PolyDoms: Supplementary tables

Supplementary File 1: Current status
No. Type Count
1 Total number of refseq (build 36.1) human protein sequences 39325
2 Number of unique human refseq genes 26378
3 Number of human genes having isoforms 6567
4 Number of coding-SNPs (cSNPs) (dbSNP build 125)
Number of nonsynonymous SNPs (nsSNPs)
Number of synonymous SNPs (synSNPs)
81606
47267
34339
5 Number of human genes with nonsynonymous SNPs (nsSNPs)
Number of human genes with synonymous SNPs (nsSNPs)
12798
11631
6 Number of ns SNPs having predictions
  • SIFT (version 2.1)
  • Polyphen (version 1.1)
  • SIFT and Polyphen
  • Deleterious (From SIFT)
  • Damaging (From Polyphen)
  • Deleterious & Damaging (From SIFT & Polyphen)
Number of unique human genes having
  • a SIFT prediction
  • a PolyPhen prediction
  • a SIFT and PolyPhen prediction
  • at least one deleterious snp (from SIFT)
  • at least one damaging snp (from Polyphen)
  • at least one snp that is deleterious and damaging
Number of unique human proteins having
  • a SIFT prediction
  • a PolyPhen prediction
  • a SIFT and PolyPhen prediction
  • at least one deleterious snp (from SIFT)
  • at least one damaging snp (from Polyphen)
  • at least one snp that is deleterious and damaging

44650
47132
44641
14819
14622
9021

 

12312
12791
12311
7458
7428
5436

 

14969
15495
14967
9055
8860
6516
7 Number of conserved domains 4334
8 Number of 3D structures 1862
9 Number of pathways
  • KEGG (human)
  • BioCarta (human)
  • BioCyc (human)
  • Reactome (human)


168
314
165
25
10 Number of Mammalian Phenotypes (MGI) 3426
11 Number of Gene Ontology terms 4960
12 Number of gene families 56

Supplementary File 2: nsSNP profile of genes associated with mammalian phenotype

Supplementary File 3: List of nsSNPs that are predicted as both deleterious (SIFT) and damaging (PolyPhen)

Supplementary File 4: List of disease-associated genes that have at least one nsSNP predicted as deleterious (SIFT) and damaging (PolyPhen)

Supplementary File 5: List of mammalian phenotype-associated genes that have at least one nsSNP predicted as deleterious (SIFT) and damaging (PolyPhen)

Supplementary File 6: List of cSNPs resulting in premature stop codons and protein truncation

Supplementary File 7: Profile of nsSNPs that are reported as disease-causing mutation (based on OMIM/SwissChange)

Supplementary File 8: Examples illustrating the utilities of PolyDoms