MiRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 47, 2013, Pages 19160-19165

  Zadran, Sohila ^a   Remacle, F ^b,c   Levine, R D ^c,d  

^a The Institute for Molecular Medicine   (United States)

^b UNIVERSITY OF LIÈGE   (Belgium)

^c HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COL11A1 PROTEIN; DLX1 PROTEIN; MESSENGER RNA; MICRORNA; MICRORNA 141; MICRORNA 206; MICRORNA 615; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ARTICLE; BREAST CARCINOMA; CANCER CELL; CANCER CELL CULTURE; CANCER GENETICS; CANCER PATIENT; CANCER SPECIFIC SIGNATURE; CELL PROLIFERATION; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION; HUMAN; HUMAN CELL; IN VITRO STUDY; LUNG ADENOCARCINOMA; MAJOR CLINICAL STUDY; MALIGNANT NEOPLASTIC DISEASE; OVARY CARCINOMA; PHENOTYPE; PRIORITY JOURNAL; PROSTATE ADENOCARCINOMA; RNA ANALYSIS; TUMOR GENE;

BIOMARKER; DEEP SEQUENCING; MAXIMAL ENTROPY; MICROARRAY; NETWORK CONNECTIVITY;

CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; INFORMATION THEORY; MICROARRAY ANALYSIS; MICRORNAS; NEOPLASMS; RNA, MESSENGER; THERMODYNAMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 84888117735     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1316991110     Document Type: Article

References (33)

1. Rhodes DR, Chinnaiyan AM (2005) Integrative analysis of the cancer transcriptome. Nat Genet 37(Suppl-S31-S37.
2. Segal E, Friedman N, Kaminski N, Regev A, Koller D (2005) From signatures to models: Understanding cancer using microarrays. Nat Genet 37(Suppl-S38-S45.
3. Bhattacharjee A, et al. (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 98(24-13790-13795.
4. Golub TR, et al. (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286(5439-531-537.
5. Schmid PR, Palmer NP, Kohane IS, Berger B (2012) Making sense out of massive data by going beyond differential expression. Proc Natl Acad Sci USA 109(15-5594-5599.
6. Nelson WG (2011) Profiling prostate cancer. Proc Natl Acad Sci USA 108(52-20861-20862.
7. Markert EK, Mizuno H, Vazquez A, Levine AJ (2011) Molecular classification of prostate cancer using curated expression signatures. Proc Natl Acad Sci USA 108(52-21276-21281.
8. Remacle F, Kravchenko-Balasha N, Levitzki A, Levine RD (2010) Information-theoretic analysis of phenotype changes in early stages of carcinogenesis. Proc Natl Acad Sci USA 107(22-10324-10329.
9. Levine RD, Bernstein RB (1974) Energy disposal and energy consumption in elementary chemical reactions. Information theoretic approach. Acc Chem Res 7(12-393-400.
10. Gross A, Levine RD (2013) Surprisal analysis of transcripts expression levels in the presence of noise: A reliable determination of the onset of a tumor phenotype. PLoS ONE 8(4-e61554.
11. Shin YS, et al. (2011) Protein signaling networks from single cell fluctuations and information theory profiling. Biophys J 100(10-2378-2386.
12. Gross A, Li CM, Remacle F, Levine RD (2013) Free energy rhythms in Saccharomyces cerevisiae: A dynamic perspective with implications for ribosomal biogenesis. Biochemistry 52(9-1641-1648.
13. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z (2009) GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10:48.
14. Kravchenko-Balasha N, et al. (2012) On a fundamental structure of gene networks in living cells. Proc Natl Acad Sci USA 109(12-4702-4707.
15. Kravchenko-Balasha N, et al. (2011) Convergence of logic of cellular regulation in different premalignant cells by an information theoretic approach. BMC Syst Biol 5:42.
16. Amson R, Pece S, Marine J-C, Di Fiore PP, Telerman A (2013) TPT1/ TCTP-regulated pathways in phenotypic reprogramming. Trends Cell Biol 23(1-37-46.
17. Cornu M, Albert V, Hall MN (2013) mTOR in aging, metabolism, and cancer. Curr Opin Genet Dev 23(1-53-62.
18. Hainaut P, Plymoth A (2013) Targeting the hallmarks of cancer: Towards a rational approach to next-generation cancer therapy. Curr Opin Oncol 25(1-50-51.
19. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: The next generation. Cell 144(5-646-674.
20. Fisher J, et al. (2007) Ferritin: A novel mechanism for delivery of iron to the brain and other organs. Am J Physiol Cell Physiol 293(2-C641-C649.
21. Gautier EL, et al.; Immunological Genome Consortium (2012) Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat Immunol 13(11-1118-1128.
22. Ng EKO, et al. (2013) Circulating microRNAs as specific biomarkers for breast cancer detection. PLoS ONE 8(1-e53141.
23. Yang Z, et al. (2012) Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs. BMC Genomics 13(Suppl 7-S14.
24. Gommans WM, Berezikov E (2012) Controlling miRNA regulation in disease. Methods Mol Biol 822:1-18.
25. Krell J, Frampton AE, Stebbing J (2013) MicroRNAs in the cancer clinic. Front Biosci (Elite Ed) 5:204-213.
26. Zhao L, et al. (2012) MiRNA expression analysis of cancer-Associated fibroblasts and normal fibroblasts in breast cancer. Int J Biochem Cell Biol 44(11-2051-2059.
27. Wang X, Ling C, Bai Y, Zhao J (2011) MicroRNA-206 is associated with invasion and metastasis of lung cancer. Anatom Record 294(1-88-92.
28. Chang HJ, et al. (2009) MMP13 is potentially a new tumor marker for breast cancer diagnosis. Oncol Rep 22(5-1119-1127.
29. Kunert-Keil C, Steinmüller F, Jeschke U, Gredes T, Gedrange T (2011) Immunolocalization of glycodelin in human adenocarcinoma of the lung, squamous cell carcinoma of the lung and lung metastases of colonic adenocarcinoma. Acta Histochem 113(8-798-802.
30. Leber MF, Efferth T (2009) Molecular principles of cancer invasion and metastasis (review). Int J Oncol 34(4-881-895.
31. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115(7-787-798.
32. Ruepp A, Kowarsch A, Theis F (2012) PhenomiR: microRNAs in human diseases and biological processes. Methods Mol Biol 822:249-260.
33. Zadran S, Amighi A, Otiniano E, Wong K, Zadran H (2012) ENTPD5-mediated modulation of ATP results in altered metabolism and decreased survival in gliomablastoma multiforme. Tumour Biol 33(6-2411-2421.