Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Daraselia, Nikolai ^a   Yuryev, Anton ^a   Egorov, Sergei ^a   Mazo, Ilya ^a   Ispolatov, Iaroslav ^a  

^a Ariadne Genomics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SIGNIFICANCE; FUNCTIONAL ANNOTATION; FUNCTIONAL SIMILARITY; GENE ONTOLOGY ANNOTATIONS; NATURAL LANGUAGE PROCESSING; PHYSICAL INTERACTIONS; PROTEIN-PROTEIN INTERACTIONS; STRUCTURAL ORGANIZATION;

ACTIVE NETWORKS; COMPLEX NETWORKS; DATA MINING; ELECTRIC NETWORK TOPOLOGY; EXTRACTION; NATURAL LANGUAGE PROCESSING SYSTEMS; TECHNOLOGY;

PROTEINS;

ARTICLE; AUTOMATION; CLUSTER ANALYSIS; COMPUTER PROGRAM; DATA EXTRACTION; INFORMATION PROCESSING; METHODOLOGY; PERFORMANCE MEASUREMENT SYSTEM; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; VALIDATION PROCESS; AUTOMATED PATTERN RECOGNITION; BIOLOGY; CLASSIFICATION; COMPARATIVE STUDY; GENE; GENETIC DATABASE; INFORMATION RETRIEVAL; MEDLINE; NATURAL LANGUAGE PROCESSING; NOMENCLATURE; PHYSIOLOGY; PROTEIN DATABASE; REPRODUCIBILITY; STANDARD;

PROTEIN;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; GENES; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; PROTEIN INTERACTION MAPPING; PROTEINS; PUBMED; REPRODUCIBILITY OF RESULTS; TERMINOLOGY;

EID: 34547771661     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-243     Document Type: Article

References (50)

1. Hartwell LH Hopfield JJ Leibler S Murray AW From molecular to modular cell biology Nature 1999 402 C47-52 10.1038/35011540 10591225
2. Spirin V Mirny LA Protein complexes and functional modules in molecular networks Proc Natl Acad Sci USA 2003 100 12123-12128 218723 14517352 10.1073/pnas.2032324100
3. Pereira-Leal JB Enright AJ Ouzounis CA Detection of functional modules from protein interaction networks Proteins 2004 54 49-57 10.1002/ prot.10505 14705023
4. Przulj N Wigle DA Jurisica I Functional topology in a network of protein interactions Bioinformatics 2004 20 340-348 10.1093/bioinformatics/ btg415 14960460
5. Ashburner M Ball CA Blake JA Botstein D Butler H Gene Ontology: Tool for the Unification of Biology Nature Genetics 2000 25 25-29 10.1038/75556 10802651
6. Hongwei Wu Zhengchang Su Fenglou Mao Victor Olman Ying Xu Prediction of functional modules based on comparative genome analysis and Gene Ontology application Nucleic Acids Res 2005 33 2822-2837 1130488 15901854 10.1093/nar/gki573
7. Jonsson PF Cavanna T Zicha D Bates PA Cluster analysis of networks generated through homology: Automatic identification of important protein communities involved in cancer metastasis BMC Bioinformatics 2006 7 2 1363365 16398927 10.1186/1471-2105-7-2
8. Cai YD Chou KC Predicting protein localization in budding yeast Bioinformatics 2004 21 944-950 10.1093/bioinformatics/bti104 15513989
9. Chalmel F Lardenois A Thompson JD Muller J Sahel JA GOAnno: GO annotation based on multiple alignment Bioinformatics 2005 21 2095-2096 10.1093/bioinformatics/bti252 15647299
10. Hayete B Bienkowska JR Gotrees: Predicting go associations from protein domain composition using decision trees Pac Symp Biocomput 2005 10 127-138
11. Hennig S Groth D Lehrach H Automated Gene Ontology annotation for anonymous sequence data Nucleic Acids Res 2003 31 3712-3715 168988 12824400 10.1093/nar/gkg582
12. Jensen LJ Gupta R Staerfeldt HH Brunak S Prediction of human protein functions according to Gene Ontology categories Bioinformatics 2003 19 635-642 10.1093/bioinformatics/btg036 12651722
13. Pal D Eisenberg D Inference of protein functions from protein structure Structure (Camb) 2005 13 121-130 10.1016/j.str.2004.10.015
14. Pazos F Sternberg MJ Automated prediction of protein function and detection of functional sites from structure Proc Natl Acad Sci USA 2004 101 4754-14759 10.1073/pnas.0404569101
15. Schug J Diskin S Mazzarelli J Brunk BP Stoeckert CJ Jr Predicting Gene Ontology functions from ProDom and CDD protein domains Genome Res 2002 12 648-655 187511 11932249 10.1101/gr.222902
16. Vinayagam A Koenig R Moormann J Schubert F Eils R Applying Support Vector Machines for Gene Ontology based gene function prediction BMC Bioinformatics 2004 5 116 517617 15333146 10.1186/1471-2105-5-116
17. Hvidsten TR Komorowski J Sandvik AK Laegreid A Predicting gene function from gene expressions and ontologies Pac Symp Biocomput 2002 7 299-310
18. Hvidsten TR Laegreid A Komorowski J Learning rule-based models of biological process from gene expression time profiles using Gene Ontology Bioinformatics 2003 19 1116-1123 10.1093/bioinformatics/btg047 12801872
19. Lagreid A Hvidsten TR Midelfart H Komorowski J Sandvik AK Predicting Gene Ontology biological process from temporal gene expression patterns Genome Res 2003 13 965-979 430886 12695321 10.1101/gr.1144503
20. Yu H Gao L Tu K Guo Z Broadly predicting specific gene functions with expression similarity and taxonomy similarity Gene 2005 352 75-81 10.1016/j.gene.2005.03.033 15927423
21. Zhou Y Young JA Santrosyan A Chen K Yan FS Winzeler EA In silico gene function prediction using ontology-based pattern identification Bioinformatics 2004 21 1237-1245 10.1093/bioinformatics/bti111 15531612
22. Deng M Tu Z Sun F Chen T Mapping gene ontology to proteins based on protein-protein interaction data Bioinformatics 2004 20 895-902 10.1093/ bioinformatics/btg500 14751964
23. Letovsky S Kasif S Predicting protein function from protein/protein interaction data: A probabilistic approach Bioinformatics 2003 19 I197-I204 10.1093/bioinformatics/btg1026 12855458
24. Daraselia N Yuryev A Egorov S Novichkova S Nikitin A Mazo I Extracting human protein interactions from MEDLINE using a full-sentence parser Bioinformatics 2003 19 1-8 10.1093/bioinformatics/19.1.1
25. Raychaudhuri S Chang JT Sutphin PD Altman RB Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature Genome Res 2002 12 203-214 155261 11779846 10.1101/gr.199701
26. Chiang JH Yu HC MeKE: Discovering the functions of gene products from biomedical literature via sentence alignment Bioinformatics 2003 19 1417-1422 10.1093/bioinformatics/btg160 12874055
27. Koike A Niwa Y Takagi T Automatic extraction of gene/protein biological functions from biomedical text Bioinformatics 2004 21 1227-1236 10.1093/ bioinformatics/bti084 15509601
28. Blaschke C Leon EA Krallinger M Valencia A Evaluation of BioCreAtIvE assessment of task 2 BMC Bioinformatics 2005 6 Suppl 1 S16 1869008 15960828 10.1186/1471-2105-6-S1-S16
29. Yuryev A Mulyukov Z Kotelnikova E Maslov S Egorov S Automatic pathway building in biological association networks BMC Bioinformatics 2006 7 171 1435941 16563163 10.1186/1471-2105-7-171
30. Maslov S Sneppen K Specificity and stability in topology of protein networks Science 2002 296 910-913 10.1126/science.1065103 11988575
31. Ispolatov I Mazo I Yuryev A Finding mesoscopic communities in sparse networks J Stat Mech 2006 doi:10.1088/1742-5468/2006/09/P09014.
32. Reichardt J Bornholdt S Detecting fuzzy community structures in complex networks with a Potts model Phys Rev Lett 2004 93 218701 10.1103/ PhysRevLett.93.218701 15601068
33. Kiritchenko S Matwin S Famili AF Functional Annotation of Genes Using Hierarchical Text Categorization Proceedings of BioLink SIG, ISMB 2005
34. Lord P Stevens R Brass A Goble C Investigating semantic similarity measures across the Gene Ontology: The Relationship between sequence and annotation Bioinformatics 2003 19 1275-1283 10.1093/bioinformatics/ btg153 12835272
35. Camon EB Barrell DG Dimmer EC Lee V Magrane M Maslen J Binns D Apweiler R An evaluation of GO annotation retrieval for BioCreAtIvE and GOA BMC Bioinformatics 2005 6 Suppl 1 S17 1869009 15960829 10.1186/ 1471-2105-6-S1-S17
36. Egorov S Yuryev A Daraselia N A simple and practical dictionary-based approach for identification of proteins in Medline abstracts JAMA 2004 11 174-8
37. LaCount DJ Vignali M Chettier R Phansalkar A Bell R A protein interaction network of the malaria parasite Plasmodium falciparum Nature 2005 438 103-107 10.1038/nature04104 16267556
38. Krogan NJ Cagney G Yu H Zhong G Guo X Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 2006 440 637-643 10.1038/nature04670 16554755
39. Ispolatov I Yuryev A Mazo I Maslov S Binding properties and evolution of homodimers in protein-protein interaction networks Nucleic Acids Res 2005 33 3629 1160523 15983135 10.1093/nar/gki678
40. Daraselia N Egorov S Yazhuk A Novichkova S Yuryev A Mazo I Protein Function Information from MEDLINE Using a Full-Sentence Parser. Proceeding of the Second European Workshop on Data Mining and Text Mining for Bioinformatics 2004 11-18
41. Koskenniemi K Two-level Morphology: A General Computational Model for Word-Form Recognition and Production University of Helsinki Publications 1983 N11
42. Lee JH Paull TT ATM Activation by DNA Double-Strand Breaks Through the Mre11-Rad50-Nbs1 Complex Science 2005 308 551-554 10.1126/ science.1108297 15790808
43. Takahagi M Tatsumi K Aggregative organization enhances the DNA end-joining process that is mediated by DNA-dependent protein kinase FEBS J 2006 273 3063-75 10.1111/j.1742-4658.2006.05317.x 16759233
44. Li J Stern DF Regulation of CHK2 by DNA-dependent protein kinase J Biol Chem 2005 280 12041-50 10.1074/jbc.M412445200 15668230
45. Chiang J Yu H Extracting Functional Annotations of Proteins Based on Hybrid Text Mining Approaches Proc BioCreAtIvE Challenge Evaluation Workshop 2004
46. Couto F Silva M Coutinho P Finding Genomic Ontology Terms in Unstructured Text BMC Bioinformatics 2005 6 Suppl 1 S21 1869014 15960834 10.1186/1471-2105-6-S1-S21
47. Ehrler F Jimeno A Ruch P Data-poor categorization and passage retrieval for Gene Ontology annotation in Swiss-Prot BMC bioinformatics 2005 6 Suppl 1 S23 1869016 15960836 10.1186/1471-2105-6-S1-S23
48. Ray S Craven M Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text BMC bioinformatics 2005 6 Suppl 1 S18 1869010 15960830 10.1186/1471-2105-6-S1-S18
49. Rice S Nenadic G Stapley B Mining protein functions from text using term-based support vector machines BMC bioinformatics 2005 6 Suppl 1 S22 1869015 15960835 10.1186/1471-2105-6-S1-S22
50. Verspoor K Cohn J Joslyn C Mniszewski S Rechtsteiner A Rocha L Simas T Protein Annotation as Term Categorization in the Gene Ontology using Word Proximity Networks BMC bioinformatics 2005 6 Suppl 1 S20 1869013 15960833 10.1186/1471-2105-6-S1-S20