Extraction of human kinase mutations from literature, databases and genotyping studies

BMC Bioinformatics

Volumn 10, Issue SUPPL. 8, 2009, Pages

  Krallinger, Martin ^a   Izarzugaza, Jose M G ^a   Rodriguez Penagos, Carlos ^b   Valencia, Alfonso ^a  

^a Centro Nacional de Investigaciones Oncológicas   (Spain)

^b Barcelona Media   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC EXTRACTION; BIOLOGICAL CHARACTERIZATION; CLASSIFICATION APPROACH; HIGH THROUGHPUT GENOTYPING; LARGE SCALE EXPERIMENTS; MUTAGENESIS EXPERIMENT; SINGLE-POINT MUTATION; SYSTEMATIC INTEGRATION;

ABSTRACTING; DATABASE SYSTEMS; EXPERIMENTS; EXTRACTION; MUTAGENESIS; PIPELINES; PROTEINS;

ENZYMES;

PROTEIN KINASE; EPIDERMAL GROWTH FACTOR RECEPTOR;

ACCURACY; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; AUTOMATION; COMPUTER PROGRAM; DATA EXTRACTION; DATA MINING; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; GENOTYPE; GOLD STANDARD; KNOWLEDGE BASE; MEDICAL LITERATURE; MEDLINE; MUTAGENESIS; MUTATIONAL ANALYSIS; POINT MUTATION; PROTEIN DOMAIN; PROTEIN FAMILY; DNA SEQUENCE; GENETICS; GENOMICS; HUMAN; INFORMATION RETRIEVAL; METHODOLOGY; MUTATION; PUBLICATION; REPRODUCIBILITY;

DATABASES, GENETIC; GENOMICS; GENOTYPE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MUTATION; PERIODICALS AS TOPIC; PROTEIN KINASES; RECEPTOR, EPIDERMAL GROWTH FACTOR; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 69549108302     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S8-S1     Document Type: Article

References (42)

1. Manning G Whyte DB Martinez R Hunter T Sudarsanam S The Protein Kinase Complement of the Human Genome Science 2002, 298:1912-1934 12471243
2. Ubersax JA Woodbury EL Quang PN Paraz M Blethrow JD Shah K Shokat KM Morgan DO Targets of the Cyclin-dependent Kinase Cdk1 Nature 2003, 425:859-864 14574415
3. Ptacek J Devgan G Michaud G Zhu H Zhu X Fasolo J Guo H Jona G Breitkreutz A Sopko R McCartney RR Schmidt MC Rachidi N Lee SJ Mah AS Meng L Stark MJR Stern DF De Virgilio C Tyers M Andrews B Gerstein M Schweitzer B Predki PF Snyder M Global Analysis of Protein Phosphorylation in Yeast Nature 2005, 438:679-684 16319894
4. Huse M Kuriyan J The conformational plasticity of protein kinases Cell 2002, 109(3):275-82 12015977
5. Burgess AW EGFR family: Structure physiology signalling and therapeutic targets Growth Factors 2008, 26(5):263-74 18800267
6. Yamada S Shiro Y Structural basis of the signal transduction in the two-component system Adv Exp Med Biol 2008, 631:22-39 18792680
7. Sanz P AMP-activated protein kinase: Structure and regulation Curr Protein Pept Sci 2008, 9(5):478-92 18855699
8. Ortutay C Väliaho J Stenberg K Vihinen M KinMutBase: A registry of disease-causing mutations in protein kinase domains Hum Mutat 2005, 25(5):435-42 15832311
9. Richardson CJ Gao Q Mitsopoulous C Zvelebil M Pearl LH Pearl FMG MoKCa Database-mutations of Kinases in Cancer Nucleic Acids Res 2009, 37:D824-D831 2686448 18986996
10. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The Protein Data Bank Nucleic Acids Res 2000, 28:235-42 102472 10592235
11. Finn RD Tate J Mistry J Coggill PC Sammut SJ Hotz HR Ceric G Forslund K Eddy SR Sonnhammer ELL Bateman A The Pfam protein families database Nucleic Acids Res 2008, 36: Database D281-8 2238907 18039703
12. Greene LH Lewis TE Addou S Cuff A Dallman T Dibley M Redfern O Pearl F Nambudiry R Reid A Sillitoe I Yeats C Thornton JM Orengo CA The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution Nucleic Acids Res 2007, 35: Database D291-7 1751535 17135200
13. Shchemelinin I Sefc L Necas E Protein kinases, their function and implication in cancer and other diseases Folia Biol (Praha) 2006, 52(3):81-100 17089919
14. Wood LD Parsons DW Jones S Lin J Sjöblom T Leary RJ Shen D Boca SM Barber TD Ptak J Silliman N Szabo S Dezso Z Ustyanksky V Nikolskaya T Nikolsky Y Karchin R Wilson PA Kaminker JS Zhang Z Croshaw R Willis J Dawson D Shipitsin M Willson JKV Sukumar S Polyak K Park BH Pethiyagoda CL Pant PVK Ballinger DG Sparks AB Hartigan J Smith DR Suh E Papadopoulos N Buckhaults P Markowitz SD Parmigiani G Kinzler KW Velculescu VE Vogelstein B The genomic landscapes of human breast and colorectal cancers Science 2007, 318(5853):1108-13 17932254
15. Sjöblom T Jones S Wood LD Parsons DW Lin J Barber TD Mandelker D Leary RJ Ptak J Silliman N Szabo S Buckhaults P Farrell C Meeh P Markowitz SD Willis J Dawson D Willson JKV Gazdar AF Hartigan J Wu L Liu C Parmigiani G Park BH Bachman KE Papadopoulos N Vogelstein B Kinzler KW Velculescu VE The consensus coding sequences of human breast and colorectal cancers Science 2006, 314(5797):268-74 16959974
16. Greenman C Stephens P Smith R Dalgliesh GL Hunter C Bignell G Davies H Teague J Butler A Stevens C Edkins S O'Meara S Vastrik I Schmidt EE Avis T Barthorpe S Bhamra G Buck G Choudhury B Clements J Cole J Dicks E Forbes S Gray K Halliday K Harrison R Hills K Hinton J Jenkinson A Jones D Menzies A Mironenko T Perry J Raine K Richardson D Shepherd R Small A Tofts C Varian J Webb T West S Widaa S Yates A Cahill DP Louis DN Goldstraw P Nicholson AG Brasseur F Looijenga L Weber BL Chiew YE DeFazio A Greaves MF Green AR Campbell P Birney E Easton DF Chenevix-Trench G Tan MH Khoo SK Teh BT Yuen ST Leung SY Wooster R Futreal PA Stratton MR Patterns of somatic mutation in human cancer genomes Nature 2007, 446(7132):153-8 17344846 2712719
17. Baudot A Real F Izarzugaza J Valencia A From cancer genomes to cancer models: Bridging the gaps EMBO Rep 2009 19305388
18. Santamaría D Barrière C Cerqueira A Hunt S Tardy C Newton K Cáceres JF Dubus P Malumbres M Barbacid M Cdk1 is sufficient to drive the mammalian cell cycle Nature 2007, 448(7155):811-5 17700700
19. Rebholz-Schuhmann D Marcel S Albert S Tolle R Casari G Kirsch H Automatic extraction of mutations from Medline and cross-validation with OMIM Nucl Acids Res 2004, 32:135-142 373272 14704350
20. Lee LC Horn F Cohen FE Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association PLoS Comput Biol 2007, 3:e16-e16 1794323 17274683
21. Baker CJO Witte R Mutation Mining - A Prospector's Tale Information Systems Frontiers (ISF) 2006, 8:47-57
22. Witte R Baker CJO Towards A Systematic Evaluation of Protein Mutation Extraction Systems J Bioinform Comput Biol 2007, 5(6):1339-1359 18172932
23. Caporaso JG Baumgartner WA 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
24. Erdogmus M Sezerman OU Application of Automatic Mutation-gene pair Extraction to Diseases J Bioinform Comput Biol 2007, 5:1261-1275 18172928
25. McDonald R Scott Winters R Ankuda CK Murphy JA Rogers AE Pereira F Greenblatt MS White PS An Automated Procedure to Identify Biomedical Articles that Contain Cancer-associated gene Variants Hum Mutat 2006, 27:957-964 16865690
26. McDonald RT Winters RS Mandel M Jin Y White PS Pereira F An Entity Tagger for Recognizing Acquired Genomic Variations in Cancer Literature Bioinformatics 2004, 20:3249-3251 15180929
27. Horn F Lau AL Cohen FE Automated Extraction of Mutation data from the Literature: Application of MuteXt to G Protein-coupled Receptors and Nuclear Hormone Receptors Bioinformatics 2004, 20:557-568 14990452
28. Yip YL Lachenal N Pillet V Veuthey AL Retrieving Mutation-specific Information for Human Proteins in UniProt/Swiss-Prot Knowledgebase J Bioinform Comput Biol 2007, 5:1215-1231 18172926
29. Kanagasabai R Choo KH Ranganathan S Baker CJO A Workflow for Mutation Extraction and Structure Annotation J Bioinform Comput Biol 2007, 5:1319-1337 18172931
30. 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, 29:361-366 18175334
31. Yip YL Scheib H Diemand AV Gattiker A Famiglietti LM Gasteiger E Bairoch A The Swiss-Prot variant page and the ModSNP database: A resource for sequence and structure information on human protein variants Human Mutation 2004, 23(5):464-470 15108278
32. Bamford S Dawson E Forbes S Clements J Pettett R Dogan A Flanagan A Teague J Futreal PA Stratton MR Wooster R The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website Br J Cancer 2004, 91(2):355-8 15188009
33. Hurst J McMillan L Porter C Allen J Fakorede A Martin A The SAAPdb web resource: A large-scale structural analysis of mutant proteins Hum Mutat 2009 19191322
34. 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 18172927
35. Morgan AA Lu Z Wang X Cohen AM Fluck J Ruch P Divoli A Fundel K Leaman R Hakenberg J Sun C Liu Hh Torres R Krauthammer M Lau WW Liu H Hsu CN Schuemie M Cohen KB Hirschman L Overview of BioCreative II gene Normalization Genome Biol 2008, 9(Suppl 2):S3-S3 2559987 18834494
36. Tam IYS Chung LP Suen WS Wang E Wong MCM Ho KK Lam WK Chiu SW Girard L Minna JD Gazdar AF Wong MP Distinct epidermal growth factor receptor and KRAS mutation patterns in non-small cell lung cancer patients with different tobacco exposure and clinicopathologic features Clin Cancer Res 2006, 12(5):1647-53 16533793
37. Altschul SF Madden TL Schäffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25(17):3389-402 146917 9254694
38. den Dunnen JT Antonarakis SE Mutation Nomenclature Curr Protoc Hum Genet 2003 Chapter 7 Unit 7.13 18428344
39. Lesk M Automatic sense disambiguation using machine readable dictionaries: How to tell a pine cone from an ice cream cone Proceedings of SIGDOC-86: 5th International Conference on Systems Documentation 1986:24-26
40. Joachims T Learning to Classify Text using Support Vector Machines Kluwer 2002 http://www.cs.cornell.edu/People/tj/
41. 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, 29:333-344 18058827
42. 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, 9:84-84 2277400 18251998