RSAT - matrix-clustering result

Analysis: hsc_lincorr_combined_dedup (12/04/2026 14:52)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix hsc_lincorr_combined_dedup $RSAT/public_html/tmp/www-data/2026/04/12/matrix-clustering_2026-04-12.145203_036hSY/matrix-clustering_query_matrices.homer homer -hclust_method average -calc sum -title hsc_lincorr_combined_dedup -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/2026/04/12/matrix-clustering_2026-04-12.145203_036hSY/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

Logo Forest (dynamic browsing)

Logo Forest (rapid overview - low image quality)

Clusters Summary

Clusters Summary Table

Cluster ID	# Motifs	Motif_Name::Collection	Number of Motifs by Collection	Root Motif (transfac Format)
cluster_1	5	homer_25.AGATAASR::hsc_lincorr_combined_dedup:: homer_17.SAGATAAGRV::hsc_lincorr_combined_dedup:: homer_22.BBCTTATCTS::hsc_lincorr_combined_dedup:: homer_12.YCTTATCTBN::hsc_lincorr_combined_dedup:: homer_13.NBWGATAAGR::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::5_motifs	Show matrix
cluster_2	13	homer_29.AWWWTGCTGAGTCAT::hsc_lincorr_combined_dedup:: homer_73.AWWNTGCTGAGTCAT::hsc_lincorr_combined_dedup:: homer_18.TGCTGAGTCA::hsc_lincorr_combined_dedup:: homer_76.TGCTGACTCA::hsc_lincorr_combined_dedup:: homer_31.VTGACTCATC::hsc_lincorr_combined_dedup:: homer_38.RATGASTCAT::hsc_lincorr_combined_dedup:: homer_39.DATGASTCAT::hsc_lincorr_combined_dedup:: homer_37.NDATGASTCAYN::hsc_lincorr_combined_dedup:: homer_41.NNATGASTCATH::hsc_lincorr_combined_dedup:: homer_52.GGATGACTCATC::hsc_lincorr_combined_dedup:: homer_46.NATGASTCABNN::hsc_lincorr_combined_dedup:: homer_36.DATGASTCATHN::hsc_lincorr_combined_dedup:: homer_47.GATGASTCATCN::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::13_motifs	Show matrix
cluster_3	28	homer_70.MGGAAGTGAAAC::hsc_lincorr_combined_dedup:: homer_43.GAAASYGAAASY::hsc_lincorr_combined_dedup:: homer_35.GAAAGTGAAAGT::hsc_lincorr_combined_dedup:: homer_48.AGTTTCASTTTC::hsc_lincorr_combined_dedup:: homer_33.GRAASTGAAAST::hsc_lincorr_combined_dedup:: homer_40.AGTTTCAKTTTC::hsc_lincorr_combined_dedup:: homer_55.SVYTTCCNGGAARB::hsc_lincorr_combined_dedup:: homer_59.NYTTCCWGGAAR::hsc_lincorr_combined_dedup:: homer_49.RCAGGATGTGGT::hsc_lincorr_combined_dedup:: homer_32.AAAGRGGAAGTG::hsc_lincorr_combined_dedup:: homer_9.MACAGGAAGT::hsc_lincorr_combined_dedup:: homer_1.ATTTCCTGTN::hsc_lincorr_combined_dedup:: homer_23.VACAGGAAAT::hsc_lincorr_combined_dedup:: homer_60.ASWTCCTGBT::hsc_lincorr_combined_dedup:: homer_5.RACCGGAAGT::hsc_lincorr_combined_dedup:: homer_15.AVCCGGAAGT::hsc_lincorr_combined_dedup:: homer_3.AACCGGAAGT::hsc_lincorr_combined_dedup:: homer_10.ACTTCCKGKT::hsc_lincorr_combined_dedup:: homer_27.AVCAGGAAGT::hsc_lincorr_combined_dedup:: homer_11.ACVAGGAAGT::hsc_lincorr_combined_dedup:: homer_16.ANCAGGAAGT::hsc_lincorr_combined_dedup:: homer_7.NNAYTTCCTGHN::hsc_lincorr_combined_dedup:: homer_8.NRYTTCCGGH::hsc_lincorr_combined_dedup:: homer_2.ACCGGAAGTG::hsc_lincorr_combined_dedup:: homer_71.HACTTCCGGY::hsc_lincorr_combined_dedup:: homer_72.NRYTTCCGGY::hsc_lincorr_combined_dedup:: homer_4.ACAGGAAGTG::hsc_lincorr_combined_dedup:: homer_6.AGAGGAAGTG::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::28_motifs	Show matrix
cluster_4	4	homer_53.NWAACCACADNN::hsc_lincorr_combined_dedup:: homer_42.SAAACCACAG::hsc_lincorr_combined_dedup:: homer_51.GCTGTGGTTW::hsc_lincorr_combined_dedup:: homer_57.AAACCACARM::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::4_motifs	Show matrix
cluster_5	3	homer_65.CARRGKBCAAAGTYCA::hsc_lincorr_combined_dedup:: homer_30.CAAAGGTCAG::hsc_lincorr_combined_dedup:: homer_69.TTGAMCTTTG::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::3_motifs	Show matrix
cluster_6	6	homer_24.RGKGGGCGKGGC::hsc_lincorr_combined_dedup:: homer_28.RGKGGGCGGAGC::hsc_lincorr_combined_dedup:: homer_26.YGGCCCCGCCCC::hsc_lincorr_combined_dedup:: homer_61.DGGGYGKGGC::hsc_lincorr_combined_dedup:: homer_34.CCCCTCCCCCAC::hsc_lincorr_combined_dedup:: homer_68.GGGGGGGG::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::6_motifs	Show matrix
cluster_7	2	homer_50.GGGGGAATCCCC::hsc_lincorr_combined_dedup:: homer_64.VGGGRATTYCCC::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::2_motifs	Show matrix
cluster_8	2	homer_21.CYTGGCABNSTGCCAR::hsc_lincorr_combined_dedup:: homer_63.CTGGCAGSCTGCCA::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::2_motifs	Show matrix
cluster_9	2	homer_19.GCTATTTTTAGC::hsc_lincorr_combined_dedup:: homer_67.CYAAAAATAG::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::2_motifs	Show matrix
cluster_10	2	homer_14.TGGCAGTTGG::hsc_lincorr_combined_dedup:: homer_20.GGCVGTTR::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::2_motifs	Show matrix
cluster_11	3	homer_75.VTTACGTAAYNNNNN::hsc_lincorr_combined_dedup:: homer_58.RTTATGYAAB::hsc_lincorr_combined_dedup:: homer_77.ATTGCGCAAC::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::3_motifs	Show matrix
cluster_12	2	homer_44.AVCAGCTG::hsc_lincorr_combined_dedup:: homer_54.ACCATCTGTT::hsc_lincorr_combined_dedup::	hsc_lincorr_combined_dedup::2_motifs	Show matrix
cluster_13	1	homer_66.CCATTGTTNY::hsc_lincorr_combined_dedup	hsc_lincorr_combined_dedup : 1 motif	Show matrix
cluster_14	1	homer_62.TWGTCTGV::hsc_lincorr_combined_dedup	hsc_lincorr_combined_dedup : 1 motif	Show matrix
cluster_15	1	homer_74.AGGCCTAG::hsc_lincorr_combined_dedup	hsc_lincorr_combined_dedup : 1 motif	Show matrix
cluster_16	1	homer_45.SGTCACGTGR::hsc_lincorr_combined_dedup	hsc_lincorr_combined_dedup : 1 motif	Show matrix
cluster_17	1	homer_56.SCCTAGCAACAG::hsc_lincorr_combined_dedup	hsc_lincorr_combined_dedup : 1 motif	Show matrix

Note: by default the table displays the first 50 clusters. Click on the Show X entries button to display more (or less) clusters.
Click on the column names to change the order of the data.
Use the Search window to find your motif (s) of interest.

Individual Cluster View

Individual Cluster View

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cluster_12

cluster_13

cluster_14

cluster_15

cluster_16

cluster_17

Display Logo Trees

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cluster_14

cluster_15

cluster_16

cluster_17

Display Branch-Motifs

Each cluster has a different color.
Click on the upper buttons to display separately the information of each cluster.
Click on the circles at each tree to display its corresponding merged motifs.

Definitions

Logo tree.
This results shows the hierarchical tree with its logo alignment of one cluster.
The logos are shown in Forward (left logo) and Reverse (right logo) orientation.
Branch-motifs.
On the trees are displayed the branch number that is the number in which the motifs were incorporated in the tree.
The Branch-Motifs table shows the logo in both orientations and the link to the file in TRANSFAC format with the branch-motif.

Individual Motif View

Individual Motif View

Motif id	Motif name	Cluster	Collection	Width	IC	Number of sites	Consensus	Consensus (Rev)
hsc_lincorr_combined_dedup_m10_homer_10.ACTTCCKGKT	homer_10.ACTTCCKGKT	cluster_3	hsc_lincorr_combined_dedup	17	6.59	101	++++AASMGGAAGT+++	+++aCTTCCkstt++++
hsc_lincorr_combined_dedup_m44_homer_44.AVCAGCTG	homer_44.AVCAGCTG	cluster_12	hsc_lincorr_combined_dedup	10	4.53	101	arCaKmTG++	++CAKMTGYT
hsc_lincorr_combined_dedup_m46_homer_46.NATGASTCABNN	homer_46.NATGASTCABNN	cluster_2	hsc_lincorr_combined_dedup	16	4.88	101	++++SRVTGASTCAYY	rrTGAsTCAbys++++
hsc_lincorr_combined_dedup_m57_homer_57.AAACCACARM	homer_57.AAACCACARM	cluster_4	hsc_lincorr_combined_dedup	12	8.69	101	+aAACCACArm+	+KYTGTGGTTT+
hsc_lincorr_combined_dedup_m68_homer_68.GGGGGGGG	homer_68.GGGGGGGG	cluster_6	hsc_lincorr_combined_dedup	15	7.95	100	++++GGGgGGGG+++	+++CCCCCCCC++++
hsc_lincorr_combined_dedup_m50_homer_50.GGGGGAATCCCC	homer_50.GGGGGAATCCCC	cluster_7	hsc_lincorr_combined_dedup	12	10.34	100	GGGGGAATCCCC	GGGGATTCCCCC
hsc_lincorr_combined_dedup_m39_homer_39.DATGASTCAT	homer_39.DATGASTCAT	cluster_2	hsc_lincorr_combined_dedup	16	8.40	101	+++++daTGAsTCAt+	+ATGASTCATH+++++
hsc_lincorr_combined_dedup_m24_homer_24.RGKGGGCGKGGC	homer_24.RGKGGGCGKGGC	cluster_6	hsc_lincorr_combined_dedup	15	8.72	101	+rGkGGGcGkGgc++	++GCCMCGCCCMCY+
hsc_lincorr_combined_dedup_m61_homer_61.DGGGYGKGGC	homer_61.DGGGYGKGGC	cluster_6	hsc_lincorr_combined_dedup	15	8.26	101	+++wGGGyGkGGC++	++GCCMCRCCCW+++
hsc_lincorr_combined_dedup_m75_homer_75.VTTACGTAAYNNNNN	homer_75.VTTACGTAAYNNNNN	cluster_11	hsc_lincorr_combined_dedup	15	6.31	101	YARHKRTKRYRYMAY	rTKryryMAymdytr
hsc_lincorr_combined_dedup_m17_homer_17.SAGATAAGRV	homer_17.SAGATAAGRV	cluster_1	hsc_lincorr_combined_dedup	11	9.06	100	+sWGATAAGrv	BYCTTATCWS+
hsc_lincorr_combined_dedup_m38_homer_38.RATGASTCAT	homer_38.RATGASTCAT	cluster_2	hsc_lincorr_combined_dedup	16	6.06	101	+++++raTGAsTCAy+	+RTGASTCATY+++++
hsc_lincorr_combined_dedup_m31_homer_31.VTGACTCATC	homer_31.VTGACTCATC	cluster_2	hsc_lincorr_combined_dedup	16	8.59	101	+++++GMTGASTCAB+	+vTGAsTCAkc+++++
hsc_lincorr_combined_dedup_m6_homer_6.AGAGGAAGTG	homer_6.AGAGGAAGTG	cluster_3	hsc_lincorr_combined_dedup	17	10.48	100	+++++aGAGGAAGTG++	++CACTTCCTCT+++++
hsc_lincorr_combined_dedup_m21_homer_21.CYTGGCABNSTGCCAR	homer_21.CYTGGCABNSTGCCAR	cluster_8	hsc_lincorr_combined_dedup	16	9.50	101	cyTGGCwswswGCCAr	YTGGCWSWSWGCCARG
hsc_lincorr_combined_dedup_m64_homer_64.VGGGRATTYCCC	homer_64.VGGGRATTYCCC	cluster_7	hsc_lincorr_combined_dedup	12	7.51	101	rGGGrawtyCCC	GGGRAWTYCCCY
hsc_lincorr_combined_dedup_m48_homer_48.AGTTTCASTTTC	homer_48.AGTTTCASTTTC	cluster_3	hsc_lincorr_combined_dedup	17	11.83	101	++GAAASTGAAAST+++	+++asTTTCasTTTC++
hsc_lincorr_combined_dedup_m52_homer_52.GGATGACTCATC	homer_52.GGATGACTCATC	cluster_2	hsc_lincorr_combined_dedup	16	9.46	101	++++ggaTGAsTCAtc	GATGASTCATCC++++
hsc_lincorr_combined_dedup_m18_homer_18.TGCTGAGTCA	homer_18.TGCTGAGTCA	cluster_2	hsc_lincorr_combined_dedup	16	9.89	100	++++tGCTGAsTCA++	++TGASTCAGCA++++
hsc_lincorr_combined_dedup_m14_homer_14.TGGCAGTTGG	homer_14.TGGCAGTTGG	cluster_10	hsc_lincorr_combined_dedup	10	7.93	101	tGrCaGTTrg	CYAACTGYCA
hsc_lincorr_combined_dedup_m65_homer_65.CARRGKBCAAAGTYCA	homer_65.CARRGKBCAAAGTYCA	cluster_5	hsc_lincorr_combined_dedup	16	9.49	101	TGRMCTTTGRMCYYTG	carrGkyCAAAGkyCA
hsc_lincorr_combined_dedup_m49_homer_49.RCAGGATGTGGT	homer_49.RCAGGATGTGGT	cluster_3	hsc_lincorr_combined_dedup	17	12.33	101	+++++MCCACWTCCTSY	rsAGGAwGTGGk+++++
hsc_lincorr_combined_dedup_m27_homer_27.AVCAGGAAGT	homer_27.AVCAGGAAGT	cluster_3	hsc_lincorr_combined_dedup	17	8.05	100	++++acvmGGAARt+++	+++AYTTCCKBGT++++
hsc_lincorr_combined_dedup_m55_homer_55.SVYTTCCNGGAARB	homer_55.SVYTTCCNGGAARB	cluster_3	hsc_lincorr_combined_dedup	17	8.38	100	sryTTCCwGGAAry+++	+++RYTTCCWGGAARYS
hsc_lincorr_combined_dedup_m76_homer_76.TGCTGACTCA	homer_76.TGCTGACTCA	cluster_2	hsc_lincorr_combined_dedup	16	8.32	100	++++TGCTGACtca++	++TGAGTCAGCA++++
hsc_lincorr_combined_dedup_m58_homer_58.RTTATGYAAB	homer_58.RTTATGYAAB	cluster_11	hsc_lincorr_combined_dedup	15	6.52	100	+++++rTTATRyAAb	VTTRYATAAY+++++
hsc_lincorr_combined_dedup_m53_homer_53.NWAACCACADNN	homer_53.NWAACCACADNN	cluster_4	hsc_lincorr_combined_dedup	12	8.01	100	KTYTGTGGTTWK	mwaACCACAram
hsc_lincorr_combined_dedup_m20_homer_20.GGCVGTTR	homer_20.GGCVGTTR	cluster_10	hsc_lincorr_combined_dedup	10	7.90	100	+GgCvGTTr+	+YAACBGCC+
hsc_lincorr_combined_dedup_m36_homer_36.DATGASTCATHN	homer_36.DATGASTCATHN	cluster_2	hsc_lincorr_combined_dedup	16	8.94	101	++++KRRTGASTCAYY	rrTGAsTCAyym++++
hsc_lincorr_combined_dedup_m9_homer_9.MACAGGAAGT	homer_9.MACAGGAAGT	cluster_3	hsc_lincorr_combined_dedup	17	9.84	100	++++RYTTCCTGTK+++	+++mACAGGAARY++++
hsc_lincorr_combined_dedup_m22_homer_22.BBCTTATCTS	homer_22.BBCTTATCTS	cluster_1	hsc_lincorr_combined_dedup	11	8.78	101	+SWGATAAGRR	yyCTTATCWs+
hsc_lincorr_combined_dedup_m43_homer_43.GAAASYGAAASY	homer_43.GAAASYGAAASY	cluster_3	hsc_lincorr_combined_dedup	17	4.24	101	++RSTTTYRSTTTC+++	+++gaAAsyraAAsy++
hsc_lincorr_combined_dedup_m13_homer_13.NBWGATAAGR	homer_13.NBWGATAAGR	cluster_1	hsc_lincorr_combined_dedup	11	7.48	100	vswGATAAsr+	+YSTTATCWSB
hsc_lincorr_combined_dedup_m33_homer_33.GRAASTGAAAST	homer_33.GRAASTGAAAST	cluster_3	hsc_lincorr_combined_dedup	17	9.41	100	++GrAAsyGAAAst+++	+++ASTTTCRSTTYC++
hsc_lincorr_combined_dedup_m67_homer_67.CYAAAAATAG	homer_67.CYAAAAATAG	cluster_9	hsc_lincorr_combined_dedup	12	7.58	100	+CTATTTTWRG+	+CywaAAATAG+
hsc_lincorr_combined_dedup_m56_homer_56.SCCTAGCAACAG	homer_56.SCCTAGCAACAG	cluster_17	hsc_lincorr_combined_dedup	12	8.58	100	sCmTrGyAACwg	CWGTTRCYAKGS
hsc_lincorr_combined_dedup_m69_homer_69.TTGAMCTTTG	homer_69.TTGAMCTTTG	cluster_5	hsc_lincorr_combined_dedup	16	5.20	101	CMRRGKTCAA++++++	++++++tTGAmCYykg
hsc_lincorr_combined_dedup_m23_homer_23.VACAGGAAAT	homer_23.VACAGGAAAT	cluster_3	hsc_lincorr_combined_dedup	17	9.84	101	++++aaCAGGAArY+++	+++RYTTCCTGTT++++
hsc_lincorr_combined_dedup_m54_homer_54.ACCATCTGTT	homer_54.ACCATCTGTT	cluster_12	hsc_lincorr_combined_dedup	10	8.72	100	RRCAGATGGY	rCCATCTGyy
hsc_lincorr_combined_dedup_m45_homer_45.SGTCACGTGR	homer_45.SGTCACGTGR	cluster_16	hsc_lincorr_combined_dedup	10	8.81	100	sgyCACGTGr	YCACGTGRCS
hsc_lincorr_combined_dedup_m32_homer_32.AAAGRGGAAGTG	homer_32.AAAGRGGAAGTG	cluster_3	hsc_lincorr_combined_dedup	17	8.91	100	+++CASTTCCBYTTT++	++aAArvGGAAsTG+++
hsc_lincorr_combined_dedup_m63_homer_63.CTGGCAGSCTGCCA	homer_63.CTGGCAGSCTGCCA	cluster_8	hsc_lincorr_combined_dedup	16	9.88	101	++TGGCWGSCWGCCAR	yTGGCwgscwGCCA++
hsc_lincorr_combined_dedup_m62_homer_62.TWGTCTGV	homer_62.TWGTCTGV	cluster_14	hsc_lincorr_combined_dedup	8	5.98	101	twGkCTrs	SYAGMCWA
hsc_lincorr_combined_dedup_m29_homer_29.AWWWTGCTGAGTCAT	homer_29.AWWWTGCTGAGTCAT	cluster_2	hsc_lincorr_combined_dedup	16	9.87	101	wwwwTGCTGAGTCAT+	+ATGACTCAGCAWWWW
hsc_lincorr_combined_dedup_m26_homer_26.YGGCCCCGCCCC	homer_26.YGGCCCCGCCCC	cluster_6	hsc_lincorr_combined_dedup	15	9.50	100	+++GGGGCGGGRCYR	yrGyCCCGCCCc+++
hsc_lincorr_combined_dedup_m74_homer_74.AGGCCTAG	homer_74.AGGCCTAG	cluster_15	hsc_lincorr_combined_dedup	8	6.88	100	aGGCCTrg	CYAGGCCT
hsc_lincorr_combined_dedup_m4_homer_4.ACAGGAAGTG	homer_4.ACAGGAAGTG	cluster_3	hsc_lincorr_combined_dedup	17	9.14	100	+++++rCMGGAAGTg++	++CACTTCCKGY+++++
hsc_lincorr_combined_dedup_m30_homer_30.CAAAGGTCAG	homer_30.CAAAGGTCAG	cluster_5	hsc_lincorr_combined_dedup	16	8.29	101	CmRAGGtCAs++++++	++++++STGACCTYKG
hsc_lincorr_combined_dedup_m8_homer_8.NRYTTCCGGH	homer_8.NRYTTCCGGH	cluster_3	hsc_lincorr_combined_dedup	17	4.12	101	+++++RSMGGAARYG++	++crytTCCksy+++++
hsc_lincorr_combined_dedup_m28_homer_28.RGKGGGCGGAGC	homer_28.RGKGGGCGGAGC	cluster_6	hsc_lincorr_combined_dedup	15	10.35	100	+rGkGGGCGGrGC++	++GCYCCGCCCMCY+
hsc_lincorr_combined_dedup_m42_homer_42.SAAACCACAG	homer_42.SAAACCACAG	cluster_4	hsc_lincorr_combined_dedup	12	9.30	101	YTGTGGTTWS++	++swAACCACAr
hsc_lincorr_combined_dedup_m59_homer_59.NYTTCCWGGAAR	homer_59.NYTTCCWGGAAR	cluster_3	hsc_lincorr_combined_dedup	17	9.83	101	++YTTCCWGGAARY+++	+++ryTTCCwGGAAr++
hsc_lincorr_combined_dedup_m71_homer_71.HACTTCCGGY	homer_71.HACTTCCGGY	cluster_3	hsc_lincorr_combined_dedup	17	6.15	100	+++++RCCGGAARYR++	++yryTTCCGgy+++++
hsc_lincorr_combined_dedup_m2_homer_2.ACCGGAAGTG	homer_2.ACCGGAAGTG	cluster_3	hsc_lincorr_combined_dedup	17	5.73	101	+++++rCCGGAAGyg++	++CRCTTCCGGY+++++
hsc_lincorr_combined_dedup_m41_homer_41.NNATGASTCATH	homer_41.NNATGASTCATH	cluster_2	hsc_lincorr_combined_dedup	16	6.69	101	++++krrTGAsTCAyc	GRTGASTCAYYM++++
hsc_lincorr_combined_dedup_m11_homer_11.ACVAGGAAGT	homer_11.ACVAGGAAGT	cluster_3	hsc_lincorr_combined_dedup	17	8.80	101	++++AyvmGGAAGT+++	+++ACTTCCKBRT++++
hsc_lincorr_combined_dedup_m40_homer_40.AGTTTCAKTTTC	homer_40.AGTTTCAKTTTC	cluster_3	hsc_lincorr_combined_dedup	17	8.69	100	++RRAAMTGAAACY+++	+++rgTTTCakTTyy++
hsc_lincorr_combined_dedup_m16_homer_16.ANCAGGAAGT	homer_16.ANCAGGAAGT	cluster_3	hsc_lincorr_combined_dedup	17	8.99	100	++++AmvAGGAAGT+++	+++ACTTCCTBKT++++
hsc_lincorr_combined_dedup_m25_homer_25.AGATAASR	homer_25.AGATAASR	cluster_1	hsc_lincorr_combined_dedup	11	6.29	101	++YSTTATCW+	+wGATAAsr++
hsc_lincorr_combined_dedup_m35_homer_35.GAAAGTGAAAGT	homer_35.GAAAGTGAAAGT	cluster_3	hsc_lincorr_combined_dedup	17	11.51	101	++GAAAsTGAAAst+++	+++ASTTTCASTTTC++
hsc_lincorr_combined_dedup_m51_homer_51.GCTGTGGTTW	homer_51.GCTGTGGTTW	cluster_4	hsc_lincorr_combined_dedup	12	8.84	101	+WAACCACAGM+	+kcTGTGGTtw+
hsc_lincorr_combined_dedup_m3_homer_3.AACCGGAAGT	homer_3.AACCGGAAGT	cluster_3	hsc_lincorr_combined_dedup	17	9.19	101	++++arCCGGAAGT+++	+++ACTTCCGGYT++++
hsc_lincorr_combined_dedup_m7_homer_7.NNAYTTCCTGHN	homer_7.NNAYTTCCTGHN	cluster_3	hsc_lincorr_combined_dedup	17	6.22	101	++++VRCMGGAWRYRS+	+syryWTCCkgyb++++
hsc_lincorr_combined_dedup_m66_homer_66.CCATTGTTNY	homer_66.CCATTGTTNY	cluster_13	hsc_lincorr_combined_dedup	10	5.42	101	ccwTTGTtyy	RRAACAAWGG
hsc_lincorr_combined_dedup_m15_homer_15.AVCCGGAAGT	homer_15.AVCCGGAAGT	cluster_3	hsc_lincorr_combined_dedup	17	7.73	101	++++avCCGGAAGt+++	+++ACTTCCGGBT++++
hsc_lincorr_combined_dedup_m37_homer_37.NDATGASTCAYN	homer_37.NDATGASTCAYN	cluster_2	hsc_lincorr_combined_dedup	16	7.51	101	++++bkaTKAsTCAyc	GRTGASTMATMV++++
hsc_lincorr_combined_dedup_m77_homer_77.ATTGCGCAAC	homer_77.ATTGCGCAAC	cluster_11	hsc_lincorr_combined_dedup	15	8.58	100	+++++ATTGcgCAAc	GTTGCGCAAT+++++
hsc_lincorr_combined_dedup_m12_homer_12.YCTTATCTBN	homer_12.YCTTATCTBN	cluster_1	hsc_lincorr_combined_dedup	11	7.07	101	VSWGATAAGR+	+yCTTATCwsb
hsc_lincorr_combined_dedup_m60_homer_60.ASWTCCTGBT	homer_60.ASWTCCTGBT	cluster_3	hsc_lincorr_combined_dedup	17	8.32	101	++++WVCMGGAWSY+++	+++rswTCCkGbw++++
hsc_lincorr_combined_dedup_m47_homer_47.GATGASTCATCN	homer_47.GATGASTCATCN	cluster_2	hsc_lincorr_combined_dedup	16	8.98	100	++++GGRTGASTCAYC	grTGAsTCAycc++++
hsc_lincorr_combined_dedup_m70_homer_70.MGGAAGTGAAAC	homer_70.MGGAAGTGAAAC	cluster_3	hsc_lincorr_combined_dedup	17	9.16	101	+STTTCACTTCYK++++	++++mRGAAgTGAAAs+
hsc_lincorr_combined_dedup_m19_homer_19.GCTATTTTTAGC	homer_19.GCTATTTTTAGC	cluster_9	hsc_lincorr_combined_dedup	12	8.59	101	kCTATTTwTrGc	GCYAWAAATAGM
hsc_lincorr_combined_dedup_m73_homer_73.AWWNTGCTGAGTCAT	homer_73.AWWNTGCTGAGTCAT	cluster_2	hsc_lincorr_combined_dedup	16	13.13	101	wwwwTGCTGAGTCAy+	+RTGACTCAGCAWWWW
hsc_lincorr_combined_dedup_m34_homer_34.CCCCTCCCCCAC	homer_34.CCCCTCCCCCAC	cluster_6	hsc_lincorr_combined_dedup	15	14.20	100	GTGGGGGAGGGG+++	+++CCCCTCCCCCAC
hsc_lincorr_combined_dedup_m72_homer_72.NRYTTCCGGY	homer_72.NRYTTCCGGY	cluster_3	hsc_lincorr_combined_dedup	17	6.62	101	+++++ACCGGAARYR++	++yryTTCCGgt+++++
hsc_lincorr_combined_dedup_m1_homer_1.ATTTCCTGTN	homer_1.ATTTCCTGTN	cluster_3	hsc_lincorr_combined_dedup	17	9.66	101	++++SRCAGGAAAT+++	+++ATTTCCTGys++++
hsc_lincorr_combined_dedup_m5_homer_5.RACCGGAAGT	homer_5.RACCGGAAGT	cluster_3	hsc_lincorr_combined_dedup	17	5.90	101	++++ACTTCCKGYT+++	+++arCmGGAAGt++++

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Additional Files

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.
Input motifs	The input motifs analyzed with matrix-clustering.

References
1. Castro-Mondragon JA et al. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. doi: 10.1093/nar/gkx314; Nucleic Acids Research (2017)
2. Last RSAT release: Nguyen NTT et al. RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research (2018).
Additional Information
- Jacques van Helden course
Contact
- Jaime Castro-Mondragon - j.a.c.mondragon@ncmm.uio.no
- Morgane Thomas-Chollier - mthomas@biologie.ens.fr
- Jacques van Helden - Jacques.van-Helden@univ-amu.fr

RSAT - matrix-clustering result

Analysis: hsc_lincorr_combined_dedup (12/04/2026 14:52)

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