Abstract
Several technologies now exist that allow the simultaneous evaluation of the amount of RNA produced by each cellular gene. Application of these technologies to measure transcriptional activity in cancer cells has provided a rich source of information that is being used to understand tumor biology. Analysis of the resulting gene expression data has evolved from the identification of individual gene expression differences between tumor and non-diseased cells to model-based evaluation of complex signal transduction pathways. Pathway-based models that utilize gene expression data have yielded new insights into tumor cell biology by more accurately describing both pleiotropic and polygenic cell processes. Further description and integration of gene expression-based models will be critical to fully exploit the information contained in gene expression data and to develop a more in-depth understanding of tumor cell development and progression.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Alizadeh AA, Eisen MB, Davis RE et al (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503–511
Alon U, Barkai N, Notterman DA et al (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96:6745–6750
Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
Beissbart T, Speed TP (2004) GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics 20:1464–1465
Bild AH, Yao G, Chang JT et al (2005) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439:353–357
Bittner M, Meltzer P, Chen Y et al (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406:536–540
Bouton CM, Pevsner J (2002) DRAGON View: information visualization for annotated microarray data. Bioinformatics 18:323–324
Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365–371
Buyse M, Loi S, van’t Veer L et al (2006) Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 98:1183–1192
Chang HY, Nuyten DS, Sneddon JB et al (2005) Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci USA 102:3738–3743
Chen X, Cheung ST, So S et al (2002) Gene expression patterns in human liver cancer. Mol Bio Cell 13:1929–1939
Chi JT, Wang Z, Nuyten DS et al (2006) Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med 3:e47
Choe SE, Boutros M, Michelson AM et al (2005) Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 6:R16
Choi K, Creighton CJ, Stivers D et al (2007) Transcriptional profiling of non-small cell lung cancer cells with activating EGFR somatic mutations. PLoS ONE 2:e1226
Crawley JJ, Furge KA (2002) Identification of frequent cytogenetic aberrations in hepatocellular carcinoma using gene expression data. Genome Biol 3:RESEARCH0075
Creighton CJ (2008) Multiple oncogenic pathway signatures show coordinate expression patterns in human prostate tumors. PLoS ONE 3:e1816
Dabney AR, Storey JD (2006) A reanalysis of a published Affymetrix GeneChip control dataset. Genome Biol 6:R16
Dai M, Wang P, Boyd AD et al (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33:e175
Desai KV, Xiao N, Wang W et al (2002) Initiating oncogenic event determines gene-expression patterns of human breast cancer models. Proc Natl Acad Sci USA 99:6967–6972
Draghici S, Khatri P, Eklund AC et al (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22:101–109
Dudoit S, Yang YH, Callow MJ et al (2002) Statistical methods of identifying differentially expressed genes in replicated cDNA microarray experiments. Stat Sinica 12:111–129
Dumur CI, Lyons-Weiler M, Sciulli C et al (2008) Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancers. J Mol Diagn 10:67–77
Eisen MB, Spellman PT, Brown PO et al (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863–14868
Fambrough D, McClure K, Kazlauskas A et al (1999) Diverse signaling pathways activated by growth factor receptors induce broadly overlapping rather than independent, sets of genes. Cell 97:727–741
Ferrando AA, Neuberg DS, Staunton J et al (2002) Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell 1:75–87
Furge KA, Lucas KA, Takahashi M et al (2004) Robust classification of renal cell carcinoma based on gene expression data and predicted cytogenetic profiles. Cancer Res 64:4117–4121
Furge KA, Tan MH, Dykema K et al (2007a) Identification of deregulated oncogenic pathways in renal cell carcinoma: an integrated oncogenomic approach based on gene expression profiling. Oncogene 26:1346–1350
Furge KA, Chen J, Koeman J et al (2007b) Detection of DNA copy number changes and oncogenic signaling abnormalities from gene expression data reveals MYC activation in high-grade papillary renal cell carcinoma. Cancer Res 67:3171–3176
Gettman MT, Blute ML, Spotts B et al (2001) Pathologic staging of renal cell carcinoma: significance of tumor classification with the 1997 TNM staging system. Cancer 91:354–361
Glas AM, Floore A, Delahaye LJ et al (2006) Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics 7:278
Golub TR, Slonim DK, Tamayo P et al (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531–537
Habel LA, Shak S, Jacobs MK et al (2006) A population-based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients. Breast Cancer Res 8:R25
Han KR, Bleumer I, Pantuck AJ et al (2003) Validation of an integrated staging system toward improved prognostication of patients with localized renal cell carcinoma in an international population. J Urol 170:2221–2224
Hertzberg L, Betts DR, Raimondi SC et al (2006) Prediction of chromosomal aneuploidy from gene expression data. Genes Chromosomes Cancer 46:75–86
Hieronymus H, Lamb J, Ross KN et al (2006) Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell 10:321–330
Hosack DA, Dennis G Jr, Sherman BT et al (2003) Identifying biological themes within lists of genes with EASE. Genome Biol 4:R70
Huang E, Ishida S, Pittman J et al (2003) Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet 34:226–230
Hughes TR, Roberts CJ, Dai H et al (2000a) Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25:333–337
Hughes TR, Marton MJ, Jones AR et al (2000b) Functional discovery via a compendium of expression profiles. Cell 102:109–126
Hummel M, Bentink S, Berger H et al (2006) A biologic definition of Burkitt’s lymphoma from transcriptional and genomic profiling. N Engl J Med 354:2419–2430
Irizarry RA, Hobbs B, Collin F et al (2003) Exploration, normalization, and summaries of high-density oligonucleotide array probe level data. Biostatistics 2:249–264
Ishida S, Huang E, Zuzan H et al (2001) Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol Cell Biol 21:4684–4699
Joshi-Tope G, Gillespie M, Vastrik I et al (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33:D428–432
Kaposi-Novak P, Lee JS, Gomez-Quiroz L et al (2006) Met-regulated expression signature defines a subset of human hepatocellular carcinomas with poor prognosis and aggressive phenotype. J Clin Invest 116:1582–1595
Khatri P, Draghici S, Ostermeier GC et al (2002) Profiling gene expression using onto-express. Genomics 79:266–270
Kim S, Volsky DJ (2005) PAGE: Parametric Analysis of Gene Set Enrichment. BMC Bioinformatics 6:144
Koeman JM, Russell RC, Tan MH et al (2008) Somatic pairing of chromosome 19 in renal oncocytoma is associated with deregulated EGLN2-mediated oxygen sensing response. PLoS Genet 4:e1000176
Kosari F, Parker AS, Kube DM et al (2005) Clear cell renal cell carcinoma: gene expression analyses identify a potential signature for tumor aggressiveness. Clin Cancer Res 11:5128–5139
Lamb J, Crawford ED, Peck D et al (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313:1929–1935
Lander ES, Linton LM, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Li G, Barthelemy A, Feng G et al (2007) S100A1: a powerful marker to differentiate chromophobe renal cell carcinoma from renal oncocytoma. Histopathology 50:642–647
Lin F, Yang W, Betten M et al (2006) Expression of S-100 protein in renal cell neoplasms. Hum Pathol 37:462–470
Lindvall C, Furge KA, Bjorkholm M et al (2004) Combined genetic- and transcriptional profiling of acute myeloid leukemia with complex and normal karyotypes. Haematologia 89:1072–1081
Majumder PK, Febbo PG, Bikoff R et al (2004) mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways. Nat Med 10:594–601
Matar P, Rojo F, Cassia R et al (2004) Combined epidermal growth factor receptor targeting with the tyrosine kinase inhibitor gefitinib (ZD1839) and the monoclonal antibody cetuximab (IMC-C225): superiority over single-agent receptor targeting. Clin Cancer Res 10:6487–6501
Moch H, Schraml P, Bubendorf L et al (1999) High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma. Am J Pathol 154:981–986
Mukasa A, Ueki K, Matsumoto S et al (2002) Distinction in gene expression profiles of oligodendrogliomas with and without allelic loss of 1p. Oncogene 21:3961–3968
Okuda S, Yamada T, Hammajima M et al (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 36:W423–426
Paik S, Shak S, Tang G et al (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351:2817–2826
Perou CM, Sorlie T, Eisen MB et al (2000) Molecular portraits of human breast tumors. Nature 406:747–752
Phillips JL, Hayward SW, Wang Y et al (2001) The consequences of chromosomal aneuploidy on gene expression profiles in a cell line model for prostate carcinogenesis. Cancer Res 61:8143–8149
Platzer P, Upender MB, Wilson K et al (2002) Silence of chromosomal amplifications in colon cancer. Cancer Res 62:1134–1138
Pollack JR, Sorlie T, Perou CM et al (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 99:12963–12968
Quackenbush J (2006) Microarray analysis and tumor classification. N Engl J Med 354:2463–2472
Rhodes DR, Miller JC, Haab BB et al (2002) CIT: identification of differentially expressed clusters of genes from microarray data. Bioinformatics 18:205–206
Rhodes DR, Chinnaiyan AM (2005) Integrative analysis of the cancer transcriptome. Nat Genet 37:S31–37
Rocca PC, Brunelli M, Gobbo S et al (2007) Diagnostic utility of S100A1 expression in renal cell neoplasms: an immunohistochemical and quantitative RT-PCR study. Mod Pathol 20:722–708
Ross DT, Scherf U, Eisen MB et al (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24:227–235
Samuels Y, Ericson K (2006) Oncogenic PI3K and its role in cancer. Curr Opin Oncol 18:77–82
Simon R, Radmacher MD, Dobbin K et al (2003) Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 95:14–18
Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3
Staller P, Sulitkova J, Lisztwan J et al (2003) Chemokine receptor CXCR4 downregulated by von Hippel-Lindau tumor suppressor pVHL. Nature 425:307–311
Struski S, Doco-Fenzy M, Cornillet-Lefebvre P (2002) Compilation of published comparative genomic hybridization studies. Cancer Genet Cytogenet 135:63–90
Subramanian A, Tamayo P, Mootha VK et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545–15550
Sweet-Cordero A, Mukherjee S, Subramanian A et al (2005) An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 37:48–55
Takahashi M, Rhodes DR, Furge KA et al (2001) Gene expression profiling of clear cell renal cell carcinoma: gene identification and prognostic classification. Proc Natl Acad Sci USA 98:9754–9759
Takahashi M, Sugimura J, Yang XJ et al (2003) Molecular sub-classification of kidney cancer and the discovery of new diagnostic markers. Oncogene 22:6810–6818
Tiwari G, Sakaue H, Pollack JR et al (2003) Gene expression profiling in prostate cancer cells with Akt activation reveals Fra-1 as an Akt-inducible gene. Mol Cancer Res 1:475–484
Tomlins SA, Rhodes DR, Perner S et al (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310:644–648
Toschi L, Janne PA (2008) Single-agent and combination therapeutic strategies to inhibit hepatocyte growth factor/MET signaling in cancer. Clin Cancer Res 14:5941–5946
Troyanskaya OG, Garber ME, Brown PO et al (2002) Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 18:1454–1461
Tsui KH, Shvarts O, Smith RB et al (2000) Prognostic indicators for renal cell carcinoma: a multivariate analysis of 643 patients using the revised 1997 TNM staging criteria. J Urol 163:1090–1095 (quiz 1295)
Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116–5121
Van’t Veer LJ, Dai H, van de Vijver MJ et al (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530–536
Venter JC, Adams MD, Myers EW et al (2001) The sequence of the human genome. Science 291:1304–1351
Virtaneva K, Wright FA, Tanner SM et al (2001) Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. Proc Natl Acad Sci USA 98:1124–1129
Whitfield ML, Sherlock G, Saldanha AJ et al (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 13:1977–2000
Xu XR, Huang J, Xu ZG et al (2001) Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Proc Natl Acad Sci USA 98:15089–15094
Yao M, Huang Y, Shioi K et al (2007) Expression of adipose differentiation-related protein: a predictor of cancer-specific survival in clear cell renal carcinoma. Clin Cancer Res 13:152–160
Ye Q, Qin L, Forgues M et al (2003) Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med 9:416–423
Yu J, Zhang L, Hwang PM et al (1999) Identification and classification of p53-regulated genes. Proc Natl Acad Sci USA 96:14517–14522
Zhao H, Ljungberg B, Grankvist K et al (2006) Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med 3:e13
Zisman A, Pantuck AJ, Dorey F et al (2001) Improved prognostication of renal cell carcinoma using an integrated staging system. J Clin Oncol 19:1649–1657
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media B.V.
About this chapter
Cite this chapter
Klomp, J.A., Teh, B.T., Furge, K.A. (2010). An Integrated Oncogenomic Approach: From Genes to Pathway Analyses. In: Cho, W. (eds) An Omics Perspective on Cancer Research. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2675-0_3
Download citation
DOI: https://doi.org/10.1007/978-90-481-2675-0_3
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-90-481-2674-3
Online ISBN: 978-90-481-2675-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)