Database of nsSNPs for hub glycogenes identified from mouse RNA-seq data


	Home Page figure shows distribution of nsSNPs in hubs. Among the hubs identified in this work, SNPs were found for TNFRSF1B only. No SNP was detected for hubs SLC2A4, TRFR2 and UCHL1. HPXN, FLT1 and NID2 were identified as hub glycogenes in our previous work [Firoz et al., 2014]. From the menu provided at web page user can download different data used in this studies and also can get list of glycogene, hub glycogene identified and help. For the prediction of SNP to be deleterious or Damaging Three tools PROVEAN, SIFT and Polyphen2 (standalone installed for mouse) has been used. For Secondary structure and ASA (Accessible Surface Area) NetsurfP has been used for normal and mutated sequence. After data derived from above tools it is placed in MySQL table for access from web portals provided here. Search criteria: There are different search criteria simple search and advance search option are also provided at the home page. Simple Search: In the simple text search criteria user can search by its gene name, SNP Id and Uniprot Id, when the search button clicked user will get SNP ID, UniProt ID, Gene name , Amino Acid changes with position (AA Change), Polyphen2 Probability (PPH2 Prob), Polyphen2 prediction (PPH2), PROVEAN Score, PROVEAN Cutoff (prediction), SIFT Score and SIFT Cutoff (prediction). From here user can also download the searched result by clicking download result link and also can get the secondary structure & ASA value of normal & mutated by NetSurfP tools by clicking AA Change link, User will get information for particular Position of Amino Acid changes like SNP ID, Residue Normal, Position, ASA Normal, Class Normal, SS Normal, Residue SNP, SNP, ASA mutated, Class mutated and SS mutated. From here user can also sort result by selecting for particular Residue, Class changes, ASA Changes and Secondary structure. Advance Search: In the Advance Search user can select particular or all gene and residue to see prediction. When the search button clicked user will get SNP ID, UniProt ID, Gene name , Amino Acid changes with position (AA Change), Polyphen2 Probability (PPH2 Prob), Polyphen2 prediction (PPH2), PROVEAN Score, PROVEAN Cutoff (prediction), SIFT Score and SIFT Cutoff (prediction). From here user can also download the searched result by clicking download result link and also can get the secondary structure & ASA value of normal & mutated by NetSurfP tools by clicking AA Change link, User will get information for particular Position of Amino Acid changes like SNP ID, Residue Normal, Position, ASA Normal, Class Normal, SS Normal, Residue SNP, SNP, ASA mutated, Class mutated and SS mutated. From here user can also sort result by selecting for particular Residue, Class changes, ASA Changes and Secondary structure.
	Definition of Header:
	AA change	Amino Acid Change
	ASA N	ASA of residues in normal sequence
	ASA SNP	ASA of residues in SNP sequence
	Class N	Class of residues in normal sequence [Class = buried (B) or exposed (E)]
	Class SNP	Class of residues in SNP sequence [Class = buried (B) or exposed (E)]
	Gene name	Name of gene
	Position	Position of SNP (residue change)
	PPH2	PolyPhen-2 is an automatic tool for prediction of the possible impact of an amino acid substitution on the structure and function of a protein
	PPH2 Prob	probability score calculated by Polyphen-2 tool for the variant to have a damaging effect on the protein function
	PROVEAN Cutoff	PROVEAN is software tools which predicts whether an amino acid substitution has an impact on the biological function of a protein if the score, lies below a certain threshold value
	PROVEAN Score	A delta alignment score is computed by PROVEAN (Protein Variation Effect Analyzer) tool for each supporting sequence. The scores are then averaged within and across clusters to generate the final PROVEAN score
	Residue N	Residues in normal sequence
	Residue SNP	Residues in SNP sequence
	SIFT Cutoff	SIFT is also software tools which predicts whether an amino acid substitution has an impact on the biological function of a protein if the score, lies below a certain threshold value
	SIFT Score	SIFT program is multi-step algorithm, which uses sequence homology based approach to classify amino acid substitutions and gives score. SIFT score is obtained from SIFT sequence
	SNP	Single nucleotide polymorphism (Amino Acid change due to SNP)
	SNP ID	Unique ID for searching SNPs at dbSNP Database
	SS N	Secondary Structure of residues in normal sequence
	SS SNP	Secondary Structure of residues in SNP sequence
	UniProt ID	Unique ID for searching protein at UniProt database

Stat

Developed at: Biomedical Informatics Centre, PGIMER, Chandigarh