Improved mutation tagging with gene identifiers applied to membrane protein stability prediction

BMC Bioinformatics

Volumn 10, Issue SUPPL. 8, 2009, Pages

  Winnenburg, Rainer ^a   Plake, Conrad ^a   Schroeder, Michael ^a  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; BENCHMARK DATASETS; G PROTEIN COUPLED RECEPTORS; NAMED ENTITY RECOGNITION; PROTEIN MUTATIONS; PROTEIN STRUCTURES; STABILIZING REGIONS; STRUCTURE-FUNCTION RELATIONSHIP;

ABSTRACTING; AMINO ACIDS; BIOLOGICAL MEMBRANES; CHARACTER RECOGNITION; GENES; PATTERN MATCHING;

PROTEINS;

MEMBRANE PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; AUTOMATION; COMPUTER PROGRAM; GENE IDENTIFICATION; GENETIC DATABASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MEDLINE; MUTATIONAL ANALYSIS; PHENOTYPE; POINT MUTATION; PREDICTION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; QUALITY CONTROL; RELIABILITY; SCIENTIFIC LITERATURE; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; ALGORITHM; ANIMAL; AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; GENE; GENETICS; GENOMICS; HUMAN; METHODOLOGY; MUTATION; PUBLICATION;

ALGORITHMS; AMINO ACID SUBSTITUTION; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENES; GENOMICS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MEMBRANE PROTEINS; MODELS, GENETIC; MUTATION; PATTERN RECOGNITION, AUTOMATED; PERIODICALS AS TOPIC; PHENOTYPE; POINT MUTATION; PROTEIN STABILITY; PUBMED; SEQUENCE ANALYSIS;

EID: 69549112939     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S8-S3     Document Type: Article

References (46)

1. Alberts B Bray D Hopkin K Johnson A Lewis J Raff M Roberts K Walter P Essential Cell Biology London: Garland Science Textbooks 2002.
2. Ogata H Goto S Sato K Fujibuchi W Bono H Kanehisa M KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res 1999, 27:29-34. 148090 9847135 10.1093/nar/27.1.29
3. Collins FS Brooks LD Chakravarti A A DNA polymorphism discovery resource for research on human genetic variation Genome Res 1998, 8(12):1229-31. 9872978
4. Horaitis O Cotton R The challenge of documenting mutation across the genome: The human genome variation society approach Hum Mutat 2004, 23(5):447-52. 10.1002/humu.20038 15108276
5. Amberger J Bocchini CA Scott AF Hamosh A McKusick's Online Mendelian Inheritance in Man (OMIM) Nucleic Acids Res 2009, 37(Database):D793-6. 2686440 18842627 10.1093/nar/gkn665
6. Yip YL Famiglietti M Gos A Duek PD David FPA Gateau A Bairoch A Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase Hum Mutat 2008, 29(3):361-6. 10.1002/humu.20671 18175334
7. Yip YL Lachenal N Pillet V Veuthey A Retrieving mutation-specific information for human proteins in uniprot/swiss-prot knowledgebase J Bioinform Comput Biol 2007, 5(6):1215-1231. 10.1142/S021972000700320X 18172926
8. Stenson P Ball E Howells K Phillips A Mort M Cooper D Human Gene Mutation Database: Towards a comprehensive central mutation database J Med Genet 2008, 45(2):124-6. 10.1136/jmg.2007.055210 18245393
9. Béroud C Hamroun D Collod-Béroud G Boileau C Soussi T Claustres M UMD (Universal Mutation Database): 2005 update Hum Mutat 2005, 26(3):184-91. 10.1002/humu.20210 16086365
10. Thorisson GA Lancaster O Free RC Hastings RK Sarmah P Dash D Brahmachari SK Brookes AJ HGVbaseG2P: A central genetic association database Nucleic Acids Res 2009, 37(Database):D797-802. 2686551 18948288 10.1093/nar/ gkn748
11. Singh A Olowoyeye A Baenziger PH Dantzer J Kann MG Radivojac P Heiland R Mooney SD MutDB: Update on development of tools for the biochemical analysis of genetic variation Nucleic Acids Res 2008, 36(Database):D815-9. 2238958 17827212
12. Milhavet F Cuisset L Hoffman HM Slim R El-Shanti H Aksentijevich I Lesage S Waterham H Wise C de Menthiere CSdM Touitou I The infevers autoinflammatory mutation online registry: Update with new genes and functions Hum Mutat 2008, 29(6):803-8. 10.1002/humu.20720 18409191
13. Kazius J Wurdinger K Iterson MvI Kok J Bäck T Ijzerman AP GPCR NaVa database: Natural variants in human G protein-coupled receptors Hum Mutat 2008, 29:39-44. 10.1002/humu.20638 17924574
14. Kroos M Pomponio RJ Vliet LvV Palmer RE Phipps M der Helm RVdH Halley D Reuser A Consortium D Update of the Pompe disease mutation database with 107 sequence variants and a format for severity rating Hum Mutat 2008, 29(6):E13-26. 10.1002/humu.20745 18425781
15. Jensen LJ Saric J Bork P Literature mining for the biologist: From information retrieval to biological discovery Nat Rev Genet 2006, 7(2):119-29. 10.1038/nrg1768 16418747
16. Krallinger M Erhardt RAA Valencia A Text-mining approaches in molecular biology and biomedicine Drug Discov Today 2005, 10(6):439-45. 10.1016/ S1359-6446(05)03376-3 15808823
17. Zweigenbaum P Demner-Fushman D Yu H Cohen K Frontiers of biomedical text mining: Current progress Brief Bioinform 2007, 8:358-375. http://www.ncbi.nlm.nih.gov/sites/entrez 2516302 17977867 10.1093/bib/bbm045
18. Winnenburg R Wächter T Plake C Doms A Schroeder M Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies? Brief Bioinform 2008, 9:466-78. 10.1093/bib/ bbn043 19060303
19. Altman RB Bergman CM Blake J Blaschke C Cohen A Gannon F Grivell L Hahn U Hersh W Hirschman L Jensen LJ Krallinger M Mons B O'Donoghue SI Peitsch MC Rebholz-Schuhmann D Shatkay H Valencia A Text mining for biology-the way forward: Opinions from leading scientists Genome Biol 2008, 9(Suppl 2):S7. 2559991 18834498 10.1186/gb-2008-9-s2-s7
20. Leser U Hakenberg J What makes a gene name?: Named entity recognition in the biomedical literature Brief Bioinform 2005, 6:357-369. 10.1093/bib/ 6.4.357 16420734
21. Spasic I Ananiadou S McNaught J Kumar A Text mining and ontologies in biomedicine: Making sense of raw text Brief Bioinform 2005, 6(3):239-51. 10.1093/bib/6.3.239 16212772
22. Ashburner M Ball C Blake J Botstein D Butler H Cherry J Davis A Dolinski K Dwight S Eppig J Harris M Hill D Issel-Tarver L Kasarskis A Lewis S Matese J Richardson J Ringwald M Rubin G Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nature genetics 2000, 25:25-29. 10.1038/75556 10802651
23. Rebholz-Schuhmann D Marcel S Albert S Tolle R Casari G Kirsch H Automatic extraction of mutations from Medline and cross-validation with OMIM Nucleic Acids Res 2004, 32:135-42. 373272 14704350 10.1093/nar/ gkh162
24. Cantor M Lussier Y Mining OMIM for insight into complex diseases Medinfo 2004, 11(Pt 2):753-7.
25. Caporaso JG Baumgartner WA Randolph DA Cohen KB Hunter L Rapid pattern development for concept recognition systems: Application to point mutations J Bioinform Comput Biol 2007, 5:1233-1259. 10.1142/ S0219720007003144 18172927
26. Lee LC Horn F Cohen FE Automatic extraction of protein point mutations using a graph bigram association PLoS Comput Biol 2007, 3(2):e16. 1794323 17274683 10.1371/journal.pcbi.0030016
27. Klinger R Friedrich C Mevissen H Fluck J Hofmann-Apitius M Furlong L Sanz F Identifying gene-specific variations in biomedical text J Bioinform Comput Biol 2007, 5(6):1277-96. 10.1142/S0219720007003156 18172929
28. Witte R Baker C Towards a systematic evaluation of protein mutation extraction systems J Bioinform Comput Biol 2007, 5(6):1339-59. 10.1142/ S0219720007003193 18172932
29. Baker CJO Journal of Bioinformatics and Computational Biology - Special Issue: Making Sense of Mutations Requires Knowledge Management London: Imperial College Press 2007, 5.
30. Kanagasabai R Choo K Ranganathan S Baker C A workflow for mutation extraction and structure annotation J Bioinform Comput Biol 2007, 5(6):1319-37. 10.1142/S0219720007003119 18172931
31. Worth C Bickerton G Schreyer A Forman J Cheng T Lee S Gong S Burke D Blundell T A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease J Bioinform Comput Biol 2007, 5(6):1297-318. 10.1142/ S0219720007003120 18172930
32. Erdogmus M Sezerman O Application of automatic mutation-gene pair extraction to diseases J Bioinform Comput Biol 2007, 5(6):1261-75. 10.1142/S021972000700317X 18172928
33. Lage K Karlberg EO Størling ZM Olason PI Pedersen AG Rigina O Hinsby AM Tümer Z Pociot F Tommerup N Moreau Y Brunak S A human phenome-interactome network of protein complexes implicated in genetic disorders Nat Biotechnol 2007, 25(3):309-16. 10.1038/nbt1295 17344885
34. Hakenberg J Plake C Royer L Strobelt H Leser U Schroeder M Gene mention normalization and interaction extraction with context models and sentence motifs Genome Biol 2008, 9(Suppl 2):S14. 2559985 18834492 10.1186/gb-2008-9-s2-s14
35. Hakenberg J Plake C Leaman R Schroeder M Gonzalez G Inter-species normalization of gene mentions with GNAT 2008, 24(16):i126-132. 18689813
36. Caporaso JG Baumgartner JWA Randolph DA Cohen KB Hunter L MutationFinder: A high-performance system for extracting point mutation mentions from text Bioinformatics 2007, 23:1862-1865. 2516306 17495998 10.1093/bioinformatics/btm235
37. Martin A Mapping PDB chains to UniProtKB entries Bioinformatics 2005, 21(23):4297-301. 10.1093/bioinformatics/bti694 16188924
38. Plake C Royer L Winnenburg R Hakenberg J Schroeder M GoGene: Gene annotation in the fast lane Nucleic Acids Res 2009, 37(Web server issue):W300-W304. 2703922 19465383 10.1093/nar/gkp429
39. Dressel F Marsico A Tuukkanen A Winnenburg R Labudde D Schroeder M Stabilizing regions in membrane proteins From Computational Biophysics to Systems Biology (CBSB08) 2008:197-9.
40. Kono M Crouch RK Oprian DD A dark and constitutively active mutant of the tiger salamander UV pigment Biochemistry 2005, 44(2):799-804. 10.1021/bi047898f 15641808
41. International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs Nature 2007, 449(7164):851-61. 2689609 17943122 10.1038/nature06258
42. Sherry ST Ward MH Kholodov M Baker J Phan L Smigielski EM Sirotkin K dbSNP: The NCBI database of genetic variation Nucleic Acids Res 2001, 29:308-11. 29783 11125122 10.1093/nar/29.1.308
43. Horn F Bettler E Oliveira L Campagne F Cohen FE Vriend G GPCRDB information system for G protein-coupled receptors Nucleic Acids Res 2003, 31:294-7. 165550 12520006 10.1093/nar/gkg103
44. Saunders RE Perkins SJ CoagMDB: A database analysis of missense mutations within four conserved domains in five vitamin K-dependent coagulation serine proteases using a text-mining tool Hum Mutat 2008, 29(3):333-44. 10.1002/humu.20629 18058827
45. Furlong LI Dach H Hofmann-Apitius M Sanz F OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature BMC Bioinformatics 2008, 9:84. 2277400 18251998 10.1186/ 1471-2105-9-84
46. Cheng D Knox C Young N Stothard P Damaraju S Wishart DS PolySearch: A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites Nucleic Acids Res 2008, 36(Web Server):W399-405. 2447794 18487273 10.1093/nar/gkn296