peak-motifs Lsr2A_silencing

Sequence composition (test sequences)

Nb of peaks: 304
Total seq. size: 163 kb
Min length: 167 bp
Mean length: 537.062 bp
Max length: 1000 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: 16361
Total seq. size: 8197 kb
Min length: 279 bp
Mean length: 500.985 bp
Max length: 501 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=60.81; evalue=1.5e-61

wwacgGAATTCcgtww

WWACGGAATTCCGTWW

[ 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: 31 (10.20%)
Max nb of predicted sites per peak: 4
(SAM_Lsr2AHA_MP5_24h_merge_peak_619)
Mean nb of predicted sites per peak: 2.06

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=52.31; evalue=4.9e-53

wsggcATTTCcgTsw

WSACGGAAATGCCSW

[ 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: 47 (15.46%)
Max nb of predicted sites per peak: 3
(SAM_Lsr2AHA_MP5_24h_merge_peak_66)
Mean nb of predicted sites per peak: 1.13

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=52.31; evalue=4.9e-53

mrgkyATTTCCGAAAAggyyr

YRRCCTTTTCGGAAATRMCYK

[ 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: 31 (10.20%)
Max nb of predicted sites per peak: 4
(SAM_Lsr2AHA_MP5_24h_merge_peak_777)
Mean nb of predicted sites per peak: 1.23

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=60.81; evalue=1.5e-61

tmAcgGAAWKCggAARTgcccg

CGGGCAYTTCCGMWTTCCGTKA

[ 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: 29 (9.54%)
Max nb of predicted sites per peak: 2
(SAM_Lsr2AHA_MP5_24h_merge_peak_544)
Mean nb of predicted sites per peak: 1.10

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=52.31; evalue=4.9e-53

mmgGcATTTccgAATgCCra

TYGGCATTCGGAAATGCCKK

[ 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: 26 (8.55%)
Max nb of predicted sites per peak: 2
(SAM_Lsr2AHA_MP5_24h_merge_peak_781)
Mean nb of predicted sites per peak: 1.19

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

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=29.74; evalue=1.8e-30

rwgcggAATTccgcwy

RWGCGGAATTCCGCWY

[ 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: 38 (12.50%)
Max nb of predicted sites per peak: 6
(SAM_Lsr2AHA_MP5_24h_merge_peak_619)
Mean nb of predicted sites per peak: 2.16

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

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=29.74; evalue=1.8e-30

vhcccGAATTccgcwa

TWGCGGAATTCGGGDB

[ 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: 45 (14.80%)
Max nb of predicted sites per peak: 4
(SAM_Lsr2AHA_MP5_24h_merge_peak_544)
Mean nb of predicted sites per peak: 1.24

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

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=20.49; evalue=3.2e-21

ktTcgGAAAAAcgby

RVCGTTTTTCCGAAM

[ 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: 55 (18.09%)
Max nb of predicted sites per peak: 2
(SAM_Lsr2AHA_MP5_24h_merge_peak_544)
Mean nb of predicted sites per peak: 1.07

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

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=19.90; evalue=1.3e-20

ssgcATTTCcgAah

DTTCGGAAATGCSS

[ 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: 40 (13.16%)
Max nb of predicted sites per peak: 2
(SAM_Lsr2AHA_MP5_24h_merge_peak_87)
Mean nb of predicted sites per peak: 1.02

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

Motif 10 oligos_7nt_test_vs_ctrl_m5

k-mer sig=29.74; evalue=1.8e-30

wdgcgGAATTcAcss

SSGTGAATTCCGCHW

[ 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: 58 (19.08%)
Max nb of predicted sites per peak: 2
(SAM_Lsr2AHA_MP5_24h_merge_peak_736)
Mean nb of predicted sites per peak: 1.21

[ 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) ]

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: Lsr2A_silencing_df2 (24/04/2025 17:34)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results