Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction

BMC Genomics

Volumn 11, Issue SUPPL. 1, 2010, Pages

  Mlecnik, Bernhard ^a,b   Sanchez Cabo, Fatima ^a,c   Charoentong, Pornpimol ^a   Bindea, Gabriela ^a,b   Pagès, Franck ^b,d   Berger, Anne ^d   Galon, Jerome ^b,d   Trajanoski, Zlatko ^a  

^a GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^b INSERM   (France)

^c CENTRO NACIONAL DE INVESTIGACIONES CARDIOVASCULARES CNIC   (Spain)

^d HÔPITAL EUROPÉEN GEORGES POMPIDOU   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; CANCER GROWTH; CANCER IMMUNOLOGY; CELL INTERACTION; DATA BASE; FLOW CYTOMETRY; GENE CLUSTER; GENETIC ANALYSIS; GENETIC ENGINEERING AND GENE TECHNOLOGY; HUMAN; IMMUNOHISTOCHEMISTRY; INFORMATION RETRIEVAL; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MICROSATELLITE INSTABILITY; MOLECULAR DYNAMICS; SUPPORT VECTOR MACHINE; SURVIVAL; BIOLOGY; BIOMETRY; COMPUTER PROGRAM; FACTUAL DATABASE; IMMUNOLOGY; METHODOLOGY; NEOPLASM; SURVIVAL RATE;

BIOMETRY; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HUMANS; NEOPLASMS; SOFTWARE DESIGN; SURVIVAL RATE;

EID: 76849100580     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-S1-S7     Document Type: Article

References (44)

1. Steeg PS, Ouatas T, Halverson D, Palmieri D, Salerno M. Metastasis suppressor genes: basic biology and potential clinical use. Clin Breast Cancer 2003, 4:51-62. 10.3816/CBC.2003.n.012, 12744759.
2. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000, 100:57-70. 10.1016/S0092-8674(00)81683-9, 10647931.
3. Parkin DM, Bray F, Ferlay J, Pisani P. Global cancer statistics, 2002. CA Cancer J Clin 2005, 55:74-108. 10.3322/canjclin.55.2.74, 15761078.
4. Sobin LWC. TNM classification of malignant timors 2000, Wiley-Liss.
5. Locker GY, S H, J H, J J, N K, J M, M S, D H, RJ B, . ASCO: ASCO 2006 update of recommendations for the use of tumor markers in gastrointestinal cancer. J Clin Oncol 2009, 24:5313-5327. ASCO.
6. Benson AB, Schrag D, Somerfield MR, Cohen AM, Figueredo AT, Flynn PJ, Krzyzanowska MK, Maroun J, McAllister P, Van Cutsem E, et al. American Society of Clinical Oncology recommendations on adjuvant chemotherapy for stage II colon cancer. J Clin Oncol 2004, 22:3408-3419. 10.1200/JCO.2004.05.063, 15199089.
7. Dalerba P, Maccalli C, Casati C, Castelli C, Parmiani G. Immunology and immunotherapy of colorectal cancer. Crit Rev Oncol Hematol 2003, 46:33-57. 10.1016/S1040-8428(02)00159-2, 12672517.
8. Atreya I, Neurath MF. Immune cells in colorectal cancer: prognostic relevance and therapeutic strategies. Expert Rev Anticancer Ther 2008, 8:561-572. 10.1586/14737140.8.4.561, 18402523.
9. Galon J, Costes A, Sanchez-Cabo F, Kirilovsky A, Mlecnik B, Lagorce-Pages C, Tosolini M, Camus M, Berger A, Wind P, et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science 2006, 313:1960-1964. 10.1126/science.1129139, 17008531.
10. Pages F, Berger A, Camus M, Sanchez-Cabo F, Costes A, Molidor R, Mlecnik B, Kirilovsky A, Nilsson M, Damotte D, et al. Effector memory T cells, early metastasis, and survival in colorectal cancer. N Engl J Med 2005, 353:2654-2666. 10.1056/NEJMoa051424, 16371631.
11. Galon J, Fridman WH, Pages F. The adaptive immunologic microenvironment in colorectal cancer: a novel perspective. Cancer Res 2007, 67:1883-1886. 10.1158/0008-5472.CAN-06-4806, 17332313.
12. Sturn A, Quackenbush J, Trajanoski Z. Genesis: cluster analysis of microarray data. Bioinformatics 2002, 18:207-208. 10.1093/bioinformatics/18.1.207, 11836235.
13. Harrel FE. Regression modeling strategies: with applications to Linear Models, Logistic Regression and Survival analysis 2001, Springer Series in Statistics.
14. Bland JM, Altman DG. The logrank test. BMJ 2004, 328:1073. 10.1136/bmj.328.7447.1073, 403858, 15117797.
15. http://www.r-project.org
16. http://rosuda.org/Rserve/
17. Altman DG, Royston P. The cost of dichotomising continuous variables. BMJ 2006, 332:1080. 10.1136/bmj.332.7549.1080, 1458573, 16675816.
18. Altman DG, Lausen B, Sauerbrei W, Schumacher M. Dangers of using "optimal" cutpoints in the evaluation of prognostic factors. J Natl Cancer Inst 1994, 86:829-835. 10.1093/jnci/86.11.829, 8182763.
19. Heinzl HTC. A cautionary note on segmenting a cyclical covariate by minimum P-value search. Computational Statistics & Data Analysis 2009, 35:451-461.
20. Faraggi D, Simon R. A simulation study of cross-validation for selecting an optimal cutpoint in univariate survival analysis. Stat Med 1996, 15:2203-2213. 10.1002/(SICI)1097-0258(19961030)15:20<2203::AID-SIM357>3.0.CO;2-G, 8910964.
21. Hollander N, Sauerbrei W, Schumacher M. Confidence intervals for the effect of a prognostic factor after selection of an 'optimal' cutpoint. Stat Med 2004, 23:1701-1713. 10.1002/sim.1611, 15160403.
22. Pittman J, Huang E, Nevins J, Wang Q, West M. Bayesian analysis of binary prediction tree models for retrospectively sampled outcomes. Biostatistics 2004, 5:587-601. 10.1093/biostatistics/kxh011, 15475421.
23. 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, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
24. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2:2366-2382. 10.1038/nprot.2007.324, 17947979.
25. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z, Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 2009, 25:1091-1093. 10.1093/bioinformatics/btp101, 2666812, 19237447.
26. Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T. GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics 2007, 23:394-396. 10.1093/bioinformatics/btl605, 17127678.
27. 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, 25:25-29. 10.1038/75556, 10802651.
28. Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, et al. A data integration methodology for systems biology. Proc Natl Acad Sci USA 2005, 102:17296-17301. 10.1073/pnas.0508647102, 1297682, 16301537.
29. Liang S, Fuhrman S, Somogyi R. Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 1998, 18-29.
30. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla FR, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006, 7(Suppl 1):S7. 10.1186/1471-2105-7-S1-S7, 1810318, 16723010.
31. von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res 2005, 33:D433-D437. 10.1093/nar/gki005, 539959, 15608232.
32. Anderson AR, Quaranta V. Integrative mathematical oncology. Nat Rev Cancer 2008, 8:227-234. 10.1038/nrc2329, 18273038.
33. Araujo RP, McElwain DL. A history of the study of solid tumour growth: the contribution of mathematical modelling. Bull Math Biol 2004, 66:1039-1091. 10.1016/j.bulm.2003.11.002, 15294418.
34. Kozusko F, Bourdeau M. A unified model of sigmoid tumour growth based on cell proliferation and quiescence. Cell Prolif 2007, 40:824-834. 10.1111/j.1365-2184.2007.00474.x, 18021173.
35. Macklin P, McDougall S, Anderson AR, Chaplain MA, Cristini V, Lowengrub J. Multiscale modelling and nonlinear simulation of vascular tumour growth. J Math Biol 2009, 58:765-798. 10.1007/s00285-008-0216-9, 18781303.
36. Roose T, Chapman SJ, Maini PK. Mathematical models of avascular tumor growth. Siam Review 2007, 49:179-208.
37. Anderson ACMRK. Single-Cell-Based Models in Biology and Medicine (Mathematics and Biosciences in Interaction) 2001, Birkhauser Basel, 1.
38. Beverley PC. Primer: making sense of T-cell memory. Nat Clin Pract Rheumatol 2008, 4:43-49. 10.1038/ncprheum0671, 18172448.
39. De Boer RJ, Oprea M, Antia R, Murali-Krishna K, Ahmed R, Perelson AS. Recruitment times, proliferation, and apoptosis rates during the CD8(+) T-cell response to lymphocytic choriomeningitis virus. J Virol 2001, 75:10663-10669. 10.1128/JVI.75.22.10663-10669.2001, 114648, 11602708.
40. De Boer RJ, Homann D, Perelson AS. Different dynamics of CD4+ and CD8+ T cell responses during and after acute lymphocytic choriomeningitis virus infection. J Immunol 2003, 171:3928-3935.
41. Antia R, Ganusov VV, Ahmed R. The role of models in understanding CD8+ T-cell memory. Nat Rev Immunol 2005, 5:101-111. 10.1038/nri1550, 15662368.
42. Kim PS, Lee PP, Levy D. Dynamics and potential impact of the immune response to chronic myelogenous leukemia. PLoS Comput Biol 2008, 4:e1000095. 10.1371/journal.pcbi.1000095, 2427197, 18566683.
43. Moore H, Li NK. A mathematical model for chronic myelogenous leukemia (CML) and T cell interaction. J Theor Biol 2004, 227:513-523. 10.1016/j.jtbi.2003.11.024, 15038986.
44. Eikenberry S, Thalhauser C, Kuang Y. Tumor-immune interaction, surgical treatment, and cancer recurrence in a mathematical model of melanoma. PLoS Comput Biol 2009, 5:e1000362. 10.1371/journal.pcbi.1000362, 2667258, 19390606.