Clustering proteins from interaction networks for the prediction of cellular functions

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Brun, Christine ^a   Herrmann, Carl ^a   Guénoche, Alain ^b  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b AIX MARSEILLE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BINARY INTERACTIONS; EFFICIENT STRATEGY; FUNCTIONAL PREDICTIONS; GENETIC INTERACTION; HIGH-THROUGHPUT DATA; INTERACTION GRAPHS; INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTION NETWORKS;

ACTIVE NETWORKS; CLUSTERING ALGORITHMS; YEAST;

PROTEINS;

FUNGAL PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

ANALYTIC METHOD; ARTICLE; CELL FUNCTION; CLUSTER ANALYSIS; CONTROLLED STUDY; GENE INTERACTION; GENETIC ALGORITHM; MICROORGANISM; NONHUMAN; PARTITION COEFFICIENT; PREDICTION; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; YEAST; BIOLOGY; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER GRAPHICS; CYTOLOGY; PHYSIOLOGY; PREDICTIVE VALUE; SACCHAROMYCES CEREVISIAE; STATISTICS AND NUMERICAL DATA; VALIDATION STUDY;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; PREDICTIVE VALUE OF TESTS; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 13244292287     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/147-2105-5-95     Document Type: Article

References (13)

1. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623-7. [Eng Journal Article].
2. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 2001, 98(8 :4569-74. [Eng Journal Article].
3. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley JRL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM: A protein interaction map of Drosophila melanogaster. Science 2003, 302(5651 :1727-36. [Journal Article].
4. Schwikowski B, Uetz P, Fields S: A network of protein-protein interactions in yeast. Nat Biotechnol 2000, 18(12): 1257-61. [Eng Journal Article].
5. Brun C, Wojcik J, Guénoche A, Jacq B: Bioinformatic study of interaction networks: PRODISTIN, a new method for a functionnal classification of proteins. In Journées Ouvertes Biologie Informatique Mathématiques (JOBIM'2002) Edited by: Nicolas J, Thermes C. Saint Malo, France; 2002:171-182.
6. Brun C, Chevenet F, Martin D, Wojcik J, Guécnoche A, Jacq B: Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol 2003, 5:R6.
7. Samanta MP, Liang S: Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci U S A 2003, 100(22):12579-83. [0027-8424 Journal Article].
8. Vazquez A, Flammini A, Maritan A, Vespignani A: Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 2003, 21(6):697-700. [Evaluation Studies Journal Article].
9. Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. [1471-2105 Evaluation Studies Journal Article].
10. Rougemont J, Hingamp P: DNA microarray data and contextual analysis of correlation graphs. BMC Bioinformatics 2003, 4: 5. [1471-2105 Journal Article Validation Studies].
11. Rives AW, Galitski T: Modular organization of cellular networks. Proc Natl Acad Sci U S A 2003, 4: 1128-1133.
12. Timblin BK, Tatchell K, Bergman LW: Deletion of the gene encoding the cyclin-dependent protein kinase Pho85 alters glycogen metabolism in Saccharomyces cerevisiae. Genetics 1996, 143: 7-66. [0016-6731 Journal Article].
13. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C: Global mapping of the yeast genetic interaction network. Science 2004, 303(5659):808-13. [1095-9203 Journal Article].