Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection

BMC Systems Biology

Volumn 5, Issue SUPPL2, 2011, Pages

  Yoon, Dukyong ^a   Kim, Hyosil ^a   Suh Kim, Haeyoung ^a   Park, Rae Woong ^a   Lee, KiYoung ^a,b  

^a Ajou University School of Medicine   (South Korea)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; DOWN REGULATION; GENE EXPRESSION PROFILING; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; METHODOLOGY; MICROARRAY ANALYSIS; PATHOGENICITY; RNA SPLICING; UPREGULATION;

ALGORITHMS; CLUSTER ANALYSIS; DOWN-REGULATION; GENE EXPRESSION PROFILING; HIV INFECTIONS; HIV-1; HUMANS; MICROARRAY ANALYSIS; RNA SPLICING; UP-REGULATION;

EID: 84870321974     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-S2-S1     Document Type: Article

References (35)

1. Pantaleo G, Graziosi C, Fauci AS. New concepts in the immunopathogenesis of human immunodeficiency virus infection. N Engl J Med 1993, 328(5):327-335. 10.1056/NEJM199302043280508, 8093551.
2. Chu C, Selwyn PA. Diagnosis and initial management of acute HIV infection. Am Fam Physician 2010, 81(10):1239-1244.
3. Grossman Z, Meier-Schellersheim M, Paul WE, Picker LJ. Pathogenesis of HIV infection: what the virus spares is as important as what it destroys. Nat Med 2006, 12(3):289-295. 10.1038/nm1380, 16520776.
4. Mothe B, Ibarrondo J, Llano A, Brander C. Virological, immune and host genetics markers in the control of HIV infection. Dis Markers 2009, 27(3):105-120.
5. Hyrcza MD, Kovacs C, Loutfy M, Halpenny R, Heisler L, Yang S, Wilkins O, Ostrowski M, Der SD. Distinct transcriptional profiles in ex vivo CD4+ and CD8+ T cells are established early in human immunodeficiency virus type 1 infection and are characterized by a chronic interferon response as well as extensive transcriptional changes in CD8+ T cells. J Virol 2007, 81(7):3477-3486. 10.1128/JVI.01552-06, 1866039, 17251300.
6. Li Q, Smith AJ, Schacker TW, Carlis JV, Duan L, Reilly CS, Haase AT. Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection. J Immunol 2009, 183(3):1975-1982. 10.4049/jimmunol.0803222, 19596987.
7. Lin CC, Hsiang JT, Wu CY, Oyang YJ, Juan HF, Huang HC. Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy. BMC Syst Biol 2010, 4:138. 10.1186/1752-0509-4-138, 2978157, 20950417.
8. Ma S, Shi M, Li Y, Yi D, Shia BC. Incorporating gene co-expression network in identification of cancer prognosis markers. BMC Bioinformatics 2010, 11:271. 10.1186/1471-2105-11-271, 2881088, 20487548.
9. Charbonnier S, Gallego O, Gavin AC. The social network of a cell: recent advances in interactome mapping. Biotechnol Annu Rev 2008, 14:1-28.
10. Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res 2008, 36(20):e136. 10.1093/nar/gkn619, 2582614, 18836191.
11. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, 32(Database issue):D449-451. 308820, 14681454.
12. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res 2001, 29(1):242-245. 10.1093/nar/29.1.242, 29820, 11125103.
13. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al. Human Protein Reference Database--2009 update. Nucleic Acids Res 2009, 37(Database issue):D767-772. 2686490, 18988627.
14. Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33(Database issue):D428-432. 540026, 15608231.
15. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437(7062):1173-1178. 10.1038/nature04209, 16189514.
16. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122(6):957-968. 10.1016/j.cell.2005.08.029, 16169070.
17. Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, et al. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 2007, 3:89. 1847948, 17353931.
18. Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol 2005, 6(5):R40. 10.1186/gb-2005-6-5-r40, 1175952, 15892868.
19. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J. TM4 microarray software suite. Methods Enzymol 2006, 411:134-193.
20. Hall M, F E, Holmes G, Pfahringer B, Reutemann P, Witten IH. The WEKA Data Mining Software: An Update. SIGKDD Explorations 2009, 11(1):10-18.
21. Xu H, Lemischka IR, Ma'ayan A. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol 2010, 4(1):173. 10.1186/1752-0509-4-173, 3019180, 21176149.
22. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2(10):2366-2382. 10.1038/nprot.2007.324, 17947979.
23. Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 10.1186/1471-2105-4-2, 149346, 12525261.
24. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
25. Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21(16):3448-3449. 10.1093/bioinformatics/bti551, 15972284.
26. Alimonti JB, Ball TB, Fowke KR. Mechanisms of CD4+ T lymphocyte cell death in human immunodeficiency virus infection and AIDS. J Gen Virol 2003, 84(Pt 7):1649-1661.
27. Bolinger C, Boris-Lawrie K. Mechanisms employed by retroviruses to exploit host factors for translational control of a complicated proteome. Retrovirology 2009, 6:8. 10.1186/1742-4690-6-8, 2657110, 19166625.
28. Hashizume C, Kuramitsu M, Zhang X, Kurosawa T, Kamata M, Aida Y. Human immunodeficiency virus type 1 Vpr interacts with spliceosomal protein SAP145 to mediate cellular pre-mRNA splicing inhibition. Microbes Infect 2007, 9(4):490-497. 10.1016/j.micinf.2007.01.013, 17347016.
29. Ropers D, Ayadi L, Gattoni R, Jacquenet S, Damier L, Branlant C, Stevenin J. Differential effects of the SR proteins 9G8, SC35, ASF/SF2, and SRp40 on the utilization of the A1 to A5 splicing sites of HIV-1 RNA. J Biol Chem 2004, 279(29):29963-29973. 10.1074/jbc.M404452200, 15123677.
30. Sobhian B, Laguette N, Yatim A, Nakamura M, Levy Y, Kiernan R, Benkirane M. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP. Mol Cell 2010, 38(3):439-451. 10.1016/j.molcel.2010.04.012, 20471949.
31. Bolinger C, Sharma A, Singh D, Yu L, Boris-Lawrie K. RNA helicase A modulates translation of HIV-1 and infectivity of progeny virions. Nucleic Acids Res 2010, 38(5):1686-1696. 10.1093/nar/gkp1075, 2836548, 20007598.
32. Klatt A, Zhang Z, Kalantari P, Hankey PA, Gilmour DS, Henderson AJ. The receptor tyrosine kinase RON represses HIV-1 transcription by targeting RNA polymerase II processivity. J Immunol 2008, 180(3):1670-1677.
33. Hadian K, Vincendeau M, Mausbacher N, Nagel D, Hauck SM, Ueffing M, Loyter A, Werner T, Wolff H, Brack-Werner R. Identification of a heterogeneous nuclear ribonucleoprotein-recognition region in the HIV Rev protein. J Biol Chem 2009, 284(48):33384-33391. 10.1074/jbc.M109.021659, 2785182, 19808671.
34. Hofmann W, Reichart B, Ewald A, Muller E, Schmitt I, Stauber RH, Lottspeich F, Jockusch BM, Scheer U, Hauber J, et al. Cofactor requirements for nuclear export of Rev response element (RRE)- and constitutive transport element (CTE)-containing retroviral RNAs. An unexpected role for actin. J Cell Biol 2001, 152(5):895-910. 10.1083/jcb.152.5.895, 2198816, 11238447.
35. Lee K, Ambrose Z, Martin TD, Oztop I, Mulky A, Julias JG, Vandegraaff N, Baumann JG, Wang R, Yuen W, et al. Flexible use of nuclear import pathways by HIV-1. Cell Host Microbe 2010, 7(3):221-233. 10.1016/j.chom.2010.02.007, 2841689, 20227665.