Integrated Bioinformatics Analysis for Cancer Target Identification

Methods in Molecular Biology

Volumn 719, Issue , 2011, Pages 527-545

  Yang, Yongliang ^a,b   Adelstein, S James ^a   Kassis, Amin I ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

False discovery rate; Integrated bioinformatics analysis; Literature data analysis; Microarray data analysis; Pathway analysis; Subcellular location; Tissue specificity

Indexed keywords

ANIMAL; ARTICLE; BIOLOGY; DATA MINING; DNA MICROARRAY; ENZYMOLOGY; HUMAN; LITERATURE; METABOLISM; METHODOLOGY; MOLECULAR IMAGING; NEOPLASM;

ANIMALS; COMPUTATIONAL BIOLOGY; DATA MINING; HUMANS; LITERATURE, MODERN; MOLECULAR IMAGING; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 79958254401     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-027-0_25     Document Type: Chapter

References (35)

1. Yang Y, Adelstein SJ, and Kassis AI. (2009) Target discovery from data mining approaches. Drug Discov Today 14(3–4), 147–54.
2. Chen X, Ji ZL, and Chen YZ. (2002) TTD: Therapeutic Target Database. Nucleic Acids Res 30(1), 412–5.
3. Zheng C, Han L, Yap CW, Xie B et al. (2006) Progress and problems in the exploration of therapeutic targets. Drug Discov Today 11 (9–10), 412–20.
4. Sams-Dodd F. (2005) Target-based drug discovery: is something wrong? Drug Discov Today 10(2), 139–47.
5. Butcher SP. (2003) Target discovery and validation in the post-genomic era. Neurochem Res 28(2), 367–71.
6. Rhodes DR, and Chinnaiyan AM. (2005) Integrative analysis of the cancer transcriptome. Nat Genet 37, 31–7.
7. Pawitan Y, Michiels S, Koscielny S, Gusnanto A et al. (2005) False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 21(13), 3017–24.
8. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R et al. (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9, 166–80.
9. Li S, Becich MJ, and Gilbertson J. (2004) Microarray data mining using Gene Ontology. Medinfo 107, 778–82.
10. Welsh JB, Sapinoso LM, Kern SG, Brown DA et al. (2003) Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum. Proc Natl Acad Sci USA 100, 3410–15.
11. Curtis RK, Oresic M, and Vidal-Puig A. (2005) Pathways to the analysis of microarray data. Trends Biotechnol 23(8), 429–35.
12. Bredel M, Scholtens DM, Harsh GR, Bredel C et al. (2009) A network model of a cooperative genetic landscape in brain tumors. JAMA 302(3), 261–75.
13. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34(3), 267–73.
14. Yue QX, Cao ZW, Guan SH, Liu XH et al. (2008) Proteomics characterization of the cytotoxicity mechanism of ganoderic acid D and computer-automated estimation of the possible drug target network. Mol Cell Proteomics 7(5), 949–61.
15. Liang S, Li Y, Be X, Howes S et al. (2006) Detecting and profiling tissue-selective genes. Physiol Genomics 26(2), 158–62.
16. Yang Y, Pospisil P, Adelstein SJ, and Kassis AI. (2008) Integrative genomic data mining for discovery of potential blood-borne biomarkers for early diagnosis of cancer. PLoS ONE 3(11), e3661.
17. Chen K, Aowad AF, Adelstein SJ, and Kassis AI. (2007) Molecular-docking-guided design, synthesis, and biologic evaluation of radioio-dinated quinazolinone prodrugs. J Med Chem 50(4), 663–73.
18. Pospisil P, Wang K, Al Aowad AF, Iyer LK et al. (2007) Computational modeling and experimental evaluation of a novel prodrug for targeting the extracellular space of prostate tumors. Cancer Res 67, 2197–205.
19. Kassis AI, Korideck H, Wang K, Pospisil P et al. (2008) Novel prodrugs for targeting diagnostic and therapeutic radionuclides to solid tumors. Molecules 13(2), 391–404.
20. Pospisil P, Iyer LK, Adelstein SJ, and Kassis AI. (2006) A combined approach to data mining of textual and structured data to identify cancer-related targets. BMC Bioinformatics 7, 354.
21. Griffith OL, Melck A, Jones SJ, and Wiseman SM. (2006) Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers. J Clin Oncol 24(31), 5043–51.
22. Harris MA, Clark J, Ireland A, Lomax J et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32, D258–61.
23. Doms A, and Schroeder M. (2005) GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res 33, 783–6.
24. Chang JT, Schütze H, and Altman RB. (2004) GAPSCORE: finding gene and protein names one word at a time. Bioinformatics 20(2), 216–25.
25. Schülke N, Varlamova OA, Donovan GP, Ma D et al. (2003) The homodimer of prostate-specific membrane antigen is a functional target for cancer therapy. Proc Natl Acad Sci USA 100(22), 12590–5.
26. Banerjee SR, Foss CA, Castanares M, Mease RC et al. (2008) Synthesis and evaluation of technetium-99m-and rhenium-labeled inhibitors of the prostate-specific membrane antigen (PSMA). J Med Chem 51(15), 4504–17.
27. Humblet V, Lapidus R, Williams LR, Tsukamoto T et al. (2005) High-affinity near-infrared fluorescent small-molecule contrast agents for in vivo imaging of prostate-specific membrane antigen. Mol Imaging 4(4), 448–62.
28. Poola I, DeWitty RL, Marshalleck JJ, Bhatnagar R et al. (2005) Identification of MMP-1 as a putative breast cancer predictive marker by global gene expression analysis. Nat Med 11, 481–83.
29. Kuhlmann KFD, van Till JWO, Boermeester MA, de Reuver PR et al. (2007) Evaluation of matrix metalloproteinase 7 in plasma and pancreatic juice as a biomarker for pancreatic cancer. Cancer Epidemiol Biomarkers Prev 16, 886–91.
30. Vihinen P, and Kähäri V-M. (2002) Matrix metalloproteinases in cancer: prognostic markers and therapeutic targets. Int J Cancer 99, 157–66.
31. Abiatari I, Kleeff J, Li J, Felix K et al. (2006) Hsulf-1 regulates growth and invasion of pancreatic cancer cells. J Clin Pathol 59, 1052–58.
32. Duffy MJ. (2004) The urokinase plasminogen activator system: role in malignancy. Curr Pharm Des 10(1), 39–49.
33. Law B, Curino A, Bugge TH, Weissleder R et al. (2004) Design, synthesis, and characterization of urokinase plasminogen-activator-sensitive near-infrared reporter. Chem Biol 11(1), 99–106.
34. Li ZB, Niu G, Wang H, He L et al. (2008) Imaging of urokinase-type plasminogen activator receptor expression using a 64Cu-labeled linear peptide antagonist by microPET. Clin Cancer Res 14(15), 4758–66.
35. Huang da W, Sherman BT, and Lempicki RA. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1), 44–5.