Liu ET: Classification of cancers by expression profiling. Curr Opin Genet Dev. 2003, 13 (1): 97-103. 10.1016/S0959-437X(03)00008-X.
Article
CAS
PubMed
Google Scholar
Sancho E, Batlle E, Clevers H: Signaling pathways in intestinal development and cancer. Annu Rev Cell Dev Biol. 2004, 20: 695-723. 10.1146/annurev.cellbio.20.010403.092805.
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
Khalil IG, Hill C: Systems biology for cancer. Curr Opin Oncol. 2005, 17 (1): 44-48. 10.1097/01.cco.0000150951.38222.16.
Article
CAS
PubMed
Google Scholar
Kitano H: Cancer as a robust system: implications for anticancer therapy. Nat Rev Cancer. 2004, 4 (3): 227-235. 10.1038/nrc1300.
Article
CAS
PubMed
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
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Barrette TR, Ghosh D, Chinnaiyan AM: Mining for regulatory programs in the cancer transcriptome. Nat Genet. 2005, 37 (6): 579-583. 10.1038/ng1578.
Article
CAS
PubMed
Google Scholar
Segal E, Friedman N, Koller D, Regev A: A module map showing conditional activity of expression modules in cancer. Nat Genet. 2004, 36 (10): 1090-1098.
Article
CAS
PubMed
Google Scholar
Rhodes DR, Chinnaiyan AM: Integrative analysis of the cancer transcriptome. Nat Genet. 2005, 37 Suppl: S31-7. 10.1038/ng1570.
Article
PubMed
Google Scholar
Wachi S, Yoneda K, Wu R: Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics. 2005, 21 (23): 4205-4208. 10.1093/bioinformatics/bti688.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jonsson PF, Bates PA: Global topological features of cancer proteins in the human interactome. Bioinformatics. 2006, 22 (18): 2291-2297. 10.1093/bioinformatics/btl390.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A: Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet. 2006, 38 (3): 285-293. 10.1038/ng1747.
Article
CAS
PubMed
Google Scholar
Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A: Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 2004, 32 (Database issue): D497-501. 10.1093/nar/gkh070.
Article
CAS
PubMed Central
PubMed
Google Scholar
Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D'Amico AV, Richie JP, Lander ES, Loda M, Kantoff PW, Golub TR, Sellers WR: 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
Stuart RO, Wachsman W, Berry CC, Wang-Rodriguez J, Wasserman L, Klacansky I, Masys D, Arden K, Goodison S, McClelland M, Wang Y, Sawyers A, Kalcheva I, Tarin D, Mercola D: In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci U S A. 2004, 101 (2): 615-620. 10.1073/pnas.2536479100.
Article
CAS
PubMed Central
PubMed
Google Scholar
Notterman DA, Alon U, Sierk AJ, Levine AJ: Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays. Cancer Res. 2001, 61 (7): 3124-3130.
CAS
PubMed
Google Scholar
Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M: Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A. 2001, 98 (24): 13790-13795. 10.1073/pnas.191502998.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM: ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004, 6 (1): 1-6.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mathivanan S, Periaswamy B, Gandhi TK, Kandasamy K, Suresh S, Mohmood R, Ramachandra YL, Pandey A: An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics. 2006, 7 Suppl 5: S19-10.1186/1471-2105-7-S5-S19.
Article
PubMed
Google Scholar
Futschik ME, Chaurasia G, Herzel H: Comparison of human protein-protein interaction maps. Bioinformatics. 2007, 23 (5): 605-611. 10.1093/bioinformatics/btl683.
Article
CAS
PubMed
Google Scholar
Jonsson PF, Cavanna T, Zicha D, Bates PA: Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinformatics. 2006, 7: 2-10.1186/1471-2105-7-2.
Article
PubMed Central
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
Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature. 2001, 411 (6833): 41-42. 10.1038/35075138.
Article
CAS
PubMed
Google Scholar
Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M: Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 2004, 430 (6995): 88-93. 10.1038/nature02555.
Article
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006, 34 (Database issue): D354-7. 10.1093/nar/gkj102.
Article
CAS
PubMed Central
PubMed
Google Scholar
Papatsoris AG, Karamouzis MV, Papavassiliou AG: Novel insights into the implication of the IGF-1 network in prostate cancer. Trends Mol Med. 2005, 11 (2): 52-55. 10.1016/j.molmed.2004.12.005.
Article
CAS
PubMed
Google Scholar
Gonzalez-Guerrico AM, Meshki J, Xiao L, Benavides F, Conti CJ, Kazanietz MG: Molecular mechanisms of protein kinase C-induced apoptosis in prostate cancer cells. J Biochem Mol Biol. 2005, 38 (6): 639-645.
Article
CAS
PubMed
Google Scholar
Mika S, Rost B: Protein-protein interactions more conserved within species than across species. PLoS Comput Biol. 2006, 2 (7): e79-10.1371/journal.pcbi.0020079.
Article
PubMed Central
PubMed
Google Scholar
Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M: Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 2001, 11 (12): 2120-2126. 10.1101/gr.205301.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M: Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 2004, 14 (6): 1107-1118. 10.1101/gr.1774904.
Article
CAS
PubMed Central
PubMed
Google Scholar
Brown KR, Jurisica I: Online predicted human interaction database. Bioinformatics. 2005, 21 (9): 2076-2082. 10.1093/bioinformatics/bti273.
Article
CAS
PubMed
Google Scholar
Lehner B, Fraser AG: A first-draft human protein-interaction map. Genome Biol. 2004, 5 (9): R63-10.1186/gb-2004-5-9-r63.
Article
PubMed Central
PubMed
Google Scholar
Han JD, Dupuy D, Bertin N, Cusick ME, Vidal M: Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol. 2005, 23 (7): 839-844. 10.1038/nbt1116.
Article
CAS
PubMed
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13 (11): 2498-2504. 10.1101/gr.1239303.
Article
CAS
PubMed Central
PubMed
Google Scholar
[http://www.analytictech.com/ucinet]
Montaner D, Tarraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MA, Alloza E, Herrero J, Al-Shahrour F, Dopazo J: Next station in microarray data analysis: GEPAS. Nucleic Acids Res. 2006, 34 (Web Server issue): W486-91. 10.1093/nar/gkl197.
Article
CAS
PubMed Central
PubMed
Google Scholar
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31 (4): e15-10.1093/nar/gng015.
Article
PubMed Central
PubMed
Google Scholar
Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J: BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 2005, 33 (Web Server issue): W460-4. 10.1093/nar/gki456.
Article
CAS
PubMed Central
PubMed
Google Scholar
Freeman LC: A set of measures of centrality based on betweenness. Sociometry. 1977, 40: 35-10.2307/3033543.
Article
Google Scholar
Sabidussi G: The centrality of a graph. Psychometrika. 1966, 31 (4): 581-603. 10.1007/BF02289527.
Article
CAS
PubMed
Google Scholar
Burt RS: Structural Holes: The social structure of competition. 1992, Cambridge , Harvard University Press
Google Scholar
Bron C, Kerbosch J: Finding all cliques of an undirected graph. Commun ACM. 1973, 16 (9): 575-577. 10.1145/362342.362367.
Article
Google Scholar
Luce R, Perry A: A method of matrix analysis of group structure. Psychometrika. 1949, 14: 95-116. 10.1007/BF02289146.
Article
CAS
PubMed
Google Scholar
Website title [www.r-project.org].
Al-Shahrour F, Diaz-Uriarte R, Dopazo J: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004, 20 (4): 578-580. 10.1093/bioinformatics/btg455.
Article
CAS
PubMed
Google Scholar