Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000, 403 (6769): 503-511. 10.1038/35000501.
Article
PubMed
CAS
Google Scholar
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA: Molecular classification of cancer class discovery and class prediction by gene expression monitoring. Science. 1999, 286 (5439): 531-537. 10.1126/science.286.5439.531.
Article
PubMed
CAS
Google Scholar
van de Vijver MJ, He YD, van’t Veer LJ, Dai H, Hart AAM, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med. 2002, 347 (25): 1999-2009. 10.1056/NEJMoa021967.
Article
PubMed
CAS
Google Scholar
Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim CJ, Kusanovic JP, Romero R, Kim Js: A novel signaling pathway impact analysis. Bioinformatics. 2009, 25: 75-82. 10.1093/bioinformatics/btn577.
Article
PubMed Central
PubMed
CAS
Google Scholar
Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM: Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010, 26 (12): i237-i245. 10.1093/bioinformatics/btq182.
Article
PubMed Central
PubMed
CAS
Google Scholar
Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002, 18 (Suppl 1): S233-S240. 10.1093/bioinformatics/18.suppl_1.S233.
Article
PubMed
Google Scholar
Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T: Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics. 2008, 24 (13): i223-i231. 10.1093/bioinformatics/btn161.
Article
PubMed Central
PubMed
CAS
Google Scholar
Kanehisa M, Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28: 27-30. 10.1093/nar/28.1.27.
Article
PubMed Central
PubMed
CAS
Google Scholar
Mitra K, Carvunis AR, Ramesh SK, Ideker T: Integrative approaches for finding modular structure in biological networks. Nat Rev Genet. 2013, 14 (10): 719-732. 10.1038/nrg3552.
Article
PubMed Central
PubMed
CAS
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: 25-29. 10.1038/75556.
Article
PubMed Central
PubMed
CAS
Google Scholar
Battista G, Eades P, Tamassia R, Tollis I: Graph drawing: algorithms for the visualization of graphs. 1998, Upper Saddle River, NJ, USA: Prentice Hall PTR
Google Scholar
Herman I, Melançon G, Marshall MS: Graph visualization and navigation in information visualization: A survey. IEEE Trans Vis Comput Graph. 2000, 6: 24-43. 10.1109/2945.841119.
Article
Google Scholar
von Landesberger T, Kuijper A, Schreck T, Kohlhammer J, van Wijk J, Fekete JD, Fellner D: Visual analysis of large graphs: state-of-the-art and future research challenges. Comput Graph Forum. 2011, 30 (6): 1719-1749. 10.1111/j.1467-8659.2011.01898.x.
Article
Google Scholar
Gehlenborg N, O’Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC: Visualization of omics data for systems biology. Nat Methods. 2010, 7 (3s): S56-S68. 10.1038/nmeth.1436.
Article
PubMed
CAS
Google Scholar
Smooth ME, Ono K, Ruscheinski J, Wang PL, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011, 27 (3): 431-432. 10.1093/bioinformatics/btq675.
Article
Google Scholar
van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C: Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008, 9: 399-10.1186/1471-2105-9-399.
Article
PubMed Central
PubMed
Google Scholar
Venn and Euler diagrams. http://apps.cytoscape.org/apps/vennandeulerdiagrams.,
RBVI Cytoscape Plugins – Cytoscape group support. http://www.rbvi.ucsf.edu/cytoscape/groups.,
Bertault F, Eades P: Drawing Hypergraphs in the subset standard. Proceedings of the 8th International Symposium on Graph Drawing, Volume 1984 of Lecture Notes in Computer Science. 2001, Berlin, Heidelberg: Springer, 164-169.
Google Scholar
Simonetto P, Auber D, Archambault D: Fully automatic visualisation of overlapping sets. Comput Graph Forum. 2009, 28 (3): 967-974. 10.1111/j.1467-8659.2009.01452.x.
Article
Google Scholar
Riche N, Dwyer T: Untangling Euler diagrams. IEEE Trans Vis Comput Graph. 2010, 16 (6): 1090-1099.
Article
PubMed
Google Scholar
Alper B, Riche N, Ramos G, Czerwinski M: Design Study of LineSets, a Novel Set Visualization Technique. IEEE Trans Vis Comput Graph. 2011, 17 (12): 2259-2267.
Article
PubMed
Google Scholar
Dinkla K, van Kreveld M, Speckmann B, Westenberg M: Kelp Diagrams Point Set Membership Visualization. Comput Graph Forum. 2012, 31 (3): 875-884.
Article
Google Scholar
Collins C, Penn G, Carpendale S: Bubble Sets: revealing set relations with Isocontours over existing visualizations. IEEE Trans Vis Comput Graph. 2009, 15 (6): 1009-1016.
Article
PubMed
Google Scholar
Smith AM, Xu W, Sun Y, Faeder JR, Marai GE: RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. BMC Bioinformatics. 2012, 13 (Suppl 8): S3-10.1186/1471-2105-13-S8-S3.
Article
PubMed Central
PubMed
Google Scholar
Meulemans W, Riche NH, Speckmann B, Alper B, Dwyer T: KelpFusion: A Hybrid Set Visualization Technique. IEEE Trans Vis Comput Graph. 2013, 19 (11): 1846-1858.
Article
PubMed
Google Scholar
Sugiyama K, Misue K: Visualization of structural information: automatic drawing of compound digraphs. IEEE Trans Syst Man Cybernet. 1991, 21 (4): 876-892. 10.1109/21.108304.
Article
Google Scholar
Shneiderman B, Aris A: Network visualization by semantic substrates. IEEE Trans Vis Comput Graph. 2006, 12 (5): 733-740.
Article
PubMed
Google Scholar
Barsky A, Munzner T, Gardy J, Kincaid R: Cerebral: visualizing multiple experimental conditions on a graph with biological context. IEEE Trans Vis Comput Graph. 2008, 14 (6): 1253-1260.
Article
PubMed
Google Scholar
Dwyer T, Marriott K, Schreiber F, Stuckey P, Woodward M, Wybrow M: Exploration of networks using overview+detail with constraint-based cooperative layout. IEEE Trans Vis Comput Graph. 2008, 14 (6): 1293-1300.
Article
PubMed
Google Scholar
Gansner ER, Hu Y, Kobourov S: GMap: Visualizing graphs and clusters as maps. Pacific Visualization Symposium (PacificVis). 2010, IEEE, 201-208.
Chapter
Google Scholar
Fruchterman T, Reingold E: Graph drawing by force-directed placement. Softw: Practice Exper. 1991, 21 (11): 1129-1164. 10.1002/spe.4380211102.
Google Scholar
Dwyer T, Marriott K, Stuckey P: Fast node overlap removal. Graph Drawing, Volume 3843 of Lecture Notes in Computer Science. 2006, Berlin, Germany: Springer Berlin Heidelberg, 153-164.
Google Scholar
Kohonen T: The self-organizing map. Proc IEEE. 1990, 78 (9): 1464-1480. 10.1109/5.58325.
Article
Google Scholar
Vesanto J: SOM-based data visualization methods. Intell Data Anal. 1999, 3 (2): 111-126. 10.1016/S1088-467X(99)00013-X.
Article
Google Scholar
MacCallum R, Redmond S, Christophides G: An expression map for Anopheles gambiae. BMC Genomics. 2011, 12: 620-10.1186/1471-2164-12-620.
Article
PubMed Central
PubMed
CAS
Google Scholar
Frishman Y, Tal A: Online dynamic graph drawing. IEEE Trans Vis Comput Graph. 2008, 14 (4): 727-740.
Article
PubMed
Google Scholar
de Berg M, Cheong O, van Kreveld M, Overmars M: Computational Geometry: Algorithms and Applications. 2008, Berlin, Heidelberg: Springer
Book
Google Scholar
Vivid Solutions: Java topology suite. http://www.vividsolutions.com/jts 2003,
Harrower M, Brewer C: ColorBrewer.org: An Online Tool for Selecting Colour Schemes for Maps. 2011, Chichester, UK: John Wiley & Sons, Ltd
Google Scholar
Gandhi MK, Khanna R: Human cytomegalovirus: clinical aspects, immune regulation, and emerging treatments. Lancet Infect Dis. 2004, 4 (12): 725-738. 10.1016/S1473-3099(04)01202-2.
Article
PubMed
CAS
Google Scholar
Söderberg-Nauclér C: Does cytomegalovirus play a causative role in the development of various inflammatory diseases and cancer?. J Intern Med. 2006, 259 (3): 219-246. 10.1111/j.1365-2796.2006.01618.x.
Article
PubMed
Google Scholar
Cobbs CS, Harkins L, Samanta M, Gillespie GY, Bharara S, King PH, Nabors LB, Cobbs CG, Britt WJ: Human cytomegalovirus infection and expression in human malignant glioma. Cancer Res. 2002, 62 (12): 3347-3350.
PubMed
CAS
Google Scholar
Harkins L, Volk AL, Samanta M, Mikolaenko I, Britt WJ, Bland KI, Cobbs CS: Specific localisation of human cytomegalovirus nucleic acids and proteins in human colorectal cancer. Lancet. 2002, 360 (9345): 1557-1563. 10.1016/S0140-6736(02)11524-8.
Article
PubMed
CAS
Google Scholar
JU V, H WD, Cinatl JJ: Oncomodulatory signals by regulatory proteins encoded by human cytomegalovirus: a novel role for viral infection in tumor progression. FEMS Microbiol Rev. 2004, 28: 59-77. 10.1016/j.femsre.2003.07.005.
Article
Google Scholar
Randolph-Habecker J, Rahill B, Torok-Storb B, Vieira J, Kolattukudy PE, Rovin BH, Sedmak DD: The expression of the cytomegalovirus chemokine receptor homolog US28 sequesters biologically active CC chemokines and alters IL-8 production. Cytokine. 2002, 19: 37-46. 10.1006/cyto.2002.0874.
Article
PubMed
CAS
Google Scholar
Casarosa P, Bakker RA, Verzijl D, Navis M, Timmerman H, Leurs R, Smit MJ: Constitutive signaling of the human cytomegalovirus-encoded Chemokine receptor US28. J Biol Chem. 2001, 276 (2): 1133-1137. 10.1074/jbc.M008965200.
Article
PubMed
CAS
Google Scholar
Maussang D, Verzijl D, van Walsum M, Leurs R, Holl J, Pleskoff O, Michel D, van Dongen GAMS, Smit MJ: Human cytomegalovirus-encoded chemokine receptor US28 promotes tumorigenesis. Proc Nat Acad Sci. 2006, 103 (35): 13068-13073. 10.1073/pnas.0604433103.
Article
PubMed Central
PubMed
CAS
Google Scholar
Maussang D, Langemeijer E, Fitzsimons CP, Stigter-van Walsum M, Dijkman R, Borg MK, Slinger E, Schreiber A, Michel D, Tensen CP, van Dongen GA, Leurs R, Smit MJ: The human cytomegalovirus-encoded Chemokine receptor US28 promotes angiogenesis and tumor formation via Cyclooxygenase-2. Cancer Res. 2009, 69 (7): 2861-2869. 10.1158/0008-5472.CAN-08-2487.
Article
PubMed
CAS
Google Scholar
Slinger E, Maussang D, Schreiber A, Siderius M, Rahbar A, Fraile-Ramos A, Lira SA, Soderberg-Naucler C, Smit MJ: HCMV-Encoded Chemokine Receptor US28 mediates proliferative signaling through the IL-6-STAT3 axis. Sci Signal. 2010, 3 (133): ra58-10.1126/scisignal.2001180.
Article
PubMed
Google Scholar
Langemeijer EV, Slinger E, de Munnik S, Schreiber A, Maussang D, Vischer H, Verkaar F, Leurs R, Siderius M, Smit MJ: Constitutiveβ-Catenin signaling by the viral Chemokine receptor US28. PLoS ONE. 2012, 7 (11): e48935-10.1371/journal.pone.0048935.
Article
PubMed Central
PubMed
CAS
Google Scholar
Gautier L, Cope L, Bolstad BM, Irizarry RA: affy—analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004, 20 (3): 307-315. 10.1093/bioinformatics/btg405.
Article
PubMed
CAS
Google Scholar
Smyth G: limma: linear models for microarray data. Bioinformatics And Computational Biology Solutions Using R and Bioconductor, Statistics for Biology and Health. Edited by: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S. 2005, New York, NY, USA: Springer New York, 397-420.
Chapter
Google Scholar
Alexa A, Rahnenfuhrer J, Lengauer T: Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006, 22 (13): 1600-1607. 10.1093/bioinformatics/btl140.
Article
PubMed
CAS
Google Scholar
Minisini R, Tulone C, Lüske A, Michel D, Mertens T, Gierschik P, Moepps B: Constitutive inositol phosphate formation in cytomegalovirus-infected human fibroblasts is due to expression of the chemokine receptor homologue pUS28. J Virol. 2003, 77 (8): 4489-4501. 10.1128/JVI.77.8.4489-4501.2003.
Article
PubMed Central
PubMed
CAS
Google Scholar
Zhurinsky J, Shtutman M, Ben-Ze’ev A: Differential mechanisms of LEF/TCF family-dependent transcriptional activation byβ-Catenin and Plakoglobin. Mol Cell Biol. 2000, 20 (12): 4238-4252. 10.1128/MCB.20.12.4238-4252.2000.
Article
PubMed Central
PubMed
CAS
Google Scholar
Streblow DN, Soderberg-Naucler C, Vieira J, Smith P, Wakabayashi E, Ruchti F, Mattison K, Altschuler Y, Nelson JA: The human cytomegalovirus chemokine receptor US28 mediates vascular smooth muscle cell migration. Cell. 1999, 99 (5): 511-520. 10.1016/S0092-8674(00)81539-1.
Article
PubMed
CAS
Google Scholar
Streblow DN, Vomaske J, Smith P, Melnychuk R, Hall L, Pancheva D, Smit M, Casarosa P, Schlaepfer DD, Nelson JA: Human Cytomegalovirus Chemokine receptor US28-induced smooth muscle cell migration is mediated by focal adhesion kinase and Src. J Biol Chem. 2003, 278 (50): 50456-50465. 10.1074/jbc.M307936200.
Article
PubMed
CAS
Google Scholar
Herynk MH, Tsan R, Radinsky R, Gallick GE: Activation of c-Met in colorectal carcinoma cells leads to constitutive association of tyrosine-phosphorylatedβ-catenin. Clin & Exp Metastasis. 2003, 20 (4): 291-300. 10.1023/A:1024024218529.
Article
CAS
Google Scholar
Purcell R, Childs M, Maibach R, Miles C, Turner C, Zimmermann A, Sullivan M: HGF/c-Met related activation of beta-catenin in hepatoblastoma. J Exp & Clin Cancer Res. 2011, 30: 96-10.1186/1756-9966-30-96.
Article
CAS
Google Scholar