matrix-clustering oct4_motifs_found_in_chen_2008_peak_sets_discovered_by_peak-motifs,_meme-chip_and

matrix-clustering  -v 1 -max_matrices 300 -matrix oct4_peak_motifs $RSAT/public_html/tmp/www-data/2025/05/30/matrix-clustering_2025-05-30.102627_UMluAO/matrix-clustering_query_matrices.transfac transfac -matrix oct4_meme-chip $RSAT/public_html/tmp/www-data/2025/05/30/matrix-clustering_2025-05-30.102627_UMluAO/matrix-clustering_second_matrices. transfac -matrix oct4_homer $RSAT/public_html/tmp/www-data/2025/05/30/matrix-clustering_2025-05-30.102627_UMluAO/matrix-clustering_third_matrices.transfac transfac -hclust_method average -calc sum -title oct4_motifs_found_in_chen_2008_peak_sets_discovered_by_peak-motifs,_meme-chip_and_homer -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -quick -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2025/05/30/matrix-clustering_2025-05-30.102627_UMluAO/matrix-clustering

Results Summary

Nb Input motifs

Nb Input collections

Nb Clusters Found

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Root motifs

Complete results [zip]

Parameters used

Linkage method

Similarity metric

Thresholds to partition the tree

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average

Ncor

Ncor = 0.4
cor = 0.6

Individual Motif View

Motif id	Motif name	Cluster	Collection	Width	IC	Number of sites	Consensus	Consensus (Rev)
oct4_meme-chip_m13_MEME_ChIP_13	MEME_ChIP_13	cluster_1	oct4_meme-chip	24	10.81	21	++KYKMATTWGCATAMWA++++++	++++++twkTATGCWAATkmrm++
oct4_homer_m10_homer_10	homer_10	cluster_8	oct4_homer	10	5.38	10526	sCWkkstyWg	CWRASMMWGS
oct4_peak_motifs_m21_positions_8nt_m3	positions_8nt_m3	cluster_1	oct4_peak_motifs	24	8.25	335	++GCATATGCGCATATGC++++++	++++++gcaTATGCGCATAtgc++
oct4_peak_motifs_m19_positions_8nt_m1	positions_8nt_m1	cluster_1	oct4_peak_motifs	24	10.11	548	+++KWCATTTGCATAACAATRS++	++syaTTgTtATGCAAATgwm+++
oct4_peak_motifs_m18_local_words_8nt_m3	local_words_8nt_m3	cluster_1	oct4_peak_motifs	24	7.34	944	++++dmATATGCATrw++++++++	++++++++WYATGCATATKH++++
oct4_peak_motifs_m3_oligos_7nt_mkv5_m3	oligos_7nt_mkv5_m3	cluster_4	oct4_peak_motifs	11	6.53	1681	SSGAGGGCGSS	ssCGCCCTCss
oct4_homer_m7_homer_7	homer_7	cluster_12	oct4_homer	14	11.18	184	kCCCAgCaCCCACa	TGTGGGTGCTGGGM
oct4_meme-chip_m6_MEME_ChIP_6	MEME_ChIP_6	cluster_13	oct4_meme-chip	8	10.56	236	CAAGGTCA	TGACCTTG
oct4_homer_m2_homer_2	homer_2	cluster_7	oct4_homer	14	7.46	5787	aGgCwGGsCTkGrr	YYCMAGSCCWGCCT
oct4_homer_m18_homer_18	homer_18	cluster_3	oct4_homer	20	4.44	289	++++++TTTTTTTTTT++++	++++AAAAAAAAAA++++++
oct4_meme-chip_m19_MEME_ChIP_19	MEME_ChIP_19	cluster_1	oct4_meme-chip	24	10.70	20	+++CTMATTWGCATAWT+++++++	+++++++awTATGCwAATkAg+++
oct4_meme-chip_m14_MEME_ChIP_14	MEME_ChIP_14	cluster_1	oct4_meme-chip	24	10.37	21	++KYTMATTWGCATAHWR++++++	++++++ywdTATGCWAATkarm++
oct4_homer_m13_homer_13	homer_13	cluster_1	oct4_homer	24	7.74	2056	++++kmATtWGCAW++++++++++	++++++++++WTGCWAATKM++++
oct4_homer_m4_homer_4	homer_4	cluster_2	oct4_homer	14	9.16	519	MSYGCGCATGCGCR	yGCGCAtGCGCrsk
oct4_peak_motifs_m1_oligos_7nt_mkv5_m1	oligos_7nt_mkv5_m1	cluster_1	oct4_peak_motifs	24	7.64	1053	++++WCATTTGCATWW++++++++	++++++++wwATGCAAATgw++++
oct4_meme-chip_m12_MEME_ChIP_12	MEME_ChIP_12	cluster_1	oct4_meme-chip	24	9.00	21	+++++MATTWGCATAWT+++++++	+++++++awTATGCwAATk+++++
oct4_meme-chip_m5_MEME_ChIP_5	MEME_ChIP_5	cluster_2	oct4_meme-chip	14	9.76	307	++TGCGCAkr++++	++++YMTGCGCA++
oct4_meme-chip_m1_MEME_ChIP_1	MEME_ChIP_1	cluster_1	oct4_meme-chip	24	8.47	1856	+++++++TTWRCAT++++++++++	++++++++++ATGYwAA+++++++
oct4_meme-chip_m23_MEME_ChIP_23	MEME_ChIP_23	cluster_1	oct4_meme-chip	24	10.48	2287	+++ykmATTTGCATrw++++++++	++++++++WYATGCAAATKMR+++
oct4_meme-chip_m4_MEME_ChIP_4	MEME_ChIP_4	cluster_6	oct4_meme-chip	10	6.59	5320	++++rGGAAr	YTTCCY++++
oct4_homer_m9_homer_9	homer_9	cluster_1	oct4_homer	24	11.37	148	++++AWATGCGCATAYSM++++++	++++++ksrTATGCGCATwt++++
oct4_homer_m14_homer_14	homer_14	cluster_6	oct4_homer	10	2.84	7519	YTSCWGRRAR	ytyyCwgsar
oct4_meme-chip_m20_MEME_ChIP_20	MEME_ChIP_20	cluster_1	oct4_meme-chip	24	9.83	21	++++++ATTWGCATA+++++++++	+++++++++TATGCwAAT++++++
oct4_meme-chip_m25_MEME_ChIP_25	MEME_ChIP_25	cluster_1	oct4_meme-chip	24	9.96	135	++++++aTtwGCATawsAAwr+++	+++YWTTSWTATGCWAAT++++++
oct4_peak_motifs_m16_local_words_8nt_m1	local_words_8nt_m1	cluster_1	oct4_peak_motifs	24	9.43	744	++++WHATTTGCATAACAAWRS++	++sywTTgTTATGCAAATdw++++
oct4_meme-chip_m3_MEME_ChIP_3	MEME_ChIP_3	cluster_1	oct4_meme-chip	24	9.09	752	++++++++++++WTTGTYAT++++	++++ATrACAAw++++++++++++
oct4_meme-chip_m2_MEME_ChIP_2	MEME_ChIP_2	cluster_4	oct4_meme-chip	11	9.38	1298	CCMCdCCC+++	+++GGGHGKGG
oct4_meme-chip_m16_MEME_ChIP_16	MEME_ChIP_16	cluster_1	oct4_meme-chip	24	8.60	21	++++WMATTWRCATAW++++++++	++++++++wTATGywAATkw++++
oct4_peak_motifs_m14_oligos_8nt_mkv6_m3	oligos_8nt_mkv6_m3	cluster_2	oct4_peak_motifs	14	7.34	674	++SSCGGAAGCGSS	ssCGCTTCCGss++
oct4_peak_motifs_m20_positions_8nt_m2	positions_8nt_m2	cluster_1	oct4_peak_motifs	24	8.84	505	+++++yayATGCATATGCATrtr+	+YAYATGCATATGCATRTR+++++
oct4_homer_m19_homer_19	homer_19	cluster_2	oct4_homer	14	11.03	589	++TGCGCATGCG++	++CGCATGCGCA++
oct4_homer_m6_homer_6	homer_6	cluster_3	oct4_homer	20	9.98	270	++CAAAACAAAACAAA++++	++++TTTGTTtTGtTtTG++
oct4_peak_motifs_m5_local_words_7nt_m1	local_words_7nt_m1	cluster_1	oct4_peak_motifs	24	9.30	806	++++WHATTTGCATAACAAWRS++	++sywTTgTtATGCAAAtdw++++
oct4_meme-chip_m15_MEME_ChIP_15	MEME_ChIP_15	cluster_1	oct4_meme-chip	24	10.68	20	++++++ATTTGCATA+++++++++	+++++++++TATGCAAAT++++++
oct4_homer_m12_homer_12	homer_12	cluster_4	oct4_homer	11	7.15	9841	YYYYYYYYYY+	+rRrrrrrrrR
oct4_homer_m8_homer_8	homer_8	cluster_11	oct4_homer	14	7.99	154	kkrGgTGTGgycyt	ARGRCCACACCYMM
oct4_peak_motifs_m15_oligos_8nt_mkv6_m4	oligos_8nt_mkv6_m4	cluster_2	oct4_peak_motifs	14	7.47	881	++SSCGGCTGCGSS	ssCGCAGCCGss++
oct4_peak_motifs_m2_oligos_7nt_mkv5_m2	oligos_7nt_mkv5_m2	cluster_1	oct4_peak_motifs	24	6.43	1500	+++++AATTAGCATWW++++++++	++++++++wwATGCTAAtt+++++
oct4_peak_motifs_m22_positions_8nt_m4	positions_8nt_m4	cluster_1	oct4_peak_motifs	24	7.98	678	+++++++++wrCATGACAAwr+++	+++YWTTGTCATGYW+++++++++
oct4_homer_m17_homer_17	homer_17	cluster_9	oct4_homer	10	4.37	256	TGTGTGTGTG	CACACACACA
oct4_meme-chip_m18_MEME_ChIP_18	MEME_ChIP_18	cluster_1	oct4_meme-chip	24	10.32	21	++++WMATTWGCATAW++++++++	++++++++wTATGcwAATkw++++
oct4_meme-chip_m11_MEME_ChIP_11	MEME_ChIP_11	cluster_1	oct4_meme-chip	24	7.82	21	+++++AATTWGCATAW++++++++	++++++++wTATGcwAATt+++++
oct4_meme-chip_m8_MEME_ChIP_8	MEME_ChIP_8	cluster_4	oct4_meme-chip	11	9.34	714	++GGMGGMGG+	+CCkCCkCC++
oct4_meme-chip_m21_MEME_ChIP_21	MEME_ChIP_21	cluster_1	oct4_meme-chip	24	7.67	21	++++++ATTWGCATA+++++++++	+++++++++TATGcwAAT++++++
oct4_peak_motifs_m4_oligos_7nt_mkv5_m4	oligos_7nt_mkv5_m4	cluster_1	oct4_peak_motifs	24	7.56	655	++++++++++rmATAACAATrr++	++YYATTGTTATKY++++++++++
oct4_homer_m3_homer_3	homer_3	cluster_5	oct4_homer	14	9.09	7145	sCtsCTGCTgCybs	SVRGCAGCAGSAGS
oct4_meme-chip_m7_MEME_ChIP_7	MEME_ChIP_7	cluster_6	oct4_meme-chip	10	6.64	3566	+++CwGGrA+	+TYCCWG+++
oct4_meme-chip_m10_MEME_ChIP_10	MEME_ChIP_10	cluster_1	oct4_meme-chip	24	10.26	1367	++++++ATTTGCATRWSAAWR+++	+++ywTTswyATGCAaAt++++++
oct4_meme-chip_m17_MEME_ChIP_17	MEME_ChIP_17	cluster_1	oct4_meme-chip	24	10.01	21	++++WAATTWGCATAWW+++++++	+++++++wwTATGCwAATtw++++
oct4_homer_m16_homer_16	homer_16	cluster_3	oct4_homer	20	5.35	4038	++++++YTKKKTTTTK++++	++++mAaAammmAr++++++
oct4_homer_m11_homer_11	homer_11	cluster_7	oct4_homer	14	4.59	9257	+++SWRRGCWGRG+	+cyCwGcyyws+++
oct4_meme-chip_m22_MEME_ChIP_22	MEME_ChIP_22	cluster_3	oct4_meme-chip	20	12.60	27	CMWWMWAAAMAMARMAAMMK	mKkTTkyTkTkTttwkwwkG
oct4_homer_m15_homer_15	homer_15	cluster_5	oct4_homer	14	6.46	4947	SCWGCWGCWG++++	++++CwGCwGCwGs
oct4_peak_motifs_m17_local_words_8nt_m2	local_words_8nt_m2	cluster_1	oct4_peak_motifs	24	9.43	743	++++whATTTGCATAAcAAwrs++	++SYWTTGTTATGCAAATDW++++
oct4_peak_motifs_m9_positions_7nt_m1	positions_7nt_m1	cluster_1	oct4_peak_motifs	24	10.18	285	++++WYATTTGCATATGCAAATRW	wyaTtTgCATATGcAaAtrw++++
oct4_peak_motifs_m10_positions_7nt_m2	positions_7nt_m2	cluster_1	oct4_peak_motifs	24	9.36	781	++++whaTTTGCATaAcAAwrs++	++SYWTTGTTATGCAAATDW++++
oct4_peak_motifs_m8_local_words_7nt_m4	local_words_7nt_m4	cluster_1	oct4_peak_motifs	24	10.02	191	kyaTTgTTaTGCAtAAcAAtrm++	++KYATTGTTATGCATAACAATRM
oct4_homer_m5_homer_5	homer_5	cluster_10	oct4_homer	14	12.64	480	rGGGGCGGRGCsks	SMSGCYCCGCCCCY
oct4_peak_motifs_m7_local_words_7nt_m3	local_words_7nt_m3	cluster_1	oct4_peak_motifs	24	7.58	1083	++++WCATTTGCATATSW++++++	++++++wsATATGCAAATgw++++
oct4_peak_motifs_m11_positions_7nt_m4	positions_7nt_m4	cluster_1	oct4_peak_motifs	24	7.88	397	+++yaTATGCGCATAtr+++++++	+++++++YATATGCGCATATR+++
oct4_peak_motifs_m6_local_words_7nt_m2	local_words_7nt_m2	cluster_1	oct4_peak_motifs	24	9.31	803	++++whaTTTGCATaAcAAwrs++	++SYWTTGTTATGCAAATDW++++
oct4_meme-chip_m24_MEME_ChIP_24	MEME_ChIP_24	cluster_1	oct4_meme-chip	24	7.71	21	++++++ATTWRCATA+++++++++	+++++++++TATGywAAT++++++
oct4_meme-chip_m9_MEME_ChIP_9	MEME_ChIP_9	cluster_4	oct4_meme-chip	11	10.41	58	CCCCwCCyCCm	KGGRGGWGGGG
oct4_peak_motifs_m12_oligos_8nt_mkv6_m1	oligos_8nt_mkv6_m1	cluster_2	oct4_peak_motifs	14	7.44	1056	++sgCGCAGGCGss	SSCGCCTGCGCS++
oct4_homer_m1_homer_1	homer_1	cluster_1	oct4_homer	24	7.11	3620	+++++++TTTGCATAWSAAWR+++	+++ywTTswtATGcAaA+++++++
oct4_peak_motifs_m13_oligos_8nt_mkv6_m2	oligos_8nt_mkv6_m2	cluster_2	oct4_peak_motifs	14	8.33	759	++ygCGCatGCGcr	YGCGCATGCGCR++

Click on the column names to change the order of the data.
Write the name of one cluster, collection or a pattern in the Search window.

Exported files

File	Description
Pairwise comparison	This table shows the pairwise comparison between all the input motifs using different metrics. This is the compare-matrices result.
Matrix description	This table shows information of each input motif.
Cluster-wise Motif Files [zip]	One TRANSFAC file is generated for each cluster including all the input motifs grouped in the corresponding cluster.
Root motifs	A file with the root matrix of each cluster.
Motif collections per cluster	A tab separated file containing the counts of motif of each collection on each cluster.
Clusters	A tab separated file containing the clusters and their correspondng motifs.
Central motifs IDs	A tab separated file containing the central motif, that one who is the most similar to all the others motif in the same cluster.
Central motifs (in TRANSFAC format)	A transfac file containing the central motif, that one who is the most similar to all the others motif within the same cluster.
Collections Complementarity	A dynamic heatmap showing how many motifs contribute each collection to each cluster.
Input motifs	The input motifs analyzed with matrix-clustering.

RSAT - matrix-clustering result

Analysis: oct4_motifs_found_in_chen_2008_peak_sets_discovered_by_peak-motifs,_meme-chip_and_homer (30/05/2025 10:27)

Command

Results Summary

Clusters Summary Table

Individual Cluster View

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Definitions

Individual Motif View

Heatmap View

Exported files