Interspecies data mining to predict novel ING-protein interactions in human

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Gordon, Paul M K ^a   Soliman, Mohamed A ^a,b   Bose, Pinaki ^a   Trinh, Quang ^a   Sensen, Christoph W ^a   Riabowol, Karl ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b CAIRO UNIVERSITY   (Egypt)

Author keywords

[No Author keywords available]

Indexed keywords

ING PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE KINASE KINASE 4; MITOGEN ACTIVATED PROTEIN KINASE P38; RAD50 PROTEIN; TUMOR SUPPRESSOR PROTEIN; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; DROSOPHILA PROTEIN; ING1 PROTEIN, HUMAN; NUCLEAR PROTEIN; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; RAD50 PROTEIN, HUMAN; SACCHAROMYCES CEREVISIAE PROTEIN; SIGNAL PEPTIDE;

ACCURACY; ARTICLE; BIOINFORMATICS; CELL STRESS; COMPUTER PREDICTION; CONTROLLED STUDY; DATA MINING; DNA DAMAGE; FLY; HUMAN; HUMAN CELL; NONHUMAN; PROBABILITY; PROTEIN PROTEIN INTERACTION; SIGNAL NOISE RATIO; SPECIES COMPARISON; VALIDITY; YEAST; AMINO ACID SEQUENCE; ANIMAL; BIOLOGY; CELL LINE; CHEMISTRY; DROSOPHILA MELANOGASTER; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN TERTIARY STRUCTURE; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; VALIDATION STUDY;

AMINO ACID SEQUENCE; ANIMALS; CELL LINE; COMPUTATIONAL BIOLOGY; DNA REPAIR ENZYMES; DNA-BINDING PROTEINS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MAP KINASE KINASE KINASE 4; NUCLEAR PROTEINS; P38 MITOGEN-ACTIVATED PROTEIN KINASES; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT; TUMOR SUPPRESSOR PROTEINS;

EID: 53749097778     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-426     Document Type: Article

References (79)

1. Goffeau A Barrell BG Bussey H Davis RW Dujon B Feldmann H Life with 6000 genes Science 1996, 274(546):5635-46, 567 10.1126/science.274.5287.546 8849441
2. Bader GD Heilbut A Andrews B Tyers M Hughes T Boone C Functional genomics and proteomics: Charting a multidimensional map of the yeast cell Trends Cell Biol 2003, 13:344-356. 10.1016/S0962-8924(03)00127-2 12837605
3. Jorgensen P Breitkreutz BJ Breitkreutz K Stark C Liu G Cook M Harvesting the genome's bounty: Integrative genomics Cold Spring Harb Symp Quant Biol 2003, 68:431-443. 10.1101/sqb.2003.68.431 15338646
4. Garkavtsev I Kazarov A Gudkov A Riabowol K Suppression of the novel growth inhibitor p33ING1 promotes neoplastic transformation Nat Genet 1996, 14:415-420. 10.1038/ng1296-415 8944021
5. He GH Helbing CC Wagner MJ Sensen CW Riabowol K Phylogenetic analysis of the ING family of PHD finger proteins Mol Biol Evol 2005, 22:104-116. 10.1093/molbev/msh256 15356280
6. Gong W Suzuki K Russell M Riabowol K Function of the ING family of PHD proteins in cancer Int J Biochem Cell Biol 2005, 37:1054-1065. 10.1016/ j.biocel.2004.09.008 15743678
7. Nouman GS Anderson JJ Lunec J Angus B The role of the tumour suppressor p33 ING1b in human neoplasia J Clin Pathol 2003, 56:491-496. 1769994 12835293 10.1136/jcp.56.7.491
8. Russell M Berardi P Gong W Riabowol K Grow-ING, Age-ING and Die-ING: ING proteins link cancer, senescence and apoptosis Exp Cell Res 2006, 312:951-961. 10.1016/j.yexcr.2006.01.020 16516887
9. Loewith R Meijer M Lees-Miller SP Riabowol K Young D Three yeast proteins related to the human candidate tumor suppressor p33(ING1) are associated with histone acetyltransferase activities Mol Cell Biol 2000, 20:3807-3816. 85704 10805724 10.1128/MCB.20.11.3807-3816.2000
10. Vieyra D Toyama T Hara Y Boland D Johnston R Riabowol K et al ING1 isoforms differentially affect apoptosis in a cell age-dependent manner Cancer Res 2002, 62:4445-4452. 12154053
11. Doyon Y Cayrou C Ullah M Landry AJ Cote V Selleck W ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation Mol Cell 2006, 21:51-64. 10.1016/ j.molcel.2005.12.007 16387653
12. Shi X Hong T Walter KL Ewalt M Michishita E Hung T et al ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression Nature 2006, 442:96-99. 10.1038/nature05140 16728974
13. Pena PV Davrazou F Shi X Walter KL Verkhusha VV Gozani O et al Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2 Nature 2006, 442:100-103. 16728977
14. Martin DG Baetz K Shi X Walter KL MacDonald VE Wlodarski MJ et al The Yng1p plant homeodomain finger is a methyl-histone binding module that recognizes lysine 4-methylated histone H3 Mol Cell Biol 2006, 26:7871-7879. 1636756 16923967 10.1128/MCB.00573-06
15. Kaadige MR Ayer DE The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding J Biol Chem 2006, 281:28831-28836. 10.1074/jbc.M605624200 16893883
16. Scott M Bonnefin P Vieyra D Boisvert FM Young D Bazett-Jones DP et al UV-induced binding of ING1 to PCNA regulates the induction of apoptosis J Cell Sci 2001, 114:3455-3462. 11682605
17. Gong W Russell M Suzuki K Riabowol K Subcellular targeting of p33ING1b by phosphorylation-dependent 14-3-3 binding regulates p21WAF1 expression Mol Cell Biol 2006, 26:2947-2954. 1446971 16581770 10.1128/ MCB.26.8.2947-2954.2006
18. Shen JC Unoki M Ythier D Duperray A Varticovski L Kumamoto K et al Inhibitor of growth 4 suppresses cell spreading and cell migration by interacting with a novel binding partner, liprin alpha1 Cancer Res 2007, 67:2552-2558. 10.1158/0008-5472.CAN-06-3870 17363573
19. Krogan NJ Cagney G Yu H Zhong G Guo X et al Ignatchenko A Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 2006, 440:637-643. 10.1038/nature04670 16554755
20. Needleman SB Wunsch CD general method applicable to the search for similarities in the amino acid sequence of two proteins J Mol Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4 5420325
21. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22:46730-4680. 308517 7984417 10.1093/nar/22.22.4673
22. Notredame C Higgins DG Heringa J A novel method for fast and accurate multiple sequence alignment J Mol Biol 2000, 302:205-217. 10.1006/ jmbi.2000.4042 10964570
23. Gandhi TK Zhong J Mathivanan S Karthick L Chandrika KN Mohan SS et al Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets Nat Genet 2006, 38:285-293. 10.1038/ ng1747 16501559
24. Kelley BP Yuan B Lewitter F Sharan R Stockwell BR Ideker T PathBLAST: A tool for alignment of protein interaction networks Nucleic Acids Res 2004, 32:W83-W88. 441549 15215356 10.1093/nar/gkh411
25. Mika S Rost B et al Protein-protein interactions more conserved within species than across species PLoS Comput Biol 2006, 2:e79. 1513270 16854211 10.1371/journal.pcbi.0020079
26. Sharan R Suthram S Kelley RM Kuhn T McCuine S Uetz P Conserved patterns of protein interaction in multiple species Proc Natl Acad Sci USA 2005, 102:1974-1979. 548573 15687504 10.1073/pnas.0409522102
27. Itzhaki Z Akiva E Altuvia Y Margalit H Evolutionary conservation of domain-domain interactions Genome Biol 2006, 7:R125. 1794438 17184549 10.1186/gb-2006-7-12-r125
28. Gaasterland T Sensen CW Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture Biochimie 1996, 78:302-310. 10.1016/0300-9084(96)84761-4 8905148
29. Gaasterland T Sensen CW MAGPIE: Automated genome interpretation Trends Genet 1996, 12:76-78. 10.1016/0168-9525(96)81406-5 8851977
30. Crosby MA Goodman JL Strelets VB Zhang P Gelbart WM FlyBase: Genomes by the dozen Nucleic Acids Res 2007, 35:D486-D491. 1669768 17099233 10.1093/ nar/gkl827
31. Giot L Bader JS Brouwer C Chaudhuri A Kuang B Li Y et al A protein interaction map of Drosophila melanogaster Science 2003, 302:1727-1736. 10.1126/science.1090289 14605208
32. von Mering C Jensen LJ Kuhn M Chaffron S Doerks T Kruger B STRING 7 - recent developments in the integration and prediction of protein interactions Nucleic Acids Res 2007, 35:D358-D362. 1669762 17098935 10.1093/nar/gkl825
33. Bettinger BT Amberg DC The MEK kinases MEKK4/Ssk2p facilitate complexity in the stress signaling responses of diverse systems J Cell Biochem 2007, 101:34-43. 10.1002/jcb.21289 17348032
34. Hart GT Ramani AK Marcotte EM How complete are current yeast and human protein-interaction networks? Genome Biol 2006, 7:120. 1794583 17147767 10.1186/gb-2006-7-11-120
35. Shoemaker BA Panchenko AR Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners PLoS Comput Biol 2007, 3:e43. 1857810 17465672 10.1371/ journal.pcbi.0030043
36. Jansen R Yu H Greenbaum D Kluger Y Krogan NJ Chung S et al A Bayesian networks approach for predicting protein-protein interactions from genomic data Science 2003, 302:449-453. 10.1126/science.1087361 14564010
37. Ramani AK Marcotte EM Exploiting the co-evolution of interacting proteins to discover interaction specificity J Mol Biol 2003, 327:273-284. 10.1016/S0022-2836(03)00114-1 12614624
38. Pazos F Valencia A In silico two-hybrid system for the selection of physically interacting protein pairs Proteins 2002, 47:219-227. 10.1002/ prot.10074 11933068
39. Marcotte CJ Marcotte EM Predicting functional linkages from gene fusions with confidence Appl Bioinformatics 2002, 1:93-100. 15130848
40. Espadaler J Romero-Isart O Jackson RM Oliva B Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships Bioinformatics 2005, 21:3360-3368. 10.1093/bioinformatics/bti522 15961445
41. Brown KR Jurisica I Online predicted human interaction database Bioinformatics 2005, 21:2076-2082. 10.1093/bioinformatics/bti273 15657099
42. Kemmer D Huang Y Shah SP Lim J Brumm J Yuen MM et al Ulysses - an application for the projection of molecular interactions across species Genome Biol 2005, 6:R106. 1414088 16356269 10.1186/gb-2005-6-12-r106
43. Huang TW Tien AC Huang WS Lee YC Peng CL Tseng HH et al POINT: A database for the prediction of protein-protein interactions based on the orthologous interactome Bioinformatics 2004, 20:3273-3276. 10.1093/ bioinformatics/bth366 15217821
44. Mathivanan S Periaswamy B Gandhi TK Kandasamy K Suresh S Mohmood R et al An evaluation of human protein-protein interaction data in the public domain BMC Bioinformatics 2006, 7(Suppl 5):S19. 1764475 17254303 10.1186/ 1471-2105-7-S5-S19
45. O'Brien KP Remm M Sonnhammer EL Inparanoid: A comprehensive database of eukaryotic orthologs Nucleic Acids Res 2005, 33:D476-D480. 540061 15608241 10.1093/nar/gki107
46. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V et al Database resources of the National Center for Biotechnology Information 2007, 35:D5-12.
47. Soliman MA Riabowol K After a decade of study-ING, a PHD for a versatile family of proteins Trends Biochem Sci 2007, 32:509-519. 10.1016/ j.tibs.2007.08.006 17949986
48. Shi X Gozani O The fellowships of the INGs J Cell Biochem 2005, 96:1127-1136. 10.1002/jcb.20625 16167330
49. Cheung KJ Jr Mitchell D Lin P Li G The tumor suppressor candidate p33(ING1) mediates repair of UV-damaged DNA Cancer Res 2001, 61:4974-4977. 11431327
50. Simpson F Lammerts van BK Butterfield N Bennetts JS Bowles J Adolphe C The PCNA-associated factor KIAA0101/p15(PAF) binds the potential tumor suppressor product p33ING1b Exp Cell Res 2006, 312:73-85. 10.1016/ j.yexcr.2005.09.020 16288740
51. Nagashima M Shiseki M Miura K Hagiwara K Linke SP Pedeux R DNA damage-inducible gene p33ING2 negatively regulates cell proliferation through acetylation of p53 Proc Natl Acad Sci USA 2001, 98:9671-9676. 55510 11481424 10.1073/pnas.161151798
52. Gozani O Karuman P Jones DR Ivanov D Cha J Lugovskoy AA The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor Cell 2003, 114:99-111. 10.1016/ S0092-8674(03)00480-X 12859901
53. Tallen G Riabowol K Wolff JE Expression of p33ING1 mRNA and chemosensitivity in brain tumor cells Anticancer Res 2003, 23:1631-1635. 12820433
54. Ozer A Wu LC Bruick RK The candidate tumor suppressor ING4 represses activation of the hypoxia inducible factor (HIF) Proc Natl Acad Sci USA 2005, 102:7481-7486. 1140452 15897452 10.1073/pnas.0502716102
55. Jones DR Bultsma Y Keune WJ Halstead JR Elouarrat D Mohammed S et al Nuclear PtdIns5P as a transducer of stress signaling: An in vivo role for PIP4Kbeta Mol Cell 2006, 23:685-695. 10.1016/j.molcel.2006.07.014 16949365
56. Kyriakis JM Avruch J Mammalian mitogen-activated protein kinase signal transduction pathways activated by stress and inflammation Physiol Rev 2001, 81:807-869. 11274345
57. Miyake Z Takekawa M Ge Q Saito H Activation of MTK1/MEKK4 by GADD45 through induced N-C dissociation and dimerization-mediated trans autophosphorylation of the MTK1 kinase domain Mol Cell Biol 2007, 27:2765-2776. 1899887 17242196 10.1128/MCB.01435-06
58. Kataoka H Bonnefin P Vieyra D Feng X Hara Y Miura Y et al ING1 represses transcription by direct DNA binding and through effects on p53 Cancer Res 2003, 63:5785-5792. 14522900
59. Garkavtsev I Kozin SV Chernova O Xu L Winkler F Brown E et al The candidate tumour suppressor protein ING4 regulates brain tumour growth and angiogenesis Nature 2004, 428:328-332. 10.1038/nature02329 15029197
60. Smith TF Waterman MS Identification of common molecular subsequences J Mol Biol 1981, 147:195-197. 10.1016/0022-2836(81)90087-5 7265238
61. Nash R Weng S Hitz B Balakrishnan R Christie KR Costanzo MC et al Expanded protein information at SGD: New pages and proteome browser Nucleic Acids Res 2007, 35:D468-D471. 1669759 17142221 10.1093/nar/gkl931
62. The Universal Protein Resource (UniProt) Nucleic Acids Res 2007, 35:D193-D197. 1669721 17142230 10.1093/nar/gkl929
63. Schwarz EM Antoshechkin I Bastiani C Bieri T Blasiar D Canaran P et al WormBase: Better software, richer content Nucleic Acids Res 2006, 34:D475-D478. 1347424 16381915 10.1093/nar/gkj061
64. von Mering C Jensen LJ Kuhn M Chaffron S Doerks T Kruger B STRING 7 - recent developments in the integration and prediction of protein interactions Nucleic Acids Res 2007, 35:D358-D362. 1669762 17098935 10.1093/nar/gkl825
65. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25:3389-3402. 146917 9254694 10.1093/nar/ 25.17.3389
66. Quevillon E Silventoinen V Pillai S Harte N Mulder N Apweiler R et al InterProScan: Protein domains identifier Nucleic Acids Res 2005, 33:W116-W120. 1160203 15980438 10.1093/nar/gki442
67. Crooks GE Hon G Chandonia JM Brenner SE WebLogo: A sequence logo generator Genome Res 2004, 14:1188-1190. 419797 15173120 10.1101/ gr.849004
68. Ho Y Gruhler A Heilbut A Bader GD Moore L Adams SL et al Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002, 415:180-183. 10.1038/415180a 11805837
69. Gavin AC Bosche M Krause R Grandi P Marzioch M Bauer A et al Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415:141-147. 10.1038/415141a 11805826
70. Ito T Chiba T Ozawa R Yoshida M Hattori M Sakaki Y et al A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc Natl Acad Sci USA 2001, 98:4569-4574. 31875 11283351 10.1073/pnas.061034498
71. Uetz P Giot L Cagney G Mansfield TA Judson RS Knight JR A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000, 403:623-627. 10.1038/35001009 10688190
72. Gavin AC Aloy P Grandi P Krause R Boesche M Marzioch M et al Proteome survey reveals modularity of the yeast cell machinery Nature 2006, 440:631-636. 10.1038/nature04532 16429126
73. Rual JF Venkatesan K Hao T Hirozane-Kishikawa T Dricot A Li N et al Towards a proteome-scale map of the human protein-protein interaction network Nature 2005, 437:1173-1178. 10.1038/nature04209 16189514
74. Stelzl U Worm U Lalowski M Haenig C Brembeck FH Goehler H et al A human protein-protein interaction network: A resource for annotating the proteome Cell 2005, 122:957-968. 10.1016/j.cell.2005.08.029 16169070
75. Rhodes DR Tomlins SA Varambally S Mahavisno V Barrette T Kalyana-Sundaram S et al Probabilistic model of the human protein-protein interaction network Nat Biotechnol 2005, 23:951-959. 10.1038/nbt1103 16082366
76. Lehner B Fraser AG A first-draft human protein-interaction map Genome Biol 2004, 5:R63. 522870 15345047 10.1186/gb-2004-5-9-r63
77. Lee I Li Z Marcotte EM An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae PLoS ONE 2007, 2:e988. 1991590 17912365 10.1371/journal.pone.0000988
78. Brown KR Jurisica I Unequal evolutionary conservation of human protein interactions in interologous networks Genome Biol 2007, 8:R95. 1929159 17535438 10.1186/gb-2007-8-5-r95
79. Liu Y Liu N Zhao H Inferring protein-protein interactions through high-throughput interaction data from diverse organisms Bioinformatics 2005, 21:3279-3285. 10.1093/bioinformatics/bti492 15905281