Gene pathway analysis of hepatocellular carcinoma genomic expression datasets

Journal of Surgical Research

Volumn 170, Issue 1, 2011, Pages

  Rodrigues, Richard Rosario ^a   Barry, Christopher Taylor ^b  

^a ROCHESTER INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

gene expression; gene pathway analysis; gene sets; genomics; hepatocellular carcinoma

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; PROTEIN P53; TRANSFORMING GROWTH FACTOR ALPHA; TRANSFORMING GROWTH FACTOR BETA; WNT PROTEIN;

APOPTOSIS; ARTICLE; CANCER SURVIVAL; CELL CYCLE REGULATION; CELL PROLIFERATION; DNA REPLICATION; DNA SYNTHESIS; DRUG METABOLISM; GENE; GENE EXPRESSION; GENE PATHWAY ANALYSIS; GENE SET ENRICHMENT ANALYSIS; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC CODE; HUMAN; LIPOGENESIS; LIVER CELL; LIVER CELL CARCINOMA; PRIORITY JOURNAL; RNA EXTRACTION; SYSTEMATIC REVIEW; TUMOR GENE; TUMOR RECURRENCE;

CARCINOMA, HEPATOCELLULAR; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENOMICS; HUMANS; LIVER NEOPLASMS;

EID: 80051550409     PISSN: 00224804     EISSN: 10958673     Source Type: Journal    
DOI: 10.1016/j.jss.2011.04.004     Document Type: Article

References (35)

1. L. Hood, J.R. Heath, and M.E. Phelps Systems biology and new technologies enable predictive and preventive medicine Science 306 2004 640
2. M. Sun, W. Mo, and X. Fu System biology analysis of cell cycle pathway involved in hepatocellular carcinoma Front Biosci (Schol Ed) 2 2010 1127
3. N. Kittaka, I. Takemasa, and S. Seno Exploration of potential genomic portraits associated with intrahepatic recurrence in human hepatocellular carcinoma Ann Surg Oncol 17 2010 3145
4. X. Chen, S.T. Cheung, and S. So Gene Expression patterns in human liver cancers Mol Biol Cell 13 2005 1929
5. R. Satow, M. Shitashige, and Y. Kanai Combined functional genome survey of therapeutic targets for hepatocellular carcinoma Clin Cancer Res 16 2010 2518
6. Q.H. Ye, L.X. Qin, and M. Forgues Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning Nat Med 9 2003 416
7. Available at: http://www.partek.com. Accessed: August 2010.
8. B. Harr, and C. Schlotterer Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons Nucleic Acids Research 34 2006 e8
9. Yang YH, Dudoit S, Luu P, et al. Normalization for cDNA microarray data. SPIE BiOS 2001, San Jose, California. Available at: http://www.improvedoutcomes. com/docs/WebSiteDocs/PreProcessing/Normalization/Two-Color-Datasets/ Overview-of-Lowess-Normalization.htm. Accessed: August 2010.
10. A. Subramanian, P. Tamayo, and V. Mootha Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles PNAS 102 2005 15545
11. V. Mootha, C.M. Lindgren, and K.F. Eriksson PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately down-regulated in human diabetes Nat Genet 34 2003 267
12. IPA (Ingenuity Systems) Available at: http://www.ingenuity.com. Accessed: August 2010.
13. D.W. Huang, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources Nature Protoc 4 2009 44
14. G. Dennis Jr., B.T. Sherman, and D.A. Hosack DAVID: Database for annotation, visualization, and integrated discovery Genome Biol 4 2003 P3
15. M. Kanehisa, and S. Goto KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res 28 2000 27
16. J. Campbell, A. Kejariwal, and H. Mi PANTHER: A library of protein families and subfamilies indexed by function Genome Res 13 2003 2129
17. Available at: http://www.biocarta.com/Default.aspx. Accessed: August 2010.
18. L. Matthews, G. Gopinath, and M. Gillespie Reactome knowledgebase of biological pathways and processes Nucleic Acids Res 2009 PMID: 18981052. 37(Database issue):D619-22. Epub 2008 Nov 3.
19. Q. Wu, C. Liu, and M. Yu FoxM1 is overexpressed in human hepatocellular cancer and associated with cancer progression J Am Coll Surg 211 2010 S125
20. R.M. Pascale, M.M. Simile, and M. Frau Forkhead box m1b is a determinant of rat susceptibility to hepatocarcinogenesis and sustains erk activity in human hcc J Hepatol 52 2010 S345
21. S. Jain, S. Singhal, and P. Lee Molecular genetics of hepatocellular neoplasia Am J Transl Res 2 2010 105
22. J.S. Lee, I.S. Chu, and J. Heo Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling Hepatology 40 2004 667
23. Y. Hoshida, A. Villanueva, and M. Kobayashi Gene expression in fixed tissues and outcome in hepatocellular carcinoma N Engl J Med 359 2008 1995
24. S.W. Lowe, E. Cepero, and G. Evan Intrinsic tumor suppression Nature 432 2004 307
25. M. Kitamoto, R. Nakashio, and S. Kira Long-term prognosis of small hepatocellular carcinoma (HCC) in view of proliferating cell nuclear antigen (PCNA) labeling index (LI) Gastroenterology 108 1995 A1099
26. K. Zaret Genetic programming of liver and pancreas progenitors: Lessons for stem-cell differentiation Nat Rev Genet 9 2008 329
27. K. Zaret, and M. Grompe Generation and regeneration of cells of the liver and pancreas Science 322 2008 1490
28. M.D. Thompson, and S.P. Monga WNT/β-catenin signaling in liver health and disease Hepatology 45 2007 1298
29. A. Villanueva, D.Y. Chiang, and P. Newell Pivotal role of mTorr signaling in hepatocellular carcinoma Gastroenterology 135 2008 1972
30. L. Zender, A. Villanueva, and V. Tovar Cancer gene discovery in hepatocellular carcinoma J Hepatol 52 2010 921
31. L.D. Tommaso, A. Destro, and J.Y. Seok The application of markers (HSP70 GPC3 and GS) in liver biopsies is useful for detection of hepatocellular carcinomas J Hepatol 50 2009 746
32. Y.A. Yang, G.M. Zhang, and L. Feigenbaum Smad3 reduces susceptibility to hepatocarcinoma by sensitizing hepatocytes to apoptosis through down-regulation of Bcl-2 Cancer cell 9 2006 445
33. N. Kondoh, A. Hada, and A. Ryo Activation of Galectin-1 gene in human hepatocellular carcinoma involves methylation-sensitive complex formations at the transcriptional upstream and downstream elements Int J Oncol 23 2003 1575
34. L. Ein-Dor, O. Zuk, and E. Domany Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer Proc Natl Acad Sci USA 103 2006 5923
35. X. Lu, V.V. Jain, and P.W. Finn Hubs in biological interaction networks exhibit low changes in expression in experimental asthma Mol Syst Biol 3 2007 98