Functional analysis of novel SNPs and mutations in human and mouse genomes

BMC Bioinformatics

Volumn 9, Issue SUPPL. 12, 2008, Pages

  Liu, Chuan Kun ^a   Chen, Yan Hau ^a   Tang, Cheng Yang ^a   Chang, Shu Chuan ^a   Lin, Yi Jung ^a   Tsai, Ming Fang ^a   Chen, Yuan Tsong ^a,b   Yao, Adam ^a,b  

^a ACADEMIA SINICA   (Taiwan)

^b INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARK TESTS; BIOINFORMATICS TOOLS; CODING REGION; DISEASE RISKS; IMPACT ANALYSIS; MANUAL OPERATIONS; MOUSE GENOME; PUBLIC INFORMATION; RISK LEVELS; SPLICE SITE;

BENCHMARKING; BIOINFORMATICS; GENES; TOOLS; FUNCTIONAL ANALYSIS;

FUNCTIONAL ANALYSIS; BIOINFORMATICS;

ADENOSINE; GUANOSINE; THYMIDINE;

BIOINFORMATICS; CONFERENCE PAPER; FUNCTIONAL ASSESSMENT; GENE FUNCTION; GENE MUTATION; GENETIC DATABASE; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN GENOME; INTERNET; MUTATIONAL ANALYSIS; PREDICTION; RNA SPLICING; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; ARTICLE; AUTOMATION; BIOLOGY; COMPUTER LANGUAGE; COMPUTER PROGRAM; DNA SEQUENCE; GENOME; GENOMICS; HUMAN; METHODOLOGY; MOUSE; MUTATION; RISK;

ANIMALS; AUTOMATION; COMPUTATIONAL BIOLOGY; GENETIC VARIATION; GENOME; GENOME, HUMAN; GENOMICS; HUMANS; MICE; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROGRAMMING LANGUAGES; RISK; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 57649193091     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S12-S10     Document Type: Conference Paper

References (18)

1. Kim BC Kim WY Park D Chung WH Shin KS Bhak J SNPΠromoter: A database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions BMC Bioinformatics 2008, 9(Suppl 1):S2 2259403 18315851 10.1186/1471-2105-9-S1-S2
2. Lee PH Shatkay H F-SNP: Computationally predicted functional SNPs for disease association studies Nucleic Acids Res 2008, 36:D820-824 2238878 17986460 10.1093/nar/gkm904
3. Li S Ma L Li H Vang S Hu Y Bolund L Wang J Snap: An integrated SNP annotation platform Nucleic Acids Res 2007, 35:D707-710 1751554 17135198 10.1093/nar/gkl969
4. Major JE Genomic mutation consequence calculator Bioinformatics 2007, 23:3091-3092 10.1093/bioinformatics/btm339 17599934
5. Fairbrother WG Yeo GW Yeh R Goldstein P Mawson M Sharp PA Burge CB RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons Nucleic Acids Res 2004, 32:W187-190 441531 15215377 10.1093/nar/ gkh393
6. Wang Z Rolish ME Yeo G Tung V Mawson M Burge CB Systematic identification and analysis of exonic splicing silencers Cell 2004, 119:831-845 10.1016/j.cell.2004.11.010 15607979
7. Ng PC Henikoff S SIFT: Predicting amino acid changes that affect protein function Nucleic Acids Res 2003, 31:3812-3814 168916 12824425 10.1093/ nar/gkg509
8. Ramensky V Bork P Sunyaev S Human non-synonymous SNPs: Server and survey Nucleic Acids Res 2002, 30:3894-3900 137415 12202775 10.1093/nar/gkf493
9. Yuan HY Chiou JJ Tseng WH Liu CH Liu CK Lin YJ Wang HH Yao A Chen YT Hsu CN FASTSNP: An always up-to-date and extendable service for SNP function analysis and prioritization Nucleic Acids Res 2006, 34:W635-641 1538865 16845089 10.1093/nar/gkl236
10. DePristo MA Weinreich DM Hartl DL Missense meanderings in sequence space: A biophysical view of protein evolution Nat Rev Genet 2005, 6:678-687 10.1038/nrg1672 16074985
11. Cartegni L Chew SL Krainer AR Listening to silence and understanding nonsense: Exonic mutations that affect splicing Nat Rev Genet 2002, 3:285-298 10.1038/nrg775 11967553
12. Shin C Manley JL Cell signalling and the control of pre-mRNA splicing Nat Rev Mol Cell Biol 2004, 5:727-738 10.1038/nrm1467 15340380
13. Tabor HK Risch NJ Myers RM Candidate-gene approaches for studying complex genetic traits: Practical considerations Nat Rev Genet 2002, 3:391-397 10.1038/nrg796 11988764
14. Yeo G Hoon S Venkatesh B Burge CB Variation in sequence and organization of splicing regulatory elements in vertebrate genes Proc Natl Acad Sci USA 2004, 101:15700-15705 524216 15505203 10.1073/pnas.0404901101
15. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V Church DM DiCuccio M Edgar R Federhen S Database resources of the National Center for Biotechnology Information Nucleic Acids Res 2007, 35:D5-12 1781113 17170002 10.1093/nar/gkl1031
16. Curwen V Eyras E Andrews TD Clarke L Mongin E Searle SM Clamp M The Ensembl automatic gene annotation system Genome Res 2004, 14:942-950 479124 15123590 10.1101/gr.1858004
17. Kent WJ BLAT - the BLAST-like alignment tool Genome Res 2002, 12:656-664 187518 11932250
18. Pruitt KD Tatusova T Maglott DR NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res 2005, 33:D501-504 539979 15608248 10.1093/nar/ gki025