATGtat

STAT1 MA0137.2 D 15 0.7143 0.778 0.556 ...CATTTcchgkAAATG... cayTTCChrGAAryc

Stat3 MA0144.1 D 10 0.4762 0.860 0.410 ......TTcchgkAAA..... TTCCaGGAAr

Total maches= 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: 294 (12.25%)
Max nb of predicted sites per peak: 4
(EP_1636)
Mean nb of predicted sites per peak: 1.58

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

Motif 5 local_words_7nt_m2

awaCATTTcybgkaaATGtaw

WTACATTTMCVRGAAATGTWT

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor awaCATTTcybgkaaATGtaw

Total maches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 248 (10.33%)
Max nb of predicted sites per peak: 4
(EP_1636)
Mean nb of predicted sites per peak: 1.43

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

Motif 6 local_words_7nt_m3

kdaCATTTyCcrgaAATGtmt

AKACATTTCYGGRAAATGTHM

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor kdaCATTTyCcrgaAATGtmt

STAT1 MA0137.2 D 15 0.7143 0.783 0.559 ...CATTTyCmrgaAATG... cayTTCChrGAAryc

Total maches= 1

[ 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: 332 (13.83%)
Max nb of predicted sites per peak: 3
(EP_87)
Mean nb of predicted sites per peak: 1.41

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

Motif 7 positions_7nt_m1

wsTsrtTTCCwGGAAatsasa

TSTSATTTCCWGGAAAYSASW

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor wsTsrtTTCCwGGAAatsasa

STAT1 MA0137.2 R 15 0.7143 0.945 0.675 ...srTTTCCwGGAAats... GRYTTCYDGGAARTG

Stat3 MA0144.1 D 10 0.4762 0.948 0.451 ......TTCCwGGAAa..... TTCCaGGAAr

GABPA MA0062.2 D 11 0.5238 0.778 0.408 .........CwGGAAatsAs. CCGGAAGygvc

Total maches= 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: 793 (33.04%)
Max nb of predicted sites per peak: 4
(EP_648)
Mean nb of predicted sites per peak: 1.70

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

Motif 8 positions_7nt_m2

ksTsatTTCCcrGAAATsAsr

YSTSATTTCYGGGAAATSASM

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor ksTsatTTCCcrGAAATsAsr

STAT1 MA0137.2 D 15 0.7143 0.916 0.654 ...satTTCCcrGAAATs... cayTTCChrGAAryc

Stat3 MA0144.1 R 10 0.4762 0.906 0.432 .....tTTCCcrGAA...... YTTCCTGGAA

Total maches= 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: 674 (28.08%)
Max nb of predicted sites per peak: 5
(EP_1946)
Mean nb of predicted sites per peak: 1.37

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

Motif 9 positions_7nt_m3

srTTTCYdGGAArtsr

YSAYTTCCHRGAAAYS

[ matrix: tab format transfac format ]

jaspar_core_vertebrates

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

columns aligned correlation cor srTTTCYdGGAArtsr

STAT1 MA0137.2 R 15 0.9375 0.975 0.914 srTTTCYwGGAArts. GRYTTCYDGGAARTG

Stat3 MA0144.1 D 10 0.6250 0.963 0.602 ...TTCYwGGAAr... TTCCaGGAAr

FEV MA0156.1 D 8 0.5000 0.925 0.462 ......YwGGAArt.. CAGGAArT

Total maches= 5 (2 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: 1241 (51.71%)
Max nb of predicted sites per peak: 5
(EP_479)
Mean nb of predicted sites per peak: 1.61

[ 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 ] [ graph: gml (for CytoScape) ]
Discovered motifs versus transcription factor databases
Motifs versus jaspar_core_vertebrates 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.

RSA-tools - peak-motifs result

Analysis: STAT1_motif_Analysis (11/01/2013 11:12)

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

jaspar_core_vertebrates

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

columns aligned correlation cor awaCATTTcybgkaaATGtaw

Total maches= 0

jaspar_core_vertebrates

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

columns aligned correlation cor kdaCATTTyCcrgaAATGtmt

STAT1 MA0137.2 D 15 0.7143 0.783 0.559 ...CATTTyCmrgaAATG... cayTTCChrGAAryc

Total maches= 1

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSA-tools - peak-motifs result

Analysis: STAT1_motif_Analysis (11/01/2013 11:12)

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

jaspar_core_vertebrates name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor awaCATTTcybgkaaATGtaw Total maches= 0

jaspar_core_vertebrates name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor kdaCATTTyCcrgaAATGtmt STAT1 MA0137.2 D 15 0.7143 0.783 0.559 ...CATTTyCmrgaAATG... cayTTCChrGAAryc Total maches= 1

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

jaspar_core_vertebrates

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

columns aligned correlation cor awaCATTTcybgkaaATGtaw

Total maches= 0

jaspar_core_vertebrates

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

columns aligned correlation cor kdaCATTTyCcrgaAATGtmt

STAT1 MA0137.2 D 15 0.7143 0.783 0.559 ...CATTTyCmrgaAATG... cayTTCChrGAAryc

Total maches= 1