MethMotif Batch Query

Genome assembly: tair10

"MethMotif Batch Query" is a tool implemented in MethMotif website, which allows users to study the occurrences of TFBSs and their respective DNA methylation states within a given list of genomic loci. For more details, please refer to the manual.

Demo dataset (REF6 ChIP-seq experiment in Arabidopsis thaliana [GSM3040333])

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ID	Species	TF	Family	Number of input regions with TFBS	C type	Cytosine beta scores in the TFBS	Details
1	Arabidopsis thaliana	REF6 MM3_AT_Seedling_REF6 (CG Details)	C2H2	4781	CG		Regions with REF6 motif: CG methScore in motif: CG beta score matrix:
		REF6 MM3_AT_Seedling_REF6 (CHG Details)			CHG		CHG methScore in motif:
		REF6 MM3_AT_Seedling_REF6 (CHH Details)			CHH		CHH methScore in motif:
2	Arabidopsis thaliana	REF6 MM1_AT_Seedling_REF6 (CG Details)	C2H2	3781	CG		Regions with REF6 motif: CG methScore in motif: CG beta score matrix:
		REF6 MM1_AT_Seedling_REF6 (CHG Details)			CHG		CHG methScore in motif:
		REF6 MM1_AT_Seedling_REF6 (CHH Details)			CHH		CHH methScore in motif:
3	Arabidopsis thaliana	REF6 MM1_AT_Inflorescence_REF6 (CG Details)	C2H2	3746	CG		Regions with REF6 motif: CG methScore in motif: CG beta score matrix:
		REF6 MM1_AT_Inflorescence_REF6 (CHG Details)			CHG		CHG methScore in motif:
		REF6 MM1_AT_Inflorescence_REF6 (CHH Details)			CHH		CHH methScore in motif:
4	Arabidopsis thaliana	REF6 MM2_AT_Seedling_REF6 (CG Details)	C2H2	3476	CG		Regions with REF6 motif: CG methScore in motif: CG beta score matrix:
		REF6 MM2_AT_Seedling_REF6 (CHG Details)			CHG		CHG methScore in motif:
		REF6 MM2_AT_Seedling_REF6 (CHH Details)			CHH		CHH methScore in motif:
5	Arabidopsis thaliana	TRB1 MM1_AT_Seedling_TRB1 (CG Details)	Unspecified	15	CG	No CGs	Regions with TRB1 motif: CG methScore in motif: CG beta score matrix:
		TRB1 MM1_AT_Seedling_TRB1 (CHG Details)			CHG		CHG methScore in motif:
		TRB1 MM1_AT_Seedling_TRB1 (CHH Details)			CHH		CHH methScore in motif:
6	Arabidopsis thaliana	NAC050 MM1_AT_Seedling_NAC050 (CG Details)	NAC domain	9	CG		Regions with NAC050 motif: CG methScore in motif: CG beta score matrix:
		NAC050 MM1_AT_Seedling_NAC050 (CHG Details)			CHG		CHG methScore in motif:
		NAC050 MM1_AT_Seedling_NAC050 (CHH Details)			CHH		CHH methScore in motif:
7	Arabidopsis thaliana	NAC052 MM1_AT_Seedling_NAC052 (CG Details)	NAC domain	9	CG		Regions with NAC052 motif: CG methScore in motif: CG beta score matrix:
		NAC052 MM1_AT_Seedling_NAC052 (CHG Details)			CHG		CHG methScore in motif:
		NAC052 MM1_AT_Seedling_NAC052 (CHH Details)			CHH		CHH methScore in motif:
8	Arabidopsis thaliana	LFY MM1_AT_Seedling_LFY (CG Details)	Orphan	2	CG		Regions with LFY motif: CG methScore in motif: CG beta score matrix:
		LFY MM1_AT_Seedling_LFY (CHG Details)			CHG		CHG methScore in motif:
		LFY MM1_AT_Seedling_LFY (CHH Details)			CHH		CHH methScore in motif:
9	Arabidopsis thaliana	RPS4 MM1_AT_Leaf_RPS4 (CG Details)	Disease resistance protein (TIR-NBS-LRR class) family	1	CG		Regions with RPS4 motif: CG methScore in motif: CG beta score matrix:
		RPS4 MM1_AT_Leaf_RPS4 (CHG Details)			CHG		CHG methScore in motif:
		RPS4 MM1_AT_Leaf_RPS4 (CHH Details)			CHH	No CHHs	CHH methScore in motif:
10	Arabidopsis thaliana	MYB3R3 MM1_AT_Seedling_MYB3R3 (CG Details)	MYB	1	CG		Regions with MYB3R3 motif: CG methScore in motif: CG beta score matrix:
		MYB3R3 MM1_AT_Seedling_MYB3R3 (CHG Details)			CHG	No CHGs	CHG methScore in motif:
		MYB3R3 MM1_AT_Seedling_MYB3R3 (CHH Details)			CHH		CHH methScore in motif:
11	Arabidopsis thaliana	PIF5 MM1_AT_Seedling_PIF5 (CG Details)	bHLH	1	CG	No CGs	Regions with PIF5 motif: CG methScore in motif: CG beta score matrix:
		PIF5 MM1_AT_Seedling_PIF5 (CHG Details)			CHG	No CHGs	CHG methScore in motif:
		PIF5 MM1_AT_Seedling_PIF5 (CHH Details)			CHH		CHH methScore in motif:
12	Arabidopsis thaliana	REV MM1_AT_Seedling_REV (CG Details)	Homeobox-leucine zipper family	1	CG	No CGs	Regions with REV motif: CG methScore in motif: CG beta score matrix:
		REV MM1_AT_Seedling_REV (CHG Details)			CHG		CHG methScore in motif:
		REV MM1_AT_Seedling_REV (CHH Details)			CHH		CHH methScore in motif:
13	Arabidopsis thaliana	SPCH MM1_AT_Seedling_SPCH (CG Details)	bHLH	1	CG		Regions with SPCH motif: CG methScore in motif: CG beta score matrix:
		SPCH MM1_AT_Seedling_SPCH (CHG Details)			CHG	No CHGs	CHG methScore in motif:
		SPCH MM1_AT_Seedling_SPCH (CHH Details)			CHH		CHH methScore in motif: