matrix-clustering oct4_motifs_found_in_chen_2008_peak_sets_discovered_by_peak-motifs,_meme-chip_and

RSAT - matrix-clustering result

Analysis: oct4_motifs_found_in_chen_2008_peak_sets_discovered_by_peak-motifs,_meme-chip_and_homer (04/03/2025 22:22)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix oct4_peak_motifs $RSAT/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.222138_i1gU99/matrix-clustering_query_matrices.meme meme -matrix oct4_meme-chip $RSAT/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.222138_i1gU99/matrix-clustering_second_matrices. transfac -matrix oct4_homer $RSAT/public_html/tmp/www-data/2025/03/04/matrix-clustering_2025-03-04.222138_i1gU99/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/2025/03/04/matrix-clustering_2025-03-04.222138_i1gU99/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	19	MEME_ChIP_3::oct4_meme-chip:: homer_1::oct4_homer:: MEME_ChIP_10::oct4_meme-chip:: MEME_ChIP_25::oct4_meme-chip:: MEME_ChIP_1::oct4_meme-chip:: MEME_ChIP_15::oct4_meme-chip:: MEME_ChIP_20::oct4_meme-chip:: MEME_ChIP_21::oct4_meme-chip:: MEME_ChIP_24::oct4_meme-chip:: homer_13::oct4_homer:: MEME_ChIP_13::oct4_meme-chip:: MEME_ChIP_14::oct4_meme-chip:: MEME_ChIP_11::oct4_meme-chip:: MEME_ChIP_12::oct4_meme-chip:: MEME_ChIP_17::oct4_meme-chip:: MEME_ChIP_16::oct4_meme-chip:: MEME_ChIP_18::oct4_meme-chip:: MEME_ChIP_19::oct4_meme-chip:: MEME_ChIP_23::oct4_meme-chip::	oct4_homer::2_motifs oct4_meme-chip::17_motifs	Show matrix
cluster_2	4	MEME_ChIP_22::oct4_meme-chip:: homer_6::oct4_homer:: homer_16::oct4_homer:: homer_18::oct4_homer::	oct4_homer::3_motifs oct4_meme-chip::1_motif	Show matrix
cluster_3	4	homer_9::oct4_homer:: homer_4::oct4_homer:: homer_19::oct4_homer:: MEME_ChIP_5::oct4_meme-chip::	oct4_homer::3_motifs oct4_meme-chip::1_motif	Show matrix
cluster_4	4	homer_12::oct4_homer:: MEME_ChIP_8::oct4_meme-chip:: MEME_ChIP_2::oct4_meme-chip:: MEME_ChIP_9::oct4_meme-chip::	oct4_homer::1_motif oct4_meme-chip::3_motifs	Show matrix
cluster_5	2	homer_15::oct4_homer:: homer_3::oct4_homer::	oct4_homer::2_motifs	Show matrix
cluster_6	3	homer_14::oct4_homer:: MEME_ChIP_4::oct4_meme-chip:: MEME_ChIP_7::oct4_meme-chip::	oct4_meme-chip::2_motifs oct4_homer::1_motif	Show matrix
cluster_7	2	homer_11::oct4_homer:: homer_2::oct4_homer::	oct4_homer::2_motifs	Show matrix
cluster_8	1	homer_10::oct4_homer	oct4_homer : 1 motif	Show matrix
cluster_9	1	homer_17::oct4_homer	oct4_homer : 1 motif	Show matrix
cluster_10	1	homer_5::oct4_homer	oct4_homer : 1 motif	Show matrix
cluster_11	1	homer_8::oct4_homer	oct4_homer : 1 motif	Show matrix
cluster_12	1	homer_7::oct4_homer	oct4_homer : 1 motif	Show matrix
cluster_13	1	MEME_ChIP_6::oct4_meme-chip	oct4_meme-chip : 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.

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cluster_1

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cluster_7

cluster_8

cluster_9

cluster_10

cluster_11

cluster_12

cluster_13

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