SNP2TFBS WEB-SERVER OUTPUT FORMAT DESCRIPTION

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SNPViewer - Viewing variants that affect TF-binding
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Two tables
Table1:
	- SNP identifier (with dbSNP link)
	- Chromosome (Feb 2009 GRCh37/hg19)
	- SNP position
	- Number of TF factors affected by the variant

Table2:
	- TF name
	- PWM score on ref assembly
	- PWM score on alt assembly
	- Score difference
	- Low score (threshold used to identify PWM sites)
	- High score (threshold for selecting variants with significant regulatory affect)


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SNPSelect - Annotate selected SNPs with TFBS matches
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SNP Set analysis (to check overlap of variants from SNP2TFBS in a user defined rsID list or vcf file)
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rsID based search
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Output plots
	- PLOT1: Variants affecting factors - number of user uploaded variants affecting one or more TFs.
	- PLOT2: TF Enrichment - TFs enriched that overlap user defined variants. TFs are sorted based on their enrichment.
        - PLOT3: Variants Annotation - matching variants are annotated based on RefSeq annotation.

Output data files
	- OUTPUT FILE: Variants-TF matches
		- Chromosome
		- SNP pos
		- SNP pos
		- ref allele
		- alt allele
		- Information: MATCH=(number of TF affected);TF=(TF name);ScoreDiff=(score difference sorted on absolute difference among TFs)
		- rsID

	- OUTPUT FILE: TF Enrichment
		- TF name
		- Total TF sites identified with our pipeline
		- TFs identified in user defined list
		- Ration of TF identified/ total TF

	- OUTPUT FILE: Annotated Variants
		- Chromosome number
		- SNP pos
		- ref allele
		- alt allele
		- Functional annotation of gene
		- Gene name
		- Gene details (. if absent)
		- ExonicFunc.refGeneAAChange (. if absent)
		- rsID
		- TFname

vcf based search
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Output plots
	- PLOT1: Variants affecting factors - number of user uploaded variants affecting one or more TFs.
	- PLOT2: TF Enrichment - TFs enriched that overlap user defined variants. TFs are sorted based on their enrichment.
        - PLOT3: Variants Annotation - matching variants are annotated based on RefSeq annotation.

Output data files
	- OUTPUT FILE: Variants-TF matches - same as above
	- OUTPUT FILE: TF Enrichment - same as above
	- OUTPUT FILE: Filtered Variants (VCF) - same format as user defined vcf but will contain only variants that found match in SNP2TFBS
	- OUTPUT FILE: Annotated Variants - same as above

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SNPIntersect - Intersect genomic regions with variants affecting TF-binding
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Output plots
	- PLOT1: Intersection counts - Number of user defined regions having zero/ one/ more than one variant matches from SNP2TFBS
	- PLOT2: TF Enrichment - TFs enriched in user defined regions. TFs are sorted based on their enrichment.
        - PLOT3: Variants Annotation - matching variants are annotated based on RefSeq annotation.

Output data files
	- OUTPUT FILE: Variants-TF matches
		- Chromosome
		- SNP pos
		- SNP pos
		- ref allele
		- alt allele
		- Information: MATCH=(number of TF affected);TF=(TF name);ScoreDiff=(score difference sorted on absolute difference among TFs)
		- rsID

	- OUTPUT FILE: Region/SNP Overlap Count
		- Chromosome
		- SNP pos
		- SNP pos
		- TF name
		- Counts
		- Number of variants identified in user defined region file

	- OUTPUT FILE: TF Enrichment
		- TF name
		- Total TF sites identified with our pipeline
		- TFs identified in user defined list
		- Ration of TF identified/ total TF

	- OUTPUT FILE: Annotated Variants
		- Chromosome number
		- SNP pos
		- ref allele
		- alt allele
		- Functional annotation of gene
		- Gene name
		- Gene details (. if absent)
		- ExonicFunc.refGeneAAChange (. if absent)
		- rsID
		- TFname

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PWM from library (JASPAR CORE 2014 vertebrates)
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Output plots
	- PLOT1 - Selected Variants: venn diagram showing intersection of PWM specific variants identified in reference and alternate genome.
	- PLOT2 - Variants Annotation: number of variants in genomic regions as defined by RefSeq annotation.

Output data files
	- OUTPUT FILE: Custom file
		- rsID
		- Chromosome
		- SNP pos (reference)
		- SNP pos (alternate)
		- ref-allele
		- alt-allele
		- ref PWM match start position (. if absent)
		- ref PWM match end position (. if absent)
		- ref PWM match seq (. if absent)
		- ref PWM match score (. if absent)
		- alt PWM match start position (. if absent)
		- alt PWM match end position (. if absent)
		- alt PWM match seq (. if absent)
		- alt PWM match score (. if absent)
		- strand
		- score difference alt-ref (if absent use low score threshold)
		- flag 1/0 (interesting SNP - 1 means one score >= high score threshold)

	- OUTPUT FILE: BED file
		- Chromosome
		- SNP position
		- SNP position
		- rsID
		- Allele change (ref>alt)

	- OUTPUT FILE: Annotated File
		- Chromosome
		- SNP position
		- ref allele
		- alt allele
		- Functional annotation of gene
		- Gene name
		- Gene details (. if absent)
		- ExonicFunc.refGeneAAChange (. if absent)
		- rsID
		- TFname

	- OUTPUT FILE: Alt genome SNPs
		- Same format as "custom file", ref PWM specific fields (column 7-10) are replaced by "."

	- OUTPUT FILE: Ref genome SNPs
		- Same format as "custom file", alt PWM specific fields (column 11-14) are replaced by "."

	- OUTPUT FILE: Both genomes SNPs
		- - Same format as "custom file"

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Indicate a gene of interest
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Output plots
	- PLOT1: TF Enrichment plot - TFs enriched near user defined gene. TFs are sorted based on their enrichment.
	- PLOT2: Variant annotation plot - number of variants in genomic regions as defined by RefSeq annotation.

Output data files
	- OUTPUT FILE: TF Enrichment
		- TF name
		- Total TF sites identified with our pipeline
		- TFs identified in user defined list
		- Ration of TF identified/ total TF

	- OUTPUT FILE: Annotated Variants
		- Chromosome
		- SNP position
		- ref allele
		- alt allele
		- Functional annotation of gene
		- Gene name
		- ExonicFunc.refGeneAAChange (. if absent)
		- Gene details (. if absent)
		- rsID
		- TFname