Vogelstein B, Kinzler KW: Cancer genes and the pathways they control. Nat Med. 2004, 10 (8): 789-799. 10.1038/nm1087
Article
CAS
PubMed
Google Scholar
Hanahan D, Weinberg RA: The hallmarks of cancer. Cell. 2000, 100 (1): 57-70. 10.1016/S0092-8674(00)81683-9
Article
CAS
PubMed
Google Scholar
Goymer P: Natural selection: The evolution of cancer. Nature. 2008, 454 (7208): 1046-1048. 10.1038/4541046a
Article
CAS
PubMed
Google Scholar
Fan C, Oh DS, Wessels L, Weigelt B, Nuyten DS, Nobel AB, van't Veer LJ, Perou CM: Concordance among gene-expression-based predictors for breast cancer. The New England journal of medicine. 2006, 355 (6): 560-569. 10.1056/NEJMoa052933
Article
CAS
PubMed
Google Scholar
van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, et al.: Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002, 415 (6871): 530-536. 10.1038/415530a
Article
PubMed
Google Scholar
Oberthuer A, Berthold F, Warnat P, Hero B, Kahlert Y, Spitz R, Ernestus K, König R, Haas S, Eils R, et al.: Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol. 2006, 24 (31): 5070-5078. 10.1200/JCO.2006.06.1879
Article
CAS
PubMed
Google Scholar
Chuang HY, Lee E, Liu YT, Lee D, Ideker T: Network-based classification of breast cancer metastasis. Molecular systems biology. 2007, 3: 140- 10.1038/msb4100180
Article
PubMed Central
PubMed
Google Scholar
Ergun A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ: A network biology approach to prostate cancer. Molecular systems biology. 2007, 3: 82- 10.1038/msb4100125
Article
PubMed Central
PubMed
Google Scholar
Rifkin SA, Kim J, White KP: Evolution of gene expression in the Drosophila melanogaster subgroup. Nature genetics. 2003, 33 (2): 138-144. 10.1038/ng1086
Article
CAS
PubMed
Google Scholar
Khaitovich P, Enard W, Lachmann M, Paabo S: Evolution of primate gene expression. Nature reviews. 2006, 7 (9): 693-702. 10.1038/nrg1940
Article
CAS
PubMed
Google Scholar
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M: Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004, 431 (7006): 308-312. 10.1038/nature02782
Article
CAS
PubMed
Google Scholar
Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, Yang S, Zhang S, Liu L, Lu M, O'Connor-McCourt M, et al.: A map of human cancer signaling. Molecular systems biology. 2007, 3: 152- 10.1038/msb4100200
Article
PubMed Central
PubMed
Google Scholar
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, et al.: Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome research. 2003, 13 (10): 2363-2371. 10.1101/gr.1680803
Article
PubMed Central
CAS
PubMed
Google Scholar
Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM: Human protein reference database--2006 update. Nucleic acids research. 2006, D411-414. 34 Database
Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR: The Catalogue of Somatic Mutations in Cancer (COSMIC). Current protocols in human genetics/editorial board, Jonathan L Haines [et al]. 2008, Chapter 10: Unit 10 11-
Google Scholar
Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004, 5 (2): 101-113. 10.1038/nrg1272
Article
CAS
PubMed
Google Scholar
Albert R, Jeong H, Barabasi AL: Error and attack tolerance of complex networks. Nature. 2000, 406 (6794): 378-382. 10.1038/35019019
Article
CAS
PubMed
Google Scholar
Shannon C: A Mathematical Theory of Communication. The Bell System Technical Journal. 1948, 27: 379-423. 623-656
Article
Google Scholar
Druker BJ: Translation of the Philadelphia chromosome into therapy for CML. Blood. 2008, 112 (13): 4808-4817. 10.1182/blood-2008-07-077958
Article
CAS
PubMed
Google Scholar
Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, et al.: Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science. 2005, 309 (5737): 1078-1083. 10.1126/science.1108876
Article
PubMed Central
PubMed
Google Scholar
Alon U: Network motifs: theory and experimental approaches. Nat Rev Genet. 2007, 8 (6): 450-461. 10.1038/nrg2102
Article
CAS
PubMed
Google Scholar
Stirewalt DL, Meshinchi S, Kopecky KJ, Fan W, Pogosova-Agadjanyan EL, Engel JH, Cronk MR, Dorcy KS, McQuary AR, Hockenbery D, et al.: Identification of genes with abnormal expression changes in acute myeloid leukemia. Genes, chromosomes & cancer. 2008, 47 (1): 8-20.
Article
CAS
Google Scholar
Yagi T, Morimoto A, Eguchi M, Hibi S, Sako M, Ishii E, Mizutani S, Imashuku S, Ohki M, Ichikawa H: Identification of a gene expression signature associated with pediatric AML prognosis. Blood. 2003, 102 (5): 1849-1856. 10.1182/blood-2003-02-0578
Article
CAS
PubMed
Google Scholar
Pau Ni IB, Zakaria Z, Muhammad R, Abdullah N, Ibrahim N, Aina Emran N, Hisham Abdullah N, Syed Hussain SN: Gene expression patterns distinguish breast carcinomas from normal breast tissues: the Malaysian context. Pathology, research and practice. 206 (4): 223-228.
Chen DT, Nasir A, Culhane A, Venkataramu C, Fulp W, Rubio R, Wang T, Agrawal D, McCarthy SM, Gruidl M: Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. Breast cancer research and treatment. 119 (2): 335-346.
Pyeon D, Newton MA, Lambert PF, den Boon JA, Sengupta S, Marsit CJ, Woodworth CD, Connor JP, Haugen TH, Smith EM, et al.: Fundamental differences in cell cycle deregulation in human papillomavirus-positive and human papillomavirus-negative head/neck and cervical cancers. Cancer research. 2007, 67 (10): 4605-4619. 10.1158/0008-5472.CAN-06-3619
Article
PubMed Central
CAS
PubMed
Google Scholar
Scotto L, Narayan G, Nandula SV, Arias-Pulido H, Subramaniyam S, Schneider A, Kaufmann AM, Wright JD, Pothuri B, Mansukhani M, et al.: Identification of copy number gain and overexpressed genes on chromosome arm 20q by an integrative genomic approach in cervical cancer: potential role in progression. Genes, chromosomes & cancer. 2008, 47 (9): 755-765.
Article
CAS
Google Scholar
Sun L, Hui AM, Su Q, Vortmeyer A, Kotliarov Y, Pastorino S, Passaniti A, Menon J, Walling J, Bailey R, et al.: Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer cell. 2006, 9 (4): 287-300. 10.1016/j.ccr.2006.03.003
Article
CAS
PubMed
Google Scholar
Kuriakose MA, Chen WT, He ZM, Sikora AG, Zhang P, Zhang ZY, Qiu WL, Hsu DF, McMunn-Coffran C, Brown SM, et al.: Selection and validation of differentially expressed genes in head and neck cancer. Cell Mol Life Sci. 2004, 61 (11): 1372-1383. 10.1007/s00018-004-4069-0
Article
CAS
PubMed
Google Scholar
Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, 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 (24): 13790-13795. 10.1073/pnas.191502998
Article
PubMed Central
CAS
PubMed
Google Scholar
Su LJ, Chang CW, Wu YC, Chen KC, Lin CJ, Liang SC, Lin CH, Whang-Peng J, Hsu SL, Chen CH, et al.: Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC genomics. 2007, 8: 140- 10.1186/1471-2164-8-140
Article
PubMed Central
CAS
PubMed
Google Scholar
Estilo CL, P Oc, Talbot S, Socci ND, Carlson DL, Ghossein R, Williams T, Yonekawa Y, Ramanathan Y, Boyle JO, et al.: Oral tongue cancer gene expression profiling: Identification of novel potential prognosticators by oligonucleotide microarray analysis. BMC cancer. 2009, 9: 11- 10.1186/1471-2407-9-11
Article
PubMed Central
PubMed
Google Scholar
Ye H, Yu T, Temam S, Ziober BL, Wang J, Schwartz JL, Mao L, Wong DT, Zhou X: Transcriptomic dissection of tongue squamous cell carcinoma. BMC genomics. 2008, 9: 69- 10.1186/1471-2164-9-69
Article
PubMed Central
PubMed
Google Scholar
Badea L, Herlea V, Dima SO, Dumitrascu T, Popescu I: Combined gene expression analysis of whole-tissue and microdissected pancreatic ductal adenocarcinoma identifies genes specifically overexpressed in tumor epithelia. Hepato-gastroenterology. 2008, 55 (88): 2016-2027.
CAS
PubMed
Google Scholar
Pei H, Li L, Fridley BL, Jenkins GD, Kalari KR, Lingle W, Petersen G, Lou Z, Wang L: FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt. Cancer cell. 2009, 16 (3): 259-266. 10.1016/j.ccr.2009.07.016
Article
PubMed Central
CAS
PubMed
Google Scholar
Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D'Amico AV, Richie JP, et al.: Gene expression correlates of clinical prostate cancer behavior. Cancer cell. 2002, 1 (2): 203-209. 10.1016/S1535-6108(02)00030-2
Article
CAS
PubMed
Google Scholar
Jones J, Otu H, Spentzos D, Kolia S, Inan M, Beecken WD, Fellbaum C, Gu X, Joseph M, Pantuck AJ, et al.: Gene signatures of progression and metastasis in renal cell cancer. Clin Cancer Res. 2005, 11 (16): 5730-5739. 10.1158/1078-0432.CCR-04-2225
Article
CAS
PubMed
Google Scholar
Yusenko MV, Kuiper RP, Boethe T, Ljungberg B, van Kessel AG, Kovacs G: High-resolution DNA copy number and gene expression analyses distinguish chromophobe renal cell carcinomas and renal oncocytomas. BMC cancer. 2009, 9: 152- 10.1186/1471-2407-9-152
Article
PubMed Central
PubMed
Google Scholar
Santegoets LA, Seters M, Helmerhorst TJ, Heijmans-Antonissen C, Hanifi-Moghaddam P, Ewing PC, van Ijcken WF, van der Spek PJ, van der Meijden WI, Blok LJ: HPV related VIN: highly proliferative and diminished responsiveness to extracellular signals. International journal of cancer. 2007, 121 (4): 759-766. 10.1002/ijc.22769.
Article
CAS
Google Scholar
Huber W, von Heydebreck A, Sueltmann H, Poustka A, Vingron M: Parameter estimation for the calibration and variance stabilization of microarray data. Statistical applications in genetics and molecular biology. 2003, 2: Article 3
Google Scholar
Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (Oxford, England). 2002, 18 (Suppl 1): S96-104.
Article
Google Scholar
Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A: BioMart Central Portal--unified access to biological data. Nucleic Acids Res. 2009, W23-27. 37 Web Server
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556
Article
PubMed Central
CAS
PubMed
Google Scholar
Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, et al.: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic acids research. 2003, 31 (1): 374-378. 10.1093/nar/gkg108
Article
PubMed Central
CAS
PubMed
Google Scholar
Cormen TH, Leiserson CE, Rivest RL: Introduction to algorithms. 1995, New York: McGraw-Hill
Google Scholar
Newman MEJ: Power laws, Pareto distributions and Zipf's law. Contemporary Physics. 2006, 46 (5): 323-351. 10.1080/00107510500052444.
Article
Google Scholar