RSAT - peak-motifs result

Analysis: Med_uninj_H3k4me1only_introndistalonly_6ntoligo (02/07/2025 13:38)

peak-motifs  -v 1 -title Med_uninj_H3k4me1only_introndistalonly_6ntoligo -i $RSAT/public_html/tmp/www-data/2025/07/02/peak-motifs.2025-07-02.133151_2025-07-02.133151_naV652/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos -nmotifs 10 -minol 6 -maxol 6 -no_merge_lengths -2str -origin center -motif_db JASPAR2024_CORE_vertebrates_non-redundant tf $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2025/07/02/peak-motifs.2025-07-02.133151_2025-07-02.133151_naV652

motif discovery
oligos_6nt_mkv3	oligos_6nt_mkv3_m1 assembly: agacaggaag (sig=23.27; e-value=5.4e-24) RC: cttcctgtct oligos_6nt_mkv3_m2 assembly: gaaatgtat (sig=13.62; e-value=2.4e-14) RC: atacatttc oligos_6nt_mkv3_m3 assembly: aggtcag (sig=13.48; e-value=3.3e-14) RC: ctgacct oligos_6nt_mkv3_m4 assembly: acaaacaa (sig=12.47; e-value=3.4e-13) RC: ttgtttgt oligos_6nt_mkv3_m5 assembly: gtaattac (sig=11.79; e-value=1.6e-12) RC: gtaattac oligos_6nt_mkv3_m6 assembly: aaagaaaa (sig=11.41; e-value=3.9e-12) RC: ttttcttt oligos_6nt_mkv3_m7 assembly: agacaggaaa (sig=13.34; e-value=4.6e-14) RC: tttcctgtct oligos_6nt_mkv3_m8 assembly: acacgcacacac (sig=11.07; e-value=8.5e-12) RC: gtgtgtgcgtgt oligos_6nt_mkv3_m9 assembly: atagataag (sig=10.77; e-value=1.7e-11) RC: cttatctat oligos_6nt_mkv3_m10 assembly: acccaccc (sig=10.52; e-value=3e-11) RC: gggtgggt	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]

Motif discovery
Motif 1   oligos_6nt_mkv3_m1	k-mer sig=23.27; evalue=5.4e-24 rvagaCAGGAAGvv BBCTTCCTGTCTBY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rvagaCAGGAAGvv FOXO1::ELK1 MA1954.2 D 13 0.9286 0.874 0.812 NA NA FOXO1::ELF1 MA1953.2 D 13 0.9286 0.862 0.800 NA NA FOXO1::ELK3 MA1955.2 D 13 0.9286 0.850 0.789 NA NA Total matches= 49 (46 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: 354 (36.38%) Max nb of predicted sites per peak: 19  (17:30158978-30161915) Mean nb of predicted sites per peak: 1.36	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_mkv3_m2	k-mer sig=13.62; evalue=2.4e-14 takAaATGTatwt AWATACATTTMTA	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor takAaATGTatwt DMRTA1 MA1707.2 R 9 0.6429 0.722 0.464 NA NA DMRT3 MA0610.2 D 7 0.5385 0.803 0.432 NA NA Hmga1 MA2124.1 R 7 0.5000 0.809 0.405 NA NA Total matches= 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: 316 (32.48%) Max nb of predicted sites per peak: 83  (3:10655690-10658255) Mean nb of predicted sites per peak: 2.18	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_mkv3_m3	k-mer sig=13.48; evalue=3.3e-14 rgAGGTCAGms SKCTGACCTCY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rgAGGTCAGms NR2F1 MA0017.3 D 11 0.9167 0.896 0.821 NA NA NR4A2 MA0160.3 D 8 0.7273 0.882 0.641 NA NA NR4A1 MA1112.3 D 8 0.7273 0.876 0.637 NA NA Total matches= 61 (58 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: 226 (23.23%) Max nb of predicted sites per peak: 3  (9:32552332-32554331) Mean nb of predicted sites per peak: 1.14	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_6nt_mkv3_m4	k-mer sig=12.47; evalue=3.4e-13 amACAAACAaam KTTTGTTTGTKT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor amACAAACAaam Foxq1 MA0040.2 R 10 0.8333 0.770 0.642 NA NA FOXE1 MA1487.3 D 10 0.7143 0.858 0.613 NA NA FOXC2 MA0846.2 D 10 0.7692 0.731 0.562 NA NA Total matches= 23 (20 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: 250 (25.69%) Max nb of predicted sites per peak: 4  (4:12921249-12922803) Mean nb of predicted sites per peak: 1.32	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   oligos_6nt_mkv3_m5	k-mer sig=11.79; evalue=1.6e-12 mtgTAATTAcak MTGTAATTACAK	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor mtgTAATTAcak Lhx1 MA1518.3 R 10 0.8333 0.845 0.704 NA NA Arx MA0874.2 D 10 0.8333 0.838 0.699 NA NA Lhx3 MA0135.2 D 11 0.8462 0.757 0.641 NA NA Total matches= 97 (94 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: 131 (13.46%) Max nb of predicted sites per peak: 6  (13:5541881-5544511) Mean nb of predicted sites per peak: 2.20	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   oligos_6nt_mkv3_m6	k-mer sig=11.41; evalue=3.9e-12 wwaAAGAAAAaa TTTTTTCTTTWW	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wwaAAGAAAAaa Stat2 MA1623.2 D 9 0.6923 0.761 0.527 NA NA ZNF384 MA1125.2 D 8 0.6667 0.790 0.527 NA NA Gata3 MA0037.5 R 8 0.6667 0.716 0.477 NA NA Total matches= 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: 376 (38.64%) Max nb of predicted sites per peak: 5  (23:16420251-16422259) Mean nb of predicted sites per peak: 1.35	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 7   oligos_6nt_mkv3_m7	k-mer sig=13.34; evalue=4.6e-14 rvagaCAGGAAAav BTTTTCCTGTCTBY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rvagaCAGGAAAav FOXO1::ELF1 MA1953.2 D 13 0.9286 0.795 0.738 NA NA FOXO1::ELK1 MA1954.2 D 13 0.9286 0.775 0.720 NA NA FOXO1::ELK3 MA1955.2 D 13 0.9286 0.761 0.706 NA NA Total matches= 28 (25 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: 322 (33.09%) Max nb of predicted sites per peak: 9  (17:30158978-30161915) Mean nb of predicted sites per peak: 1.28	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 8   oligos_6nt_mkv3_m8	k-mer sig=11.07; evalue=8.5e-12 aCaCACrCACACACaC GTGTGTGTGYGTGTGT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor aCaCACrCACACACaC KLF9 MA1107.3 D 11 0.6875 0.743 0.511 NA NA Total matches= 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: 336 (34.53%) Max nb of predicted sites per peak: 75  (16:10543295-10546446) Mean nb of predicted sites per peak: 7.30	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 9   oligos_6nt_mkv3_m9	k-mer sig=10.77; evalue=1.7e-11 rtatAGATAAGrr YYCTTATCTATAY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rtatAGATAAGrr Gata3 MA0037.5 R 8 0.6154 0.978 0.602 NA NA GATA6 MA1104.3 R 8 0.6154 0.974 0.599 NA NA TRPS1 MA1970.2 R 8 0.6154 0.974 0.599 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: 213 (21.89%) Max nb of predicted sites per peak: 3  (5:17333347-17336050) Mean nb of predicted sites per peak: 1.16	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   oligos_6nt_mkv3_m10	k-mer sig=10.52; evalue=3e-11 ccmCCCmCCCcc GGGGGKGGGKGG	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_vertebrates_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ccmCCCmCCCcc PATZ1 MA1961.2 R 11 0.9167 0.871 0.799 NA NA KLF5 MA0599.1 D 10 0.8333 0.878 0.731 NA NA KLF16 MA0741.1 D 11 0.9167 0.793 0.727 NA NA Total matches= 35 (32 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: 342 (35.15%) Max nb of predicted sites per peak: 34  (17:30158978-30161915) Mean nb of predicted sites per peak: 4.49	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title Med_uninj_H3k4me1only_introndistalonly_6ntoligo -i $RSAT/public_html/tmp/www-data/2025/07/02/peak-motifs.2025-07-02.133151_2025-07-02.133151_naV652/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos -nmotifs 10 -minol 6 -maxol 6 -no_merge_lengths -2str -origin center -motif_db JASPAR2024_CORE_vertebrates_non-redundant tf $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2025/07/02/peak-motifs.2025-07-02.133151_2025-07-02.133151_naV652