Bicluster and Pathway Enrichment Analysis of HCV-induced Cirrhosis and Hepatocellular Carcinoma |
Cheng, Peng
(Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University)
Cheng, You (Department of Otolaryngology-Head and Neck Surgery, PLA General Hospital of Nanjing Commond, Clinical Medical College of Nanjing University) Su, Mei X. (Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University) Li, Dong (Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University) Zhao, Guo Z. (Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University) Gao, Hui (Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University) Li, Yan (Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University) Zhu, Jie Y. (Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University) Li, Hua (Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University) Zhang, Tao (Department of Oncology, PLA general hospital of Chengdu Commond, Clinical Medical College of The Third Medical Military University) |
1 | Abedi-Ardekani B, Gouas D, Villar S, et al (2011). TP53 Mutations and HBX Status Analysis in Hepatocellular Carcinomas from Iran: Evidence for Lack of Association between HBV Genotype D and TP53 R249S Mutations. Hepat Res Treat, 2011, 475965. |
2 | Amitrano L, Guardascione MA, Brancaccio V, Balzano A (2002). Coagulation disorders in liver disease. Semin Liver Dis, 22, 83-96. DOI |
3 | Avila MA, Berasain C, Sangro B, Prieto J (2006). New therapies for hepatocellular carcinoma. Oncogene, 25, 3866-84. DOI |
4 | Barazani Y, Hiatt JR, Tong MJ, Busuttil RW (2007). Chronic viral hepatitis and hepatocellular carcinoma. World J Surg, 31, 1243-8. |
5 | Bashirova AA, Geijtenbeek TB, van Duijnhoven GC, et al (2001). A dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN)-related protein is highly expressed on human liver sinusoidal endothelial cells and promotes HIV-1 infection. J Exp Med, 193, 671-8. DOI |
6 | Befeler AS, Di Bisceglie AM (2002). Hepatocellular carcinoma: diagnosis and treatment. Gastroenterology, 122, 1609-19. DOI |
7 | Benjamini YH, Y (1995). Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J Royal Stat Society Series B (Methodological), 57, 289-300. |
8 | Bieche I, Asselah T, Laurendeau I, et al (2005). Molecular profiling of early stage liver fibrosis in patients with chronic hepatitis C virus infection. Virology, 332, 130-44. DOI |
9 | Block TM, Mehta AS, Fimmel CJ, Jordan R (2003). Molecular viral oncology of hepatocellular carcinoma. Oncogene, 22, 5093-107. DOI ScienceOn |
10 | Bruix J, Sherman M, Llovet JM, et al (2001). Clinical management of hepatocellular carcinoma. Conclusions of the Barcelona-2000 EASL conference. European Association for the Study of the Liver. J Hepatol, 35, 421-30. DOI ScienceOn |
11 | Capurro M, Wanless IR, Sherman M, et al (2003). Glypican-3: a novel serum and histochemical marker for hepatocellular carcinoma. Gastroenterology, 125, 89-97. DOI ScienceOn |
12 | Chuma M, Sakamoto M, Yamazaki K, et al (2003). Expression profiling in multistage hepatocarcinogenesis: identification of HSP70 as a molecular marker of early hepatocellular carcinoma. Hepatology, 37, 198-207. DOI |
13 | Cocquerel L, Voisset C, Dubuisson J (2006). Hepatitis C virus entry: potential receptors and their biological functions. J Gen Virol, 87, 1075-84. DOI |
14 | Cormier EG, Durso RJ, Tsamis F, et al (2004). L-SIGN (CD209L) and DC-SIGN (CD209) mediate transinfection of liver cells by hepatitis C virus. Proc Natl Acad Sci U S A, 101, 14067-72. DOI |
15 | Degos F, Christidis C, Ganne-Carrie N, et al (2000). Hepatitis C virus related cirrhosis: time to occurrence of hepatocellular carcinoma and death. Gut, 47, 131-6. DOI ScienceOn |
16 | Donato F, Tagger A, Gelatti U, et al (2002). Alcohol and hepatocellular carcinoma: the effect of lifetime intake and hepatitis virus infections in men and women. Am J Epidemiol, 155, 323-31. DOI ScienceOn |
17 | El-Serag HB, Hampel H, Javadi F (2006). The association between diabetes and hepatocellular carcinoma: a systematic review of epidemiologic evidence. Clin Gastroenterol Hepatol, 4, 369-80. DOI ScienceOn |
18 | Ferlay J, Shin HR, Bray F, et al (2010). Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer, 127, 2893-917. DOI |
19 | Gentleman RC, Carey VJ, Bates DM, et al (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol, 5, R80. DOI |
20 | Gardner JP, Durso RJ, Arrigale RR, et al (2003). L-SIGN (CD 209L) is a liver-specific capture receptor for hepatitis C virus. Proc Natl Acad Sci USA, 100, 4498-503. DOI |
21 | Hochreiter S, Bodenhofer U, Heusel M, et al (2010). FABIA: factor analysis for bicluster acquisition. Bioinformatics, 26, 1520-7. DOI |
22 | Hui AM, Makuuchi M, Li X (1998). Cell cycle regulators and human hepatocarcinogenesis. Hepatogastroenterology, 45, 1635-42. |
23 | Hulsegge I, Kommadath A, Smits MA (2009). Globaltest and GOEAST: two different approaches for Gene Ontology analysis. BMC Proc, 3 Suppl 4, S10. |
24 | Jaskiewicz K, Chasen MR, Robson SC (1993). Differential expression of extracellular matrix proteins and integrins in hepatocellular carcinoma and chronic liver disease. Anticancer Res, 13, 2229-37. |
25 | Kanehisa M (2002). The KEGG database. Novartis Found Symp, 247, 91-101; discussion -3, 19-28, 244-52. |
26 | Koppel EA, van Gisbergen KP, Geijtenbeek TB, van Kooyk Y (2005). Distinct functions of DC-SIGN and its homologues L-SIGN (DC-SIGNR) and mSIGNR1 in pathogen recognition and immune regulation. Cell Microbiol, 7, 157-65. |
27 | Kumar M, Sarin SK (2007). Is cirrhosis of the liver reversible? Indian J Pediatr, 74, 393-9. DOI |
28 | Levine AJ, Puzio-Kuter AM (2010). The control of the metabolic switch in cancers by oncogenes and tumor suppressor genes. Science, 330, 1340-4. DOI ScienceOn |
29 | Lozach PY, Amara A, Bartosch B, et al (2004). C-type lectins L-SIGN and DC-SIGN capture and transmit infectious hepatitis C virus pseudotype particles. J Biol Chem, 279, 32035-45. DOI |
30 | Li J, Tibshirani R (2011). Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res. |
31 | Maere S, Heymans K, Kuiper M (2005). BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448-9. DOI |
32 | Marcellin P (1999). Hepatitis C: the clinical spectrum of the disease. J Hepatol, 31 Suppl 1, 9-16. DOI |
33 | Marrero JA, Lok AS (2004). Newer markers for hepatocellular carcinoma. Gastroenterology, 127, S113-9. DOI |
34 | Seyer JM, Hutcheson ET, Kang AH (1977). Collagen polymorphism in normal and cirrhotic human liver. J Clin Invest, 59, 241-8. DOI |
35 | Smith MW, Yue ZN, Geiss, et al (2003). Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma. Cancer Res, 63, 859-64. |
36 | Soini Y, Chia SC, Bennett WP, et al (1996). An aflatoxinassociated mutational hotspot at codon 249 in the p53 tumor suppressor gene occurs in hepatocellular carcinomas from Mexico. Carcinogenesis, 17, 1007-12. DOI |
37 | Swann JB, Smyth MJ (2007). Immune surveillance of tumors. J Clin Invest, 117, 1137-46. DOI ScienceOn |
38 | Tai DI, Tsai SL, Chen YM, et al (2000). Activation of nuclear factor kappaB in hepatitis C virus infection: implications for pathogenesis and hepatocarcinogenesis. Hepatology, 31, 656-64. DOI ScienceOn |
39 | Warburg O (1956). On the origin of cancer cells. Science, 123, 309-14. DOI |
40 | Thorgeirsson SS, Grisham JW (2002). Molecular pathogenesis of human hepatocellular carcinoma. Nat Genet, 31, 339-46. DOI ScienceOn |
41 | Wideroff L, Gridley G, Mellemkjaer L, et al (1997). Cancer incidence in a population-based cohort of patients hospitalized with diabetes mellitus in Denmark. J Natl Cancer Inst, 89, 1360-5. DOI ScienceOn |
42 | Wu ZL, Prather B, Ethen CM, et al (2011). Detection of specific glycosaminoglycans and glycan epitopes by in vitro sulfation using recombinant sulfotransferases. Glycobiology, 21, 625-33. DOI |
43 | Zhu N, Ware CF, Lai MM (2001). Hepatitis C virus core protein enhances FADD-mediated apoptosis and suppresses TRADD signaling of tumor necrosis factor receptor. Virology, 283, 178-87. DOI |
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