RSAT - matrix-clustering result

Analysis: JASPAR_2020_insects (08/10/2019 11:48)

Command

matrix-clustering  -v 2 -matrix CORE_insects data/motifs/Motifs_parsed_ID/JASPAR2020_CORE_insects.tf tf -matrix NV_insects data/motifs/Motifs_parsed_ID/JASPAR2020_Unvalidated_insects.tf tf -hclust_method average -calc sum -title 'JASPAR 2020 insects' -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -label_in_tree name -return json,heatmap -calc mean -quick -o results/JASPAR_2020_matrix_clustering/insects_CORE_+_UNVALIDATED/interactive_trees/JASPAR_2020_CORE_+_UNVALIDATED_matrix_clustering_insects

Results Summary

Nb Input motifs

Nb Input collections

Nb Clusters Found

Download
Root motifs

Complete results [zip]

Parameters used

Linkage method ?

Similarity metric ?

Thresholds to partition the tree?

146

Download

Download

average

Ncor

Ncor = 0.4
cor = 0.6

Logo Forest (dynamic browsing)

Logo Forest (rapid overview - low image quality)

Clusters Summary

Clusters Summary Table

Show entries

Search:

Cluster ID	# Motifs	Motif_Name::Collection	Number of Motifs by Collection	Root Motif (transfac Format)
cluster_1	2	prd::CORE_insects:: ovo::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_2	70	bap::CORE_insects:: onecut::CORE_insects:: Dll::CORE_insects:: Dr::CORE_insects:: lbe::CORE_insects:: lbl::CORE_insects:: Vsx2::CORE_insects:: inv::CORE_insects:: Ubx::CORE_insects:: HHEX::CORE_insects:: CG4328-RA::CORE_insects:: Abd-B::CORE_insects:: Dbx::CORE_insects:: H2_0::CORE_insects:: zen::CORE_insects:: zen2::CORE_insects:: E5::CORE_insects:: ap::CORE_insects:: ind::CORE_insects:: pb::CORE_insects:: CG18599::CORE_insects:: ems::CORE_insects:: eve::CORE_insects:: Lim3::CORE_insects:: Awh::CORE_insects:: HGTX::CORE_insects:: Vsx1::CORE_insects:: otp::CORE_insects:: btn::CORE_insects:: Scr::CORE_insects:: Dfd::CORE_insects:: Antp::CORE_insects:: ftz::CORE_insects:: abd-A::CORE_insects:: lab::CORE_insects:: CG15696-RA::CORE_insects:: Lim1::CORE_insects:: CG11294::CORE_insects:: al::CORE_insects:: repo::CORE_insects:: CG32105::CORE_insects:: exex::CORE_insects:: ro::CORE_insects:: Pph13::CORE_insects:: Rx::CORE_insects:: CG9876::CORE_insects:: OdsH::CORE_insects:: PHDP::CORE_insects:: hbn::CORE_insects:: unpg::CORE_insects:: CG32532::CORE_insects:: en::CORE_insects:: C15::CORE_insects:: B-H2::CORE_insects:: B-H1::CORE_insects:: unc-4::CORE_insects:: Hmx::CORE_insects:: CG11085::CORE_insects:: CG34031::CORE_insects:: tup::CORE_insects:: NK7_1::CORE_insects:: bsh::CORE_insects:: slou::CORE_insects:: lms::CORE_insects:: ttk::CORE_insects:: dve::CORE_insects:: Ptx1::CORE_insects:: Gsc::CORE_insects:: bcd::CORE_insects:: oc::CORE_insects::	CORE_insects::70_motifs	Show matrix
cluster_3	10	hth::CORE_insects:: vis::CORE_insects:: achi::CORE_insects:: Optix::CORE_insects:: Six4::CORE_insects:: so::CORE_insects:: CG11617::CORE_insects:: caup::CORE_insects:: ara::CORE_insects:: mirr::CORE_insects::	CORE_insects::10_motifs	Show matrix
cluster_4	3	BEAF-32::CORE_insects:: pnr::CORE_insects:: Dref::CORE_insects::	CORE_insects::3_motifs	Show matrix
cluster_5	2	Eip74EF::CORE_insects:: Ets21C::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_6	2	su_Hw_::CORE_insects:: *Cp190::NV_insects::	NV_insects::1_motif CORE_insects::1_motif	Show matrix
cluster_7	3	ct::CORE_insects:: tin::CORE_insects:: vnd::CORE_insects::	CORE_insects::3_motifs	Show matrix
cluster_8	6	cad::CORE_insects:: hb::CORE_insects:: slp1::CORE_insects:: fkh::CORE_insects:: br::CORE_insects:: br_var_4_::CORE_insects::	CORE_insects::6_motifs	Show matrix
cluster_9	5	z::CORE_insects:: Trl::CORE_insects:: trx::NV_insects:: Clamp::CORE_insects:: Dsp1::NV_insects::	CORE_insects::3_motifs NV_insects::2_motifs	Show matrix
cluster_10	2	dl::CORE_insects:: dl_var_2_::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_11	2	Pdp1::CORE_insects:: gt::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_12	2	br_var_3_::CORE_insects:: D::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_13	2	sna::CORE_insects:: vfl::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_14	3	opa::CORE_insects:: btd::CORE_insects:: hkb::CORE_insects::	CORE_insects::3_motifs	Show matrix
cluster_15	2	grh::CORE_insects:: Kr::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_16	1	Bgb::run::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_17	1	gcm2::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_18	1	twi::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_19	1	Cf2::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_20	1	schlank::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_21	1	Deaf1::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_22	1	Hsf::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_23	2	tll::CORE_insects:: exd::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_24	2	br_var_2_::CORE_insects:: kni::CORE_insects::	CORE_insects::2_motifs	Show matrix
cluster_25	3	Mad::CORE_insects:: brk::CORE_insects:: CTCF::CORE_insects::	CORE_insects::3_motifs	Show matrix
cluster_26	1	slbo::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_27	1	vvl::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_28	1	odd::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_29	1	sd::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_30	1	Stat92E::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_31	1	nub::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_32	1	usp::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_33	1	h::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_34	1	Su_H_::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_35	1	M1BP::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_36	1	pho::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_37	1	pan::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_38	1	EcR::usp::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_39	1	dmrt99B::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_40	1	sv::CORE_insects	CORE_insects : 1 motif	Show matrix
cluster_41	1	cnc::maf-S::CORE_insects	CORE_insects : 1 motif	Show matrix

Showing 1 to 41 of 41 entries

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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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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

Show entries

Search:

Motif id	Motif name	Cluster	Collection	Width	IC	Number of sites	Consensus	Consensus (Rev)
CORE_insects_m107_MA0239_1	prd	cluster_1	CORE_insects	9	6.66	21	wgtAACwGt	ACWGTTACW
CORE_insects_m99_MA0126_1	ovo	cluster_1	CORE_insects	9	6.66	21	wgtAACwGt	ACWGTTACW
CORE_insects_m45_MA0022_1	dl	cluster_10	CORE_insects	12	8.94	13	sGGGtTTTTCCs	SGGAAAAACCCS
CORE_insects_m46_MA0023_1	dl_var_2_	cluster_10	CORE_insects	12	9.79	9	-GGGGwtTTCC-	-GGAAAWCCCC-
CORE_insects_m66_MA0447_1	gt	cluster_11	CORE_insects	12	9.68	60	-rTTACGTAAy-	-RTTACGTAAY-
CORE_insects_m102_MA1702_1	Pdp1	cluster_11	CORE_insects	12	8.25	4816	WRTTRCATAAYW	wrTTATGYAAyw
CORE_insects_m41_MA0445_1	D	cluster_12	CORE_insects	11	8.89	29	ARAACAAWRGR	yCyWTTGTTyT
CORE_insects_m17_MA0012_1	br_var_3_	cluster_12	CORE_insects	11	6.47	12	wAAACwArwhs	SDWYTWGTTTW
CORE_insects_m119_MA0086_2	sna	cluster_13	CORE_insects	13	8.98	1001	kbrACAGGTGyaa	TTRCACCTGTYVM
CORE_insects_m135_MA1462_1	vfl	cluster_13	CORE_insects	13	7.60	11731	-htgCAGGTAgrh	DYCTACCTGCAD-
CORE_insects_m73_MA0450_1	hkb	cluster_14	CORE_insects	12	9.72	32	---kRGGCGTGA	TCACGCCYM---
CORE_insects_m21_MA0443_1	btd	cluster_14	CORE_insects	12	8.83	30	-arkGGGCGkr-	-YMCGCCCMYT-
CORE_insects_m96_MA0456_1	opa	cluster_14	CORE_insects	12	10.33	18	CAGCGGGGGGKC	GmCCCCCCGCtG
CORE_insects_m80_MA0452_2	Kr	cluster_15	CORE_insects	14	9.82	1296	ytyAACCCTTTyty	RARAAAGGGTTRAR
CORE_insects_m64_MA1457_1	grh	cluster_15	CORE_insects	14	8.76	3332	-raAACCrGTTtty	RAAAACYGGTTTY-
CORE_insects_m14_MA0242_1	Bgb::run	cluster_16	CORE_insects	9	9.61	29	wAACCGCAR	YTGCGGTTW
CORE_insects_m63_MA0917_1	gcm2	cluster_17	CORE_insects	8	7.15	1001	ATGCGGGy	RCCCGCAT
CORE_insects_m130_MA0249_2	twi	cluster_18	CORE_insects	11	7.55	2896	ryACACATGta	TACATGTGTRY
CORE_insects_m26_MA0015_1	Cf2	cluster_19	CORE_insects	10	7.61	80	rTATATrTry	RYAYATATAY
CORE_insects_m81_MA0230_1	lab	cluster_2	CORE_insects	10	8.11	16	-TTAATkA--	--TMATTAA-

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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.

Heatmap View

Cluster composition by collection

Collections Overlap

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.
Collections Complementarity	A dynamic heatmap showing how many motifs contribute each collection to each 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. Fornes O, Castro-Mondragon JA et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research (2019)
Contact
- Jaime A Castro-Mondragon - j[dot]a[dot]c[dot]mondragon[at]ncmm[dot]uio[dot]no
- Anthony Mathelier - anthony[dot]mathelier[at]ncmm[dot]uio[dot]no

RSAT - matrix-clustering result

Analysis: JASPAR_2020_insects (08/10/2019 11:48)

Command

Results Summary

Clusters Summary Table

Individual Cluster View

Branch Motifs

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Definitions

Individual Motif View

Heatmap View

Exported files