Edgetic perturbation models of human inherited disorders

Molecular Systems Biology

Volumn 5, Issue , 2009, Pages

  Zhong, Quan ^a,b   Simonis, Nicolas ^a,b   Li, Qian Ru ^a,b   Charloteaux, Benoit ^a,b,c   Heuze, Fabien ^a,b,c   Klitgord, Niels ^a,b   Tam, Stanley ^a,b   Yu, Haiyuan ^a,b   Venkatesan, Kavitha ^a,b   Mou, Danny ^a,b   Swearingen, Venus ^a,b   Yildirim, Muhammed A ^a,b   Yan, Han ^a,b   Dricot, Amélie ^a,b   Szeto, David ^a,b   Lin, Chenwei ^a,b   Hao, Tong ^a,b   Fan, Changyu ^a,b   Milstein, Stuart ^a,b   Dupuy, Denis ^a,b   Brasseur, Robert ^c   Hill, David E ^a,b   Cusick, Michael E ^a,b   Vidal, Marc ^a,b   more..

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Binary protein interaction; Genotype to phenotype relationships; Human Mendelian disorders; Network perturbation

Indexed keywords

DNA; GENE PRODUCT; PROTEIN; RNA; TRANSCRIPTION FACTOR;

ALLELE; ARTICLE; BIOCHEMISTRY; CELL FUNCTION; CORRELATION ANALYSIS; GENE MUTATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC DISORDER; GENOTYPE; HUMAN; MACROMOLECULE; MATHEMATICAL ANALYSIS; METABOLITE; OPEN READING FRAME; PATHOGENESIS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; BIOLOGICAL MODEL; GENERAL ASPECTS OF DISEASE; GENETICS; MUTATION;

ALLELES; DISEASE; GENETIC DISEASES, INBORN; HUMANS; MODELS, GENETIC; MUTATION;

EID: 72849142731     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2009.80     Document Type: Article

References (37)

1. Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM (2000) Integrating functional genomic information into the Saccharomyces genome database. Nucleic Acids Res 28: 77-80
2. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33 : 228-237
3. Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, Sahalie JM, Murray RR, Roncari L, de Smet AS, Venkatesan K, Rual JF, Vandenhaute J, Cusick ME, Pawson T, Hill DE, Tavernier J, Wrana JL, Roth FP, Vidal M (2009) An experimentally derived confidence score for binary protein-protein interactions. Nat Methods 6: 91-97
4. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500
5. Chik JK, Lindberg U, Schutt CE (1996) The structure of an open state of b-actin at 2.65A° resolution. J Mol Biol 263: 607-623
6. Day PJ, Cleasby A, Tickle IJ, O'Reilly M, Coyle JE, Holding FP, McMenamin RL, Yon J, Chopra R, Lengauer C, Jhoti H (2009) Crystal structure of human CDK4 in complex with a D-type cyclin. Proc Natl Acad Sci USA 106: 4166-4170
7. DrezeM, Charloteaux B,Milstein S, Vidalain PO, YildirimMA, Zhong Q, Svrzikapa N, Romero V, Laloux G, Brasseur R, Vandenhaute J, Boxem M, Cusick ME, Hill DE, Vidal M (in press) 'Edgetic' perturbation of a C. elegans BCL2 ortholog. Nat Methods
8. 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 (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34: D247-D251
9. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL (2007) The human disease network. Proc Natl Acad Sci USA 104: 8685-8690
10. Gunsalus KC, Yueh WC, MacMenamin P, Piano F (2004) RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res 32: D406-D410
11. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33: D514-D517
12. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M et al (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-D261
13. Hsu WT, Pang CN, Sheetal J, Wilkins MR (2007) Protein-protein interactions and disease: use of S. cerevisiae as a model system.. Biochim Biophys Acta 1774: 838-847
14. Jeffrey PD, Tong L, Pavletich NP (2000) Structural basis of inhibition of CDK-cyclin complexes by INK4 inhibitors. Genes Dev 14: 3115-3125
15. Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M (2007) hORFeome v3.1: a resource of human open reading frames representing over 10 0human genes. Genomics 89: 307-315
16. Lassing I, Schmitzberger F, Bjornstedt M, Holmgren A, Nordlund P, Schutt CE, Lindberg U (2007) Molecular and structural basis for redox regulation of b-actin. J Mol Biol 370: 331-348
17. Maglott D, Ostell J, Pruitt KD, Tatusova T (2005) Entrez Gene: genecentered information at NCBI. Nucleic Acids Res 33: D54-D58
18. Meier M, Janosik M, Kery V, Kraus JP, Burkhard P (2001) Structure of human cystathionine b-synthase: a unique pyridoxal 50-phosphatedependent heme protein. EMBO J 20: 3910-3916
19. Mihel J, Sikic M, Tomic S, Jeren B, Vlahovicek K (2008) PSAIA- protein structure and interaction analyzer. BMC Struct Biol 8: 21
20. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV,Wong SL, Franklin G, Li S et al (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178
21. Sammut SJ, Finn RD, Bateman A (2008) Pfam 10 years on: 10 0families and still growing. Brief Bioinform 9: 210-219
22. Schuster-Böckler B, Bateman A (2008) Protein interactions in human genetic diseases. Genome Biol 9: R9
23. Schutt CE, Myslik JC, Rozycki MD, Goonesekere NC, Lindberg U (1993) The structure of crystalline profilin-b-actin. Nature 365: 810-816
24. Seidman JG, Seidman C (2002) Transcription factor haploinsufficiency: when half a loaf is not enough. J Clin Invest 109: 451-455
25. Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN (2003) Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat 21: 577-581
26. Subramanian S, Kumar S (2006) Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics 7: 306
27. Suzuki Y, Kagawa N, Fujino T, Sumiya T, Andoh T, Ishikawa K, Kimura R, Kemmochi K, Ohta T, Tanaka S (2005) A novel highthroughput (HTP) cloning strategy for site-directed designed chimeragenesis and mutation using the Gateway cloning system. Nucleic Acids Res 33: e109
28. Titus GP, Mueller HA, Burgner J, Rodriguez De Cordoba S, Penalva MA, Timm DE (2000) Crystal structure of human homogentisate dioxygenase. Nat Struct Biol 7: 542-546
29. van Bokhoven H, Brunner HG (2002) Splitting p63. Am J Hum Genet 71: 1-13
30. Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A et al (2009) An empirical framework for binary interactome mapping. Nat Methods 6: 83-90
31. Wang G, Dunbrack Jr RL (2005) PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res 33: W94-W98
32. Wang Z, Moult J (2001) SNPs, protein structure, and disease. Hum Mutat 17: 263-270
33. Wilkie AO (1994) The molecular basis of genetic dominance. J Med Genet 31: 89-98
34. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA (2008a) DBD-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res 36: D88-D92
35. Wilson RJ, Goodman JL, Strelets VB (2008b) FlyBase: integration and improvements to query tools. Nucleic Acids Res 36: D588-D593
36. Ye Y, Li Z, Godzik A (2006) Modeling and analyzing three-dimensional structures of human disease proteins. Pac Symp Biocomput 2006: 439-450
37. Yue P, Li Z, Moult J (2005) Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol 353: 459-473