Chung CH, Bernard PS, Perou CM: Molecular portraits and the family tree of cancer. Nat Genet. 2002, 32 (Suppl): 533-540. 10.1038/ng1038.
Article
CAS
PubMed
Google Scholar
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, et al: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999, 286: 531-537. 10.1126/science.286.5439.531.
Article
CAS
PubMed
Google Scholar
Weigelt B, Hu ZY, He XP, Livasy C, Carey LA, Ewend MG, et al: Molecular portraits and 70-gene prognosis signature are preserved throughout the metastatic process of breast cancer. Cancer research. 2005, 65: 9155-9158. 10.1158/0008-5472.CAN-05-2553.
Article
CAS
PubMed
Google Scholar
Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, et al: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA. 2003, 100: 8418-8423. 10.1073/pnas.0932692100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hayes DN, Monti S, Parmigiani G, Gilks CB, Naoki K, Bhattacharjee A, et al: Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. Journal of Clinical Oncology. 2006, 24: 5079-5090. 10.1200/JCO.2005.05.1748.
Article
CAS
PubMed
Google Scholar
Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, et al: Molecular portraits of human breast tumours. Nature. 2000, 406: 747-752. 10.1038/35021093.
Article
CAS
PubMed
Google Scholar
Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, et al: Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proceedings of the National Academy of Sciences of the United States of America. 2001, 98: 13790-13795. 10.1073/pnas.191502998.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alizadeh A, Eisen M, Davis E, Ma C, Lossos I, Rosenwald A, et al: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000, 403: 503-511. 10.1038/35000501.
Article
CAS
PubMed
Google Scholar
Sorlie T, Perou C, Tibshirani R, Aas T, Geisler S, Johnsen H, et al: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. PNAS. 2001, 98: 10869-10874. 10.1073/pnas.191367098.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, et al: Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA. 2001, 98: 15149-15154. 10.1073/pnas.211566398.
Article
CAS
PubMed
PubMed Central
Google Scholar
Giordano TJ, Shedden KA, Schwartz DR, Kuick R, Taylor JMG, Lee N, et al: Organ-specific molecular classification of primary lung, colon, and ovarian adenocarcinomas using gene expression profiles. American journal of pathology. 2001, 159: 1231-1238.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rhodes D, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, et al: Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences of the United States of America. 2004, 101: 9309-9314. 10.1073/pnas.0401994101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ramaswamy S, Ross KN, Lander ES, Golub TR: A molecular signature of metastasis in primary solid tumors. Nature genetics. 2003, 33: 49-54. 10.1038/ng1060.
Article
CAS
PubMed
Google Scholar
Glinsky GV, Berezovska O, Glinskii AB: Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer. Journal of Clinical Investigation. 2005, 115: 1503-1521. 10.1172/JCI23412.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pavlidis N, Fizazi K: Cancer of unknown primary (CUP). Critical Reviews in Oncology Hematology. 2005, 54: 243-250. 10.1016/j.critrevonc.2004.10.002.
Article
Google Scholar
Tothill RW, Kowalczyk A, Rischin D, Bousioutas A, Haviv I, van Laar RK, et al: An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. Cancer Res. 2005, 65: 4031-4040. 10.1158/0008-5472.CAN-04-3617.
Article
CAS
PubMed
Google Scholar
Bender RA, Erlander MG: Molecular classification of unknown primary cancer. Semin Oncol. 2009, 36: 38-43. 10.1053/j.seminoncol.2008.10.002.
Article
CAS
PubMed
Google Scholar
Bloom G, Yang IV, Boulware D, Kwong KY, Coppola D, Eschrich S, et al: Multi-platform, multi-site, microarray-based human tumor classification. American journal of pathology. 2004, 164: 9-16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma XJ, Patel R, Wang XQ, Salunga R, Murage J, Desai R, et al: Molecular classification of human cancers using a 92-gene real-time quantitative polymerase chain reaction assay. Archives of Pathology & Laboratory Medicine. 2006, 130: 465-473.
CAS
Google Scholar
Talantov D, Baden J, Jatkoe T, Hahn K, Yu J, Rajpurohit Y, et al: Quantitative reverse transcriptase-polyme rase chain reaction assay to identify metastatic carcinoma tissue of origin. Journal of Molecular Diagnostics. 2006, 8: 320-329. 10.2353/jmoldx.2006.050136.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, et al: NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 2005, D562-6. 33 Database
Wilson CL, Miller CJ: Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics. 2005, 21: 3683-3685. 10.1093/bioinformatics/bti605.
Article
CAS
PubMed
Google Scholar
Dai M, Wang P, Boyd A, Kostov G, Athey B, Jones E, et al: Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic acids research. 2005, 33: e175-10.1093/nar/gni179.
Article
PubMed
PubMed Central
Google Scholar
Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M, et al: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS. 2005, 102: 15545-15550. 10.1073/pnas.0506580102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, et al: DAVID: Database for annotation, visualization, and integrated discovery. Genome biology. 2003, 4: P3-10.1186/gb-2003-4-5-p3.
Article
PubMed
Google Scholar
Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, et al: The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome biology. 2007, 8: R183-10.1186/gb-2007-8-9-r183.
Article
PubMed
PubMed Central
Google Scholar
Nelson PS, Clegg N, Arnold H, Ferguson C, Bonham M, White J, et al: The program of androgen-responsive genes in neoplastic prostate epithelium. Proceedings of the National Academy of Sciences of the United States of America. 2002, 99: 11890-11895. 10.1073/pnas.182376299.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cuatrecasas M, Catasus L, Palacios J, Prat J: Transitional Cell Tumors of the Ovary A Comparative Clinicopathologic, Immunohistochemical, and Molecular Genetic Analysis of Brenner Tumors and Transitional Cell Carcinomas. American Journal of Surgical Pathology. 2009, 33: 556-567. 10.1097/PAS.0b013e318188b84c.
Article
PubMed
Google Scholar
Eichhorn JH, Young RH: Transitional cell carcinoma of the ovary - A morphologic study of 100 cases with emphasis on differential diagnosis. American Journal of Surgical Pathology. 2004, 28: 453-463. 10.1097/00000478-200404000-00004.
Article
PubMed
Google Scholar
Tickoo SK, Gopalan A: Pathologic features of renal cortical tumors. Urol Clin North Am. 2008, 35: 551-561. 10.1016/j.ucl.2008.07.001.
Article
PubMed
Google Scholar
Ayala G, Tuxhorn JA, Wheeler TM, Frolov A, Scardino PT, Ohori M, et al: Reactive stroma as a predictor of biochemical-free recurrence in prostate cancer. Clin Cancer Res. 2003, 9: 4792-4801.
CAS
PubMed
Google Scholar
Brugarolas J: Renal-cell carcinoma - Molecular pathways and therapies. New England Journal of Medicine. 2007, 356: 185-187. 10.1056/NEJMe068263.
Article
CAS
PubMed
Google Scholar
Staller P, Sulitkova J, Liszlwan J, Moch H, Oakeley EJ, Krek W: Chemokine receptor CXCR4 downregulated by von Hippel-Lindau tumour suppressor pVHL. Nature. 2003, 425: 307-311. 10.1038/nature01874.
Article
CAS
PubMed
Google Scholar
Liu X, Yu XP, Zack DJ, Zhu H, Qian J: TiGER: A database for tissue-specific gene expression and regulation. BMC Bioinformatics. 2008, 9: 271-10.1186/1471-2105-9-271.
Article
PubMed
PubMed Central
Google Scholar
Yoder BJ, Wilkinson EJ, Massoll NA: Molecular and morphologic distinctions between infiltrating ductal and lobular carcinoma of the breast. Breast Journal. 2007, 13: 172-179. 10.1111/j.1524-4741.2007.00393.x.
Article
CAS
PubMed
Google Scholar
Lacroix M, Toillon RA, Leclercq G: Stable 'portrait' of breast tumors during progression: data from biology, pathology and genetics. Endocrine-related cancer. 2004, 11: 497-522. 10.1677/erc.1.00758.
Article
CAS
PubMed
Google Scholar
Weigelt B, Horlings HM, Kreike B, Hayes MM, Hauptmann M, Wessels LF, et al: Refinement of breast cancer classification by molecular characterization of histological special types. J Pathol. 2008, 216: 141-150. 10.1002/path.2407.
Article
CAS
PubMed
Google Scholar
Sotiriou C, Pusztai L: Gene-expression signatures in breast cancer. N Engl J Med. 2009, 360: 790-800. 10.1056/NEJMra0801289.
Article
CAS
PubMed
Google Scholar
Rakha EA, Elsheikh SE, Aleskandarany MA, Habashi HO, Green AR, Powe DG, et al: Triple-negative breast cancer: distinguishing between basal and nonbasal subtypes. Clin Cancer Res. 2009, 15: 2302-2310. 10.1158/1078-0432.CCR-08-2132.
Article
CAS
PubMed
Google Scholar
Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, et al: Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis. Journal of the National Cancer Institute. 2006, 98: 262-272. 10.1093/jnci/djj052.
Article
CAS
PubMed
Google Scholar
Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, et al: Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer research. 2006, 66: 10292-10301. 10.1158/0008-5472.CAN-05-4414.
Article
CAS
PubMed
Google Scholar
Ignatiadis M, Sotiriou C: Understanding the molecular basis of histologic grade. Pathobiology. 2008, 75: 104-111. 10.1159/000123848.
Article
CAS
PubMed
Google Scholar
Yu JX, Sieuwerts AM, Zhang Y, Martens JWM, Smid M, Klijn JGM, et al: Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC cancer. 2007, 7: 182-10.1186/1471-2407-7-182.
Article
PubMed
PubMed Central
Google Scholar
Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, et al: The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics. 2006, 7: 96-10.1186/1471-2164-7-96.
Article
PubMed
PubMed Central
Google Scholar
Sloan EK, Ciocca DR, Pouliot N, Natoli A, Restall C, Henderson MA, et al: Stromal Cell Expression of Caveolin-1 Predicts Outcome in Breast Cancer. Am J Pathol. 2009, 174 (6): 2035-43. 10.2353/ajpath.2009.080924.
Article
CAS
PubMed
PubMed Central
Google Scholar
Witkiewicz AK, Dasgupta A, Sotgia F, Mercier I, Pestell RG, Sabel M, et al: An Absence of Stromal Caveolin-1 Expression Predicts Early Tumor Recurrence and Poor Clinical Outcome in Human Breast Cancers. Am J Pathol. 2009, 174 (6): 2023-34. 10.2353/ajpath.2009.080873.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lukes L, Crawford NPS, Walker R, Hunter KW: The Origins of Breast Cancer Prognostic Gene Expression Profiles. Cancer research. 2009, 69: 310-318. 10.1158/0008-5472.CAN-08-3520.
Article
CAS
PubMed
PubMed Central
Google Scholar
Witkiewicz AK, Dasgupta A, Nguyen KH, Liu C, Kovatich AJ, Schwartz GF, et al: Stromal caveolin-1 levels predict early DCIS progression to invasive breast cancer. Cancer Biol Ther. 2009, 8: 1167-1175.
Article
Google Scholar
Ma XJ, Dahiya S, Richardson E, Erlander M, Sgroi DC: Gene expression profiling of the tumor microenvironment during breast cancer progression. Breast Cancer Res. 2009, 11: R7-10.1186/bcr2222.
Article
PubMed
PubMed Central
Google Scholar
Pavlakis K, Messini I, Vrekoussis T, Yiannou P, Keramopoullos D, Louvrou N, et al: The assessment of angiogenesis and fibroblastic stromagenesis in hyperplastic and pre-invasive breast lesions. BMC cancer. 2008, 8: 88-10.1186/1471-2407-8-88.
Article
PubMed
PubMed Central
Google Scholar
Troup S, Njue C, Kliewer EV, Parisien M, Roskelley C, Chakravarti S, et al: Reduced expression of the small leucine-rich proteoglycans, lumican, and decorin is associated with poor outcome in node-negative invasive breast cancer. Clin Cancer Res. 2003, 9: 207-214.
CAS
PubMed
Google Scholar
Wennmalm K, Ostman A, Bergh J: Stromal signature identifies basal breast cancers. Nat Med. 2009, 15: 237-238. 10.1038/nm0309-237.
Article
CAS
PubMed
Google Scholar
Schedin P, Borges V: Breaking down barriers: the importance of the stromal microenvironment in acquiring invasiveness in young women's breast cancer. Breast Cancer Res. 2009, 11: 102-10.1186/bcr2235.
Article
PubMed
PubMed Central
Google Scholar
Finak G, Bertos N, Pepin F, Sadekova S, Souleimanova M, Zhao H, et al: Stromal gene expression predicts clinical outcome in breast cancer. Nat Med. 2008, 14: 518-527. 10.1038/nm1764.
Article
CAS
PubMed
Google Scholar
Oien KA: Pathologic Evaluation of Unknown Primary Cancer. Seminars in Oncology. 2009, 36: 8-37. 10.1053/j.seminoncol.2008.10.009.
Article
CAS
PubMed
Google Scholar
Laberke HG, Klingebiel T, Quack G: A Contribution to the Morphology and Pathogenesis of Thyroid-Like Lesions in the Kidney. Pathology Research and Practice. 1983, 176: 284-296.
Article
CAS
Google Scholar
Amin MB, Gupta R, Ondrej H, McKenney JK, Michal M, Young AN, et al: Primary Thyroid-like Follicular Carcinoma of the Kidney Report of 6 Cases of a Histologically Distinctive Adult Renal Epithelial Neoplasm. American Journal of Surgical Pathology. 2009, 33: 393-400. 10.1097/PAS.0b013e31818cb8f5.
Article
PubMed
Google Scholar
Jung SJ, Il Chung J, Park SH, Ayala AG, Ro JY: Thyroid follicular carcinoma-like tumor of kidney - A case report with morphologic, immunohistochemical, and genetic analysis. American Journal of Surgical Pathology. 2006, 30: 411-415.
Article
PubMed
Google Scholar
Bast RC, Hennessy B, Mills GB: The biology of ovarian cancer: new opportunities for translation. Nat Rev Cancer. 2009, 9: 415-428. 10.1038/nrc2644.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seidman JD, Russell P, Kurman RJ: Surface epithelial tumors of the ovary. Blaustein's pathology of the female genital tract. Edited by: Ancell Blaustein, Robert J Kurman. 2002, New York: Springer-Verlag, 791-904.
Google Scholar
Kang H, O'Connell JB, Maggard MA, Sack J, Ko CY: A 10-year outcomes evaluation of mucinous and signet-ring cell carcinoma of the colon and rectum. Dis Colon Rectum. 2005, 48: 1161-1168. 10.1007/s10350-004-0932-1.
Article
PubMed
Google Scholar
Naora H, Montell DJ: Ovarian cancer metastasis: integrating insights from disparate model organisms. Nat Rev Cancer. 2005, 5: 355-366. 10.1038/nrc1611.
Article
CAS
PubMed
Google Scholar
Smorenburg SM, Griffini P, Tiggelman AMBC, Moorman AFM, Boers W, VanNoorden CJF: alpha 2-macroglobulin is mainly produced by cancer cells and not by hepatocytes in rats with colon carcinoma metastases in liver. Hepatology. 1996, 23: 560-570.
Article
CAS
PubMed
Google Scholar
Sukata T, Uwagawa S, Ozaki K, Sumida K, Kikuchi K, Kushida M, et al: alpha-2-macroglobulin: A novel cytochemical marker characterizing preneoplastic and neoplastic rat liver lesions negative for hitherto established cytochemical markers. American journal of pathology. 2004, 165: 1479-1488.
Article
CAS
PubMed
PubMed Central
Google Scholar
Matouk IJ, Abbasi I, Hochberg A, Galun E, Dweik H, Akkawi M: Highly upregulated in liver cancer noncoding RNA is overexpressed in hepatic colorectal metastasis. Eur J Gastroenterol Hepatol. 2009, 21: 688-692. 10.1097/MEG.0b013e328306a3a2.
Article
CAS
PubMed
Google Scholar
Khambata-Ford S, Garrett CR, Meropol NJ, Basik M, Harbison CT, Wu S, et al: Expression of epiregulin and amphiregulin and K-ras mutation status predict disease control in metastatic colorectal cancer patients treated with cetuximab. J Clin Oncol. 2007, 25: 3230-3237. 10.1200/JCO.2006.10.5437.
Article
CAS
PubMed
Google Scholar
Pantaleo MA, Astolfi A, Nannini M, Paterini P, Piazzi G, Ercolani G, et al: Gene expression profiling of liver metastases from colorectal cancer as potential basis for treatment choice. Br J Cancer. 2008, 99: 1729-1734. 10.1038/sj.bjc.6604681.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ki DH, Jeung HC, Park CH, Kang SH, Lee GY, Lee WS, et al: Whole genome analysis for liver metastasis gene signatures in colorectal cancer. Int J Cancer. 2007, 121: 2005-2012. 10.1002/ijc.22975.
Article
CAS
PubMed
Google Scholar
Ramasamy A, Mondry A, Holmes CC, Altman DG: Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets. PLoS Med. 2008, 5: e184-10.1371/journal.pmed.0050184.
Article
PubMed
PubMed Central
Google Scholar
Snyder M, Weissman S, Gerstein M: Personal phenotypes to go with personal genomes. Mol Syst Biol. 2009, 5: 273-10.1038/msb.2009.32.
Article
PubMed
PubMed Central
Google Scholar
Belmont J, McGuire AL: The futility of genomic counseling: essential role of electronic health records. Genome Med. 2009, 1: 48-10.1186/gm48.
Article
PubMed
PubMed Central
Google Scholar
Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, et al: Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006, 10: 529-541. 10.1016/j.ccr.2006.10.009.
Article
CAS
PubMed
Google Scholar
Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, et al: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA. 2005, 102: 13550-13555. 10.1073/pnas.0506230102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pittman J, Huang E, Dressman H, Horng CF, Cheng S, Tsou MH, et al: Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes. PNAS. 2004, 101: 8431-8436. 10.1073/pnas.0401736101.
Article
CAS
PubMed
PubMed Central
Google Scholar