RSAT - peak-motifs result

Analysis: 468BrM_CancerMetabolism (30/03/2026 23:29)

peak-motifs  -v 1 -title 468BrM_CancerMetabolism -i $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.204106_2026-03-30.204106_ShgQoa/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db ENCODE tf $RSAT/public_html/motif_databases/ENCODE/encode-motifs_Kheradpour_Kellis_NAR2013.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/2026/03/30/peak-motifs.2026-03-30.204106_2026-03-30.204106_ShgQoa

motif discovery
oligos_6nt_mkv3	oligos_6nt_mkv3_m1 assembly: gcctccc (sig=7.34; e-value=4.6e-08) RC: gggaggc oligos_6nt_mkv3_m2 assembly: acccagc (sig=4.45; e-value=3.5e-05) RC: gctgggt oligos_6nt_mkv3_m3 assembly: cgccccgcccg (sig=4.04; e-value=9.1e-05) RC: cgggcggggcg oligos_6nt_mkv3_m4 assembly: gcgccgc (sig=2.82; e-value=0.0015) RC: gcggcgc oligos_6nt_mkv3_m5 assembly: cgagcg (sig=1.65; e-value=0.022) RC: cgctcg	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_6nt	Not a single significant pattern	[positions_6nt]
oligos_7nt_mkv4	oligos_7nt_mkv4_m1 assembly: ccactgc (sig=2.26; e-value=0.0055) RC: gcagtgg oligos_7nt_mkv4_m2 assembly: gggattaca (sig=2.10; e-value=0.0079) RC: tgtaatccc oligos_7nt_mkv4_m3 assembly: cgctcgc (sig=2.02; e-value=0.0095) RC: gcgagcg oligos_7nt_mkv4_m4 assembly: aaaggca (sig=2.01; e-value=0.0098) RC: tgccttt oligos_7nt_mkv4_m5 assembly: aagtgct (sig=1.77; e-value=0.017) RC: agcactt	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_7nt	Not a single significant pattern	[positions_7nt]

Motif discovery
Motif 1   oligos_6nt_mkv3_m1	k-mer sig=7.34; evalue=4.6e-08 ccGCCTCCCms SKGGGAGGCGG	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ccGCCTCCCms ZNF263_disc1 ZNF263_disc1 R 10 0.9091 0.819 0.745 NA NA SP1_known6 SP1_known6 D 10 0.9091 0.780 0.709 NA NA SP1_known4 SP1_known4 R 10 0.9091 0.752 0.684 NA NA Total matches= 24 (21 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: 102 (9.62%) Max nb of predicted sites per peak: 13  (chr17:82098093-82098519) Mean nb of predicted sites per peak: 1.70	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_mkv3_m2	k-mer sig=4.45; evalue=3.5e-05 rsaCCCAGCmc GKGCTGGGTSY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rsaCCCAGCmc NANOG_disc3 NANOG_disc3 D 9 0.7500 0.809 0.607 NA NA CACBP_1 CACBP_1 R 8 0.6667 0.794 0.529 NA NA NFKB_disc2 NFKB_disc2 R 9 0.6429 0.788 0.507 NA NA Total matches= 12 (9 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: 112 (10.57%) Max nb of predicted sites per peak: 3  (chr1:225930002-225930182) Mean nb of predicted sites per peak: 1.21	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_mkv3_m3	k-mer sig=4.04; evalue=9.1e-05 ssCGCCCCGCCCsss SSSGGGCGGGGCGSS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ssCGCCCCGCCCsss IRF_disc4 IRF_disc4 R 15 1.0000 0.841 0.841 NA NA SP1_known2 SP1_known2 R 13 0.8667 0.885 0.767 NA NA SP1_known5 SP1_known5 R 13 0.8667 0.872 0.755 NA NA Total matches= 53 (50 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: 63 (5.94%) Max nb of predicted sites per peak: 88  (chr17:82098093-82098519) Mean nb of predicted sites per peak: 10.73	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_6nt_mkv3_m4	k-mer sig=2.82; evalue=0.0015 ssGCGCCGCss SSGCGGCGCSS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ssGCGCCGCss YY1_disc3 YY1_disc3 R 10 0.9091 0.839 0.763 NA NA E2F_disc7 E2F_disc7 R 10 0.9091 0.824 0.749 NA NA TATA_disc10 TATA_disc10 D 10 0.9091 0.779 0.708 NA NA Total matches= 30 (27 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: 53 (5.00%) Max nb of predicted sites per peak: 56  (chr17:82098093-82098519) Mean nb of predicted sites per peak: 7.28	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   oligos_6nt_mkv3_m5	k-mer sig=1.65; evalue=0.022 ssCGaGCGss SSCGCTCGSS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ssCGaGCGss EGR1_disc7 EGR1_disc7 D 10 1.0000 0.803 0.803 NA NA AHR_ARNT_HIF1A_1 AHR_ARNT_HIF1A_1 D 9 0.9000 0.797 0.718 NA NA NRF1_disc3 NRF1_disc3 D 9 0.8182 0.750 0.614 NA NA Total matches= 13 (10 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: 42 (3.96%) Max nb of predicted sites per peak: 9  (chr10:87094813-87095031) Mean nb of predicted sites per peak: 2.88	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   oligos_7nt_mkv4_m1	k-mer sig=2.26; evalue=0.0055 vsCCACTGCms SKGCAGTGGSB	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor vsCCACTGCms KLF12_1 KLF12_1 R 7 0.6364 0.928 0.590 NA NA ZBTB3_1 ZBTB3_1 D 11 0.6471 0.874 0.566 NA NA GFI1B_1 GFI1B_1 D 10 0.7692 0.705 0.542 NA NA Total matches= 17 (14 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: 70 (6.60%) Max nb of predicted sites per peak: 5  (chr15:72231133-72231729) Mean nb of predicted sites per peak: 1.14	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 7   oligos_7nt_mkv4_m2	k-mer sig=2.10; evalue=0.0079 ctgGGATTACAgg CCTGTAATCCCAG	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ctgGGATTACAgg PITX2_1 PITX2_1 R 11 0.8462 0.798 0.675 NA NA GSC2_1 GSC2_1 R 10 0.7692 0.770 0.592 NA NA DMBX1_2 DMBX1_2 D 10 0.7692 0.762 0.586 NA NA Total matches= 19 (16 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: 86 (8.11%) Max nb of predicted sites per peak: 2  (chr1:225930002-225930182) Mean nb of predicted sites per peak: 1.06	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 8   oligos_7nt_mkv4_m3	k-mer sig=2.02; evalue=0.0095 ssCGCkCGCss SSGCGMGCGSS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ssCGCkCGCss EGR1_disc7 EGR1_disc7 R 10 0.9091 0.856 0.778 NA NA HDAC2_disc4 HDAC2_disc4 R 10 0.9091 0.815 0.741 NA NA SETDB1_disc2 SETDB1_disc2 R 10 0.9091 0.804 0.731 NA NA Total matches= 32 (29 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: 43 (4.06%) Max nb of predicted sites per peak: 18  (chr10:87094813-87095031) Mean nb of predicted sites per peak: 5.30	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 9   oligos_7nt_mkv4_m4	k-mer sig=2.01; evalue=0.0098 ktAAAGGCAyr YRTGCCTTTAM	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ktAAAGGCAyr NR2E1_3 NR2E1_3 D 9 0.8182 0.745 0.610 NA NA NR2E1_1 NR2E1_1 D 9 0.8182 0.732 0.599 NA NA E2F_disc5 E2F_disc5 D 8 0.7273 0.727 0.529 NA NA Total matches= 9 (6 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: 53 (5.00%) Max nb of predicted sites per peak: 2  (chr17:82133577-82133800) Mean nb of predicted sites per peak: 1.04	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   oligos_7nt_mkv4_m5	k-mer sig=1.77; evalue=0.017 mwAAGTGCTrr YYAGCACTTWK	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ENCODE name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor mwAAGTGCTrr NKX2-2_1 NKX2-2_1 D 10 0.9091 0.756 0.687 NA NA NKX3-2_3 NKX3-2_3 R 9 0.8182 0.804 0.658 NA NA NKX3-1_6 NKX3-1_6 R 9 0.8182 0.794 0.650 NA NA Total matches= 27 (24 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: 61 (5.75%) Max nb of predicted sites per peak: 2  (chr19:34333299-34333499) Mean nb of predicted sites per peak: 1.02	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title 468BrM_CancerMetabolism -i $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.204106_2026-03-30.204106_ShgQoa/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db ENCODE tf $RSAT/public_html/motif_databases/ENCODE/encode-motifs_Kheradpour_Kellis_NAR2013.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/2026/03/30/peak-motifs.2026-03-30.204106_2026-03-30.204106_ShgQoa

Warning: Not a single pattern was found in file tmp/www-data/2026/03/30/peak-motifs.2026-03-30.204106_2026-03-30.204106_ShgQoa/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab

Warning: Not a single pattern was found in file tmp/www-data/2026/03/30/peak-motifs.2026-03-30.204106_2026-03-30.204106_ShgQoa/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab