A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

Genome Biology

Volumn 9, Issue SUPPL. 1, 2008, Pages

  Peña Castillo, Lourdes ^a   Tasan, Murat ^b   Myers, Chad L ^c   Lee, Hyunju ^d   Joshi, Trupti ^e   Zhang, Chao ^e   Guan, Yuanfang ^c   Leone, Michele ^f   Pagnani, Andrea ^f   Kim, Wan Kyu ^g   Krumpelman, Chase ^h   Tian, Weidong ^b   Obozinski, Guillaume ⁱ   Qi, Yanjun ^j   Mostafavi, Sara ^k   Lin, Guan Ning ^e   Berriz, Gabriel F ^b   Gibbons, Francis D ^b   Lanckriet, Gert ^l   Qiu, Jian ^m   Grant, Charles ^m   Barutcuoglu, Zafer ⁿ   Hill, David P ^o   Warde Farley, David ^k   Grouios, Chris ^a   Ray, Debajyoti ^p   Blake, Judith A ^o   Deng, Minghua ^q   Jordan, Michael I ⁱ   Noble, William S ^m   Morris, Quaid ^a,k   Klein Seetharaman, Judith ^r   Bar Joseph, Ziv ^j   Chen, Ting ^s   Sun, Fengzhu ^s   Troyanskaya, Olga G ^c   Marcotte, Edward M ^g   Xu, Dong ^e   Hughes, Timothy R ^a,k   Roth, Frederick P ^b,t   more..

^a UNIVERSITY OF TORONTO   (Canada)

^b HARVARD MEDICAL SCHOOL   (United States)

^c PRINCETON UNIVERSITY   (United States)

^d Gwangju Institute of Science and Technology (GIST)   (South Korea)

^e University of Missouri   (United States)

^f ISI FOUNDATION   (Italy)

^g UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^h The University of Texas at Austin   (United States)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

^j Carnegie Mellon University   (United States)

^k UNIVERSITY OF TORONTO   (Canada)

^l UNIVERSITY OF CALIFORNIA   (United States)

^m UNIVERSITY OF WASHINGTON   (United States)

ⁿ Princeton University   (United States)

^o JACKSON LABORATORY   (United States)

^p UNIVERSITY COLLEGE LONDON   (United Kingdom)

^q PEKING UNIVERSITY   (China)

^r UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^s UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^t DANA FARBER CANCER INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; CLASSIFIER; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENE FUNCTION; GENETIC ALGORITHM; GENOME ANALYSIS; MAMMALIAN GENETICS; MOUSE; NONHUMAN; PREDICTION; ALGORITHM; ANIMAL; GENETICS; METABOLISM;

MAMMALIA; MUS MUSCULUS;

PROTEIN;

ALGORITHMS; ANIMALS; MICE; PROTEINS;

EID: 47549116997     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-s1-s2     Document Type: Article

References (57)

1. Aerts S Lambrechts D Maity S Van Loo P Coessens B De Smet F Tranchevent LC De Moor B Marynen P Hassan B Carmeliet P Moreau Y Gene prioritization through genomic data fusion. Nat Biotechnol 2006, 24:537-544. 16680138
2. Chen Y Xu D Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res 2004, 32:6414-6424. 535686 15585665
3. Joshi T Chen Y Becker JM Alexandrov N Xu D Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. OMICS 2004, 8:322-333. 15703479
4. Karaoz U Murali TM Letovsky S Zheng Y Ding C Cantor CR Kasif S Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci USA 2004, 101:2888-2893. 365715 14981259
5. Lanckriet GR De Bie T Cristianini N Jordan MI Noble WS A statistical framework for genomic data fusion. Bioinformatics 2004, 20:2626-2635. 15130933
6. Massjouni N Rivera CG Murali TM VIRGO: Computational prediction of gene functions. Nucleic Acids Res 2006, 34:W340-344. 1538839 16845022
7. Myers CL Robson D Wible A Hibbs MA Chiriac C Theesfeld CL Dolinski K Troyanskaya OG Discovery of biological networks from diverse functional genomic data. Genome Biol 2005, 6:R114. 1414113 16420673
8. Shenouda EAMA Morris Q Bonner AJ Connectionist approaches for predicting mouse gene function from gene expression. Neural Information Processing: 13th International Conference, ICONIP 2006, Hong Kong, China, October 3-6, 2006, Proceedings Heidelberg, Berlin; Springer King I, Wang J, Chan L, Wang DL 2006:280-289.
9. Troyanskaya OG Dolinski K Owen AB Altman RB Botstein D A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci USA 2003, 100:8348-8353. 166232 12826619
10. Yao Z Ruzzo WL A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data. BMC Bioinformatics 2006, 7(suppl 1):S11. 1810312 16723004
11. Abuin A Hansen GM Zambrowicz B Gene trap mutagenesis. Handb Exp Pharmacol 2007, 178:129-147. 17203654
12. Collins FS Rossant J Wurst W A mouse for all reasons. Cell 2007, 128:9-13. 17218247
13. Letovsky S Kasif S Predicting protein function from protein/protein interaction data: A probabilistic approach. Bioinformatics 2003, 19(suppl 1):i197-204. 12855458
14. Lu LJ Xia Y Paccanaro A Yu H Gerstein M Assessing the limits of genomic data integration for predicting protein networks. Genome Res 2005, 15:945-953. 1172038 15998909
15. Tanay A Steinfeld I Kupiec M Shamir R Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium. Mol Syst Biol 2005, 1:2005.0002. 1681453 16729037
16. Clare A Karwath A Ougham H King RD Functional bioinformatics for Arabidopsis thaliana. Bioinformatics 2006, 22:1130-1136. 16481336
17. King RD Karwath A Clare A Dehaspe L Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coli genomes using data mining. Yeast 2000, 17:283-293. 11119305
18. van Noort V Snel B Huynen MA Predicting gene function by conserved co-expression. Trends Genet 2003, 19:238-242. 12711213
19. Milo R Shen-Orr S Itzkovitz S Kashtan N Chklovskii D Alon U Network motifs: Simple building blocks of complex networks. Science 2002, 298:824-827. 12399590
20. Oltvai ZN Barabasi AL Systems biology. Life's complexity pyramid. Science 2002, 298:763-764. 12399572
21. Zhang W Morris QD Chang R Shai O Bakowski MA Mitsakakis N Mohammad N Robinson MD Zirngibl R Somogyi E Laurin N Eftekharpour E Sat E Grigull J Pan Q Peng WT Krogan N Greenblatt J Fehlings M Kooy van der D Aubin J Bruneau BG Rossant J Blencowe BJ Frey BJ Hughes TR The functional landscape of mouse gene expression. J Biol 2004, 3:21. 549719 15588312
22. Godzik A Jambon M Friedberg I Computational protein function prediction: Are we making progress? Cell Mol Life Sci 2007, 64:2505-2511. 17611711
23. Murali TM Wu CJ Kasif S The art of gene function prediction. Nat Biotechnol 2006, 24:1474-1475. 17160037
24. Myers CL Barrett DR Hibbs MA Huttenhower C Troyanskaya OG Finding function: Evaluation methods for functional genomic data. BMC Genomics 2006, 7:187. 1560386 16869964
25. Chen Y Xu D Computational analyses of high-throughput protein-protein interaction data. Curr Protein Pept Sci 2003, 4:159-181. 12769716
26. Grunenfelder B Winzeler EA Treasures and traps in genome-wide data sets: case examples from yeast. Nat Rev Genet 2002, 3:653-661. 12209140
27. Steinmetz LM Deutschbauer AM Gene function on a genomic scale. J Chromatogr B Analyt Technol Biomed Life Sci 2002, 782:151-163. 12458004
28. Brown KR Jurisica I Online Predicted Human Interaction Database. Bioinformatics 2005, 21:2076-2082. 15657099
29. Yu H Luscombe NM Lu HX Zhu X Xia Y Han JD Bertin N Chung S Vidal M Gerstein M Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs. Genome Res 2004, 14:1107-1118. 419789 15173116
30. MouseFunc I http://hugheslab.med.utoronto.ca/supplementary-data/ mouseFunc_I/
31. The Gene Ontology Consortium Gene ontology: Tool for the unification of biology. Nat Genet 2000, 25:25-29. 10802651
32. The Jackson Laboratory Mouse Genome Database (MGD), Mouse Genome Informatics Web Site http://www.informatics.jax.org
33. Guide to GO Evidence Codes http://www.geneontology.org/GO.evidence.shtml
34. Hanley JA McNeil BJ A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology 1983, 148:839-843. 6878708
35. Marcotte EM Pellegrini M Thompson MJ Yeates TO Eisenberg D A combined algorithm for genome-wide prediction of protein function. Nature 1999, 402:83-86. 10573421
36. Geserick P Kaiser F Klemm U Kaufmann S Zerrahn J Modulation of T cell development and activation by novel members of the Schlafen (slfn) gene family harbouring an RNA helicase-like motif. Int Immunol 2004, 16:1535-1548. 15351786
37. MFunc: Predictions of Gene Function http://llama.med.harvard.edu/cgi/ Mfunc/mfunc.py
38. Kislinger T Cox B Kannan A Chung C Hu P Ignatchenko A Scott MS Gramolini AO Morris Q Hallett MT Rossant J Hughes TR Frey B Emili A Global survey of organ and organelle protein expression in mouse: Combined proteomic and transcriptomic profiling. Cell 2006, 125:173-186. 16615898
39. Maeda N Kasukawa T Oyama R Gough J Frith M Engstrom PG Lenhard B Aturaliya RN Batalov S Beisel KW Bult CJ Fletcher CF Forrest AR Furuno M Hill D Itoh M Kanamori-Katayama M Katayama S Katoh M Kawashima T Quackenbush J Ravasi T Ring BZ Shibata K Sugiura K Takenaka Y Teasdale RD Wells CA Zhu Y Kai C et aM.: Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet 2006, 2:e62. 1449903 16683036
40. Kittler J Hatef M Duin RPW Matas J On combining classifiers. IEEE Trans Pattern Analysis Machine Intelligence 1998, 20:226-239.
41. Peng WT Robinson MD Mnaimneh S Krogan NJ Cagney G Morris Q Davierwala AP Grigull J Yang X Zhang W Mitsakakis N Ryan OW Datta N Jojic V Pal C Canadien V Richards D Beattie B Wu LF Altschuler SJ Roweis S Frey BJ Emili A Greenblatt JF Hughes TR A panoramic view of yeast noncoding RNA processing. Cell 2003, 113:919-933. 12837249
42. Fawcett T An introduction to ROC analysis. Pattern Recogn Lett 2006, 27:861-874.
43. Davis J Goadrich M The relationship between Precision-Recall and ROC curves. Proceedings of the 23rd International Conference on Machine Learning: June 25-29, 2006; Pittsburgh, Pennsylvania New York: ACM Press Cohen WW, Moore A 2006:233-240.
44. Su AI Wiltshire T Batalov S Lapp H Ching KA Block D Zhang J Soden R Hayakawa M Kreiman G Cooke MP Walker JR Hogenesch JB A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101:6062-6067. 395923 15075390
45. Siddiqui AS Khattra J Delaney AD Zhao Y Astell C Asano J Babakaiff R Barber S Beland J Bohacec S Brown-John M Chand S Charest D Charters AM Cullum R Dhalla N Featherstone R Gerhard DS Hoffman B Holt RA Hou J Kuo BY Lee LL Lee S Leung D Ma K Matsuo C Mayo M McDonald H Prabhu AL et al.: A mouse atlas of gene eLpression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci USA 2005, 102:18485-18490. 1311911 16352711
46. Finn RD Mistry J Schuster-Bockler B Griffiths-Jones S Hollich V Lassmann T Moxon S Marshall M Khanna A Durbin R Eddy SR Sonnhammer EL Bateman A Pfam: Clans, web tools and services. Nucleic Acids Res 2006, 34:D247-251. 1347511 16381856
47. Mulder NJ Apweiler R Attwood TK Bairoch A Bateman A Binns D Bradley P Bork P Bucher P Cerutti L Copley R Courcelle E Das U Durbin R Fleischmann W Gough J Haft D Harte N Hulo N Kahn D Kanapin A Krestyaninova M Lonsdale D Lopez R Letunic I Madera M Maslen J McDowall J Mitchell A Nikolskaya AN et al.: InterPro, progress and status in 2005. Nucleic Acids Res 2005, 33:D201-205. 540060 15608177
48. Eppig JT Blake JA Bult CJ Kadin JA Richardson JE The mouse genome database (MGD): New features facilitating a model system. Nucleic Acids Res 2007, 35:D630-637. 1751527 17135206
49. Phenotype Annotations from MGI http://ftp.informatics.jax.org/pub/reports
50. Kasprzyk A Keefe D Smedley D London D Spooner W Melsopp C Hammond M Rocca-Serra P Cox T Birney E EnsMart: A generic system for fast and flexible access to biological data. Genome Res 2004, 14:160-169. 314293 14707178
51. O'Brien KP Remm M Sonnhammer EL Inparanoid: A comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005, 33:D476-D480. 540061 15608241
52. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V Church DM DiCuccio M Edgar R Federhen S Geer LY Kapustin Y Khovayko O Landsman D Lipman DJ Madden TL Maglott DR Ostell J Miller V Pruitt KD Schuler GD Sequeira E Sherry ST Sirotkin K Souvorov A Starchenko G Tatusov RL Tatusova TA Wagner L Yaschenko E Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007, 35:D5-12. 1781113 17170002
53. Hamosh A Scott AF Amberger JS Bocchini CA McKusick VA Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005, 33:D514-D517. 539987 15608251
54. Disease Associations from OMIM http://ftp.ncbi.nih.gov/repository/OMIM/
55. Lee H Tu Z Deng M Sun F Chen T Diffusion kernel-based logistic regression models for protein function prediction. OMICS 2006, 10:40-55. 16584317
56. Barutcuoglu Z Schapire RE Troyanskaya OG Hierarchical multi-label prediction of gene function. Bioinformatics 2006, 22:830-836. 16410319
57. Leone M Pagnani A Predicting protein functions with message passing algorithms. Bioinformatics 2005, 21:239-247. 15377508