peak-motifs siGATA_vs_siNT

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

sssGCCGCCCCGCCss

SSGGCGGGGCGGCSSS

[ 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 sssGCCGCCCCGCCss

SP1 MA0079.2 D 9 0.5294 0.875 0.463 .......CCCCGCCss CCCCkCCCC.

KLF5 MA0599.1 D 10 0.6250 0.817 0.510 ......GCCCCGCCss gCCMCrCCCh

SP1 MA0079.3 D 10 0.5882 0.839 0.494 ......GCCCCGCCss gCCCCkCCCC.

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: 609 (8.65%)
Max nb of predicted sites per peak: 95
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 8.18

[ 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

ssgGCCGCCCCvGGGCrGggss

SSCCCYGCCCBGGGGCGGCCSS

[ 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 ssgGCCGCCCCvGGGCrGggss

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: 682 (9.69%)
Max nb of predicted sites per peak: 153
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 9.58

[ 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

ssAGGGAGCcs

SGGCTCCCTSS

[ 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 ssAGGGAGCcs

EBF1 MA0154.1 D 7 0.5000 0.884 0.442 ssAGGGA.... ...CmaGGGA

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: 602 (8.55%)
Max nb of predicted sites per peak: 7
(hg19_chr7_130790442_130790741_+)
Mean nb of predicted sites per peak: 1.29

[ 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

sssssscsCGCCCCGCCCvsssss

SSSSSBGGGCGGGGCGSGSSSSSS

[ 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 sssssscsCGCCCCGCCCvsssss

SP2 MA0516.1 D 15 0.6250 0.772 0.482 .........GCCCCGCCCvsssss gyCCCGCCyCyyccs

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: 616 (8.75%)
Max nb of predicted sites per peak: 244
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 18.90

[ 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

sssCCvGCCCCGCCCCvGGGCsss

SSSGCCCBGGGGCGGGGCBGGSSS

[ 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 sssCCvGCCCCGCCCCvGGGCsss

SP1 MA0079.3 D 11 0.4583 0.887 0.406 ......GCCCCGCCCCv....... gCCCCkCCCCy

SP2 MA0516.1 D 15 0.6250 0.781 0.488 ......GCCCCGCCCCvGggC... gyCCCGCCyCyyccs

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: 702 (9.97%)
Max nb of predicted sites per peak: 183
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 11.57

[ 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

ssGCCCCaGGgCss

SSGCCCTGGGGCSS

[ 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 ssGCCCCaGGgCss

TFAP2C MA0524.1 D 13 0.8125 0.883 0.717 csGCCCCaGGgcs. ..ydsCCyCAGGsca

TFAP2A MA0003.2 D 13 0.8125 0.841 0.684 csGCCCCaGGgcs. ..ywGCCysAGGsCa

TFAP2A MA0003.1 D 9 0.6429 0.818 0.526 ..GCCCCaGGg... GCCcbrrGs

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: 753 (10.69%)
Max nb of predicted sites per peak: 33
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 2.97

[ 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

skCCTCAGGys

SRCCTGAGGMS

[ 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 skCCTCAGGys

TFAP2C MA0524.1 D 11 0.7333 0.866 0.635 skCCTCAGGys ...dsCCyCAGGsc.

TFAP2A MA0003.2 D 11 0.7333 0.829 0.608 skCCTCAGGys ...wGCCysAGGsC.

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: 872 (12.38%)
Max nb of predicted sites per peak: 8
(hg19_chr7_56032452_56032951_+)
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 8 oligos_7nt_test_vs_ctrl_m3

ssCCCCGCCCCss

SSGGGGCGGGGSS

[ 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 ssCCCCGCCCCss

SP1 MA0079.3 D 11 0.8462 0.901 0.763 .sCcCCGCCCCs. gCCCCkCCCCy

SP2 MA0516.1 D 12 0.7500 0.886 0.665 .sCcCCGCCCCss gyCCCGCCyCyy...

SP1 MA0079.2 D 10 0.7692 0.870 0.670 ..CcCCGCCCCs. CCCCkCCCCC

Total maches= 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: 671 (9.53%)
Max nb of predicted sites per peak: 56
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 5.11

[ 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

ssGmGGGmGGCG

CGCCKCCCKCSS

[ 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 ssGmGGGmGGCG

E2F3 MA0469.1 R 9 0.5000 0.807 0.403 ssGmGGGmG... ......GGGCGGGAR

EGR1 MA0162.2 R 12 0.8571 0.761 0.652 ssGmGGGmGGcG .GMGKGGGCGGGG.

KLF5 MA0599.1 R 9 0.6923 0.762 0.528 ...mGGGmGGcG DGGGYGKGG.

Total maches= 4 (1 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: 566 (8.04%)
Max nb of predicted sites per peak: 23
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 2.17

[ 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

CrCRCACACRCG

CGYGTGTGYGYG

[ 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 CrCRCACACRCG

EGR2 MA0472.1 D 11 0.6875 0.797 0.548 CrCACACACAC. ....CrCCCACrCac

Arnt::Ahr MA0006.1 R 6 0.5000 0.813 0.407 ....CACACA.. CACGCR

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: 304 (4.32%)
Max nb of predicted sites per peak: 28
(hg19_chr7_93205532_93205880_+)
Mean nb of predicted sites per peak: 3.36

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 11 dyads_test_vs_ctrl_m1

ssCtGCCCtssGGCCvSGGCCCss

SSGGGCCSBGGCCSSAGGGCAGSS

[ 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 ssCtGCCCtssGGCCvSGGCCCss

TFAP2A MA0003.2 R 15 0.6250 0.818 0.511 ...tGCCCtssGGCCagg...... TGSCCTSRGGCWRTK

Zfx MA0146.1 R 14 0.5833 0.770 0.449 .........ssGGCCaggGCCcs. SAGGCCBVGSCSSS

TFAP2C MA0524.1 R 15 0.6250 0.809 0.506 ...tGCCCtssGGCCagg...... TGSCCTGRGGSHRKD

Total maches= 4 (1 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: 675 (9.59%)
Max nb of predicted sites per peak: 120
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 6.89

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 12 dyads_test_vs_ctrl_m2

ssGCCCCGCCCCGCCss

SSGGCGGGGCGGGGCSS

[ 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 ssGCCCCGCCCCGCCss

KLF5 MA0599.1 D 10 0.5882 0.894 0.526 ..gCCCCGCCCC..... gCCMCrCCCh

SP1 MA0079.3 D 11 0.6471 0.857 0.554 ..gCCCCGCCCCG.... gCCCCkCCCCy

SP2 MA0516.1 D 15 0.8824 0.822 0.725 ..gCCCCGCCCCGCCss gyCCCGCCyCyyccs

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: 689 (9.79%)
Max nb of predicted sites per peak: 101
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 7.23

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 13 dyads_test_vs_ctrl_m3

ssGCCbsvsGCCtss

SSAGGCSBSVGGCSS

[ 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 ssGCCbsvsGCCtss

TFAP2A MA0003.1 D 9 0.6000 0.890 0.534 ..GCCbsvsGC.... GCCcbrrGs

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: 622 (8.83%)
Max nb of predicted sites per peak: 57
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 4.52

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 14 dyads_test_vs_ctrl_m4

ssGGCssssssssssCCCss

SSGGGSSSSSSSSSSGCCSS

[ 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 ssGGCssssssssssCCCss

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: 614 (8.72%)
Max nb of predicted sites per peak: 216
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 16.47

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 15 dyads_test_vs_ctrl_m5

ssCvGsssssssssssssssssssgGCss

SSGCCSSSSSSSSSSSSSSSSSSSCBGSS

[ 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 ssCvGsssssssssssssssssssgGCss

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: 564 (8.01%)
Max nb of predicted sites per peak: 374
(hg19_chr7_140372612_140372961_+)
Mean nb of predicted sites per peak: 35.73

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

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]

RSA-tools - peak-motifs result

Analysis: siGATA_vs_siNT_r3 (07/10/2014 15:14)

Command

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 ssgGCCGCCCCvGGGCrGggss

Total maches= 0

jaspar_core_vertebrates

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

columns aligned correlation cor ssAGGGAGCcs

EBF1 MA0154.1 D 7 0.5000 0.884 0.442 ssAGGGA.... ...CmaGGGA

Total maches= 1

jaspar_core_vertebrates

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

columns aligned correlation cor sssssscsCGCCCCGCCCvsssss

SP2 MA0516.1 D 15 0.6250 0.772 0.482 .........GCCCCGCCCvsssss gyCCCGCCyCyyccs

Total maches= 1

jaspar_core_vertebrates

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

columns aligned correlation cor ssGCCbsvsGCCtss

TFAP2A MA0003.1 D 9 0.6000 0.890 0.534 ..GCCbsvsGC.... GCCcbrrGs

Total maches= 1

jaspar_core_vertebrates

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

columns aligned correlation cor ssGGCssssssssssCCCss

Total maches= 0

jaspar_core_vertebrates

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

columns aligned correlation cor ssCvGsssssssssssssssssssgGCss

Total maches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSA-tools - peak-motifs result

Analysis: siGATA_vs_siNT_r3 (07/10/2014 15:14)

Command

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 ssgGCCGCCCCvGGGCrGggss Total maches= 0

jaspar_core_vertebrates name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor ssAGGGAGCcs EBF1 MA0154.1 D 7 0.5000 0.884 0.442 ssAGGGA.... ...CmaGGGA Total maches= 1

jaspar_core_vertebrates name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor sssssscsCGCCCCGCCCvsssss SP2 MA0516.1 D 15 0.6250 0.772 0.482 .........GCCCCGCCCvsssss gyCCCGCCyCyyccs Total maches= 1

jaspar_core_vertebrates name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor CrCRCACACRCG EGR2 MA0472.1 D 11 0.6875 0.797 0.548 CrCACACACAC. ....CrCCCACrCac Arnt::Ahr MA0006.1 R 6 0.5000 0.813 0.407 ....CACACA.. CACGCR Total maches= 2

jaspar_core_vertebrates name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor ssGCCbsvsGCCtss TFAP2A MA0003.1 D 9 0.6000 0.890 0.534 ..GCCbsvsGC.... GCCcbrrGs Total maches= 1

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

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

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 ssgGCCGCCCCvGGGCrGggss

Total maches= 0

jaspar_core_vertebrates

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

columns aligned correlation cor ssAGGGAGCcs

EBF1 MA0154.1 D 7 0.5000 0.884 0.442 ssAGGGA.... ...CmaGGGA

Total maches= 1

jaspar_core_vertebrates

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

columns aligned correlation cor sssssscsCGCCCCGCCCvsssss

SP2 MA0516.1 D 15 0.6250 0.772 0.482 .........GCCCCGCCCvsssss gyCCCGCCyCyyccs

Total maches= 1

jaspar_core_vertebrates

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

columns aligned correlation cor ssGCCbsvsGCCtss

TFAP2A MA0003.1 D 9 0.6000 0.890 0.534 ..GCCbsvsGC.... GCCcbrrGs

Total maches= 1

jaspar_core_vertebrates

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

columns aligned correlation cor ssGGCssssssssssCCCss

Total maches= 0

jaspar_core_vertebrates

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

columns aligned correlation cor ssCvGsssssssssssssssssssgGCss

Total maches= 0