Estimating developmental states of tumors and normal tissues using a linear time-ordered model

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Zhang, Bo ^a,b   Chen, Beibei ^a,b   Wu, Tao ^a   Xuan, Zhenyu ^c   Zhu, Xiaopeng ^a   Chen, Runsheng ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; DEVELOPMENT PROCESS; DEVELOPMENT STAGES; EMBRYONIC DEVELOPMENT; EXPRESSION PROFILE; SEQUENCE OF EVENTS; STEM CELL DIFFERENTIATION; TUMORIGENESIS PROCESS;

GENE EXPRESSION; HISTOLOGY; STEM CELLS; TUMORS; VECTOR SPACES;

CYTOLOGY;

ANIMAL; ARTICLE; FEMALE; GENE EXPRESSION PROFILING; GENETICS; HUMAN; LIVER; LIVER TUMOR; LUNG; METABOLISM; METHODOLOGY; MOUSE; NEOPLASM; OVARY; OVARY TUMOR; PATHOLOGY; PRENATAL DEVELOPMENT; PRINCIPAL COMPONENT ANALYSIS; STATISTICAL MODEL; TIME; TUMOR GENE;

ANIMALS; FEMALE; GENE EXPRESSION PROFILING; GENES, NEOPLASM; HUMANS; LINEAR MODELS; LIVER; LIVER NEOPLASMS; LUNG; MICE; NEOPLASMS; OVARIAN NEOPLASMS; OVARY; PRINCIPAL COMPONENT ANALYSIS; TIME FACTORS;

EID: 79751535010     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-53     Document Type: Article

References (40)

1. Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev 2004, 18(6):629-640. 10.1101/gad.1182504, 387239, 15075291.
2. Lepourcelet M, Tou L, Cai L, Sawada J, Lazar AJ, Glickman JN, Williamson JA, Everett AD, Redston M, Fox EA, Nakatani Y, Shivdasani RA. Insights into developmental mechanisms and cancers in the mammalian intestine derived from serial analysis of gene expression and study of the hepatoma-derived growth factor (HDGF). Development 2005, 132(2):415-427. 10.1242/dev.01579, 15604097.
3. Quackenbush J. Microarray analysis and tumor classification. N Engl J Med 2006, 354(23):2463-2472. 10.1056/NEJMra042342, 16760446.
4. Kauffman S. Differentiation of malignant to benign cells. J Theor Biol 1971, 31(3):429-451. 10.1016/0022-5193(71)90020-8, 5556142.
5. Foster DV, Foster JG, Huang S, Kauffman SA. A model of sequential branching in hierarchical cell fate determination. J Theor Biol 2009, 260(4):589-597. 10.1016/j.jtbi.2009.07.005, 19615382.
6. Huang S, Guo YP, May G, Enver T. Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. Dev Biol 2007, 305(2):695-713. 10.1016/j.ydbio.2007.02.036, 17412320.
7. Huang AC, Hu L, Kauffman SA, Zhang W, Shmulevich I. Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Syst Biol 2009, 3:20. 10.1186/1752-0509-3-20, 2652435, 19222862.
8. Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 2008, 453(7194):544-547. 10.1038/nature06965, 18497826.
9. Huang S, Eichler G, Bar-Yam Y, Ingber DE. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys Rev Lett 2005, 94(12):128701. 10.1103/PhysRevLett.94.128701, 15903968.
10. Mar JC, Quackenbush J. Decomposition of gene expression state space trajectories. PLoS Comput Biol 2009, 5(12):e1000626. 10.1371/journal.pcbi.1000626, 2791157, 20041215.
11. Kauffman S. A proposal for using the ensemble approach to understand genetic regulatory networks. J Theor Biol 2004, 230(4):581-590. 10.1016/j.jtbi.2003.12.017, 15363677.
12. Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 2000, 97(18):10101-10106. 10.1073/pnas.97.18.10101, 27718, 10963673.
13. Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV. Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci USA 2000, 97(15):8409-8414. 10.1073/pnas.150242097, 26961, 10890920.
14. Jonnalagadda S, Srinivasan R. Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data. BMC Bioinformatics 2008, 9:267. 10.1186/1471-2105-9-267, 2435549, 18534040.
15. Ramoni MF, Sebastiani P, Kohane IS. Cluster analysis of gene expression dynamics. Proc Natl Acad Sci USA 2002, 99(14):9121-9126. 10.1073/pnas.132656399, 123104, 12082179.
16. Schliep A, Schonhuth A, Steinhoff C. Using hidden Markov models to analyze gene expression time course data. Bioinformatics 2003, 19(Suppl 1):i255-263. 10.1093/bioinformatics/btg1036, 12855468.
17. Xu XL, Olson JM, Zhao LP. A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model. Hum Mol Genet 2002, 11(17):1977-1985. 10.1093/hmg/11.17.1977, 12165559.
18. Fischer EA, Friedman MA, Markey MK. Empirical comparison of tests for differential expression on time-series microarray experiments. Genomics 2007, 89(4):460-470. 10.1016/j.ygeno.2006.10.008, 17188839.
19. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454(7205):766-770. 2896277, 18600261.
20. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462(7271):315-322. 10.1038/nature08514, 2857523, 19829295.
21. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordonez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2009,
22. Shah N, Sukumar S. The Hox genes and their roles in oncogenesis. Nat Rev Cancer 10(5):361-371. 10.1038/nrc2826, 20357775.
23. Krivtsov AV, Armstrong SA. MLL translocations, histone modifications and leukaemia stem-cell development. Nat Rev Cancer 2007, 7(11):823-833. 10.1038/nrc2253, 17957188.
24. Slany RK. The molecular biology of mixed lineage leukemia. Haematologica 2009, 94(7):984-993. 10.3324/haematol.2008.002436, 2704309, 19535349.
25. Li T, Huang J, Jiang Y, Zeng Y, He F, Zhang MQ, Han Z, Zhang X. Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics 2009, 93(3):235-242. 10.1016/j.ygeno.2008.10.006, 2995988, 19015022.
26. Small CL, Shima JE, Uzumcu M, Skinner MK, Griswold MD. Profiling gene expression during the differentiation and development of the murine embryonic gonad. Biol Reprod 2005, 72(2):492-501. 10.1095/biolreprod.104.033696, 15496517.
27. Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biol 2008, 9(7):R108. 10.1186/gb-2008-9-7-r108, 2530866, 18611264.
28. Otu HH, Naxerova K, Ho K, Can H, Nesbitt N, Libermann TA, Karp SJ. Restoration of liver mass after injury requires proliferative and not embryonic transcriptional patterns. J Biol Chem 2007, 282(15):11197-11204. 10.1074/jbc.M608441200, 17227769.
29. Khetchoumian K, Teletin M, Tisserand J, Mark M, Herquel B, Ignat M, Zucman-Rossi J, Cammas F, Lerouge T, Thibault C, Metzger D, Chambon P, Losson R. Loss of Trim24 (Tif1alpha) gene function confers oncogenic activity to retinoic acid receptor alpha. Nat Genet 2007, 39(12):1500-1506. 10.1038/ng.2007.15, 18026104.
30. Thomas RS, O'Connell TM, Pluta L, Wolfinger RD, Yang L, Page TJ. A comparison of transcriptomic and metabonomic technologies for identifying biomarkers predictive of two-year rodent cancer bioassays. Toxicol Sci 2007, 96(1):40-46. 10.1093/toxsci/kfl171, 17114358.
31. Pla P, Hirsch MR, Le Crom S, Reiprich S, Harley VR, Goridis C. Identification of Phox2b-regulated genes by expression profiling of cranial motoneuron precursors. Neural Dev 2008, 3:14. 10.1186/1749-8104-3-14, 2441621, 18565209.
32. Hendrix ND, Wu R, Kuick R, Schwartz DR, Fearon ER, Cho KR. Fibroblast growth factor 9 has oncogenic activity and is a downstream target of Wnt signaling in ovarian endometrioid adenocarcinomas. Cancer Res 2006, 66(3):1354-1362. 10.1158/0008-5472.CAN-05-3694, 16452189.
33. Rosen MB, Schmid JE, Das KP, Wood CR, Zehr RD, Lau C. Gene expression profiling in the liver and lung of perfluorooctane sulfonate-exposed mouse fetuses: comparison to changes induced by exposure to perfluorooctanoic acid. Reprod Toxicol 2009, 27(3-4):278-288. 10.1016/j.reprotox.2009.01.007, 19429403.
34. Thorrez L, Van Deun K, Tranchevent LC, Van Lommel L, Engelen K, Marchal K, Moreau Y, Van Mechelen I, Schuit F. Using ribosomal protein genes as reference: a tale of caution. PLoS One 2008, 3(3):e1854. 10.1371/journal.pone.0001854, 2267211, 18365009.
35. LaVaute TM, Yoo YD, Pankratz MT, Weick JP, Gerstner JR, Zhang SC. Regulation of neural specification from human embryonic stem cells by BMP and FGF. Stem Cells 2009, 27(8):1741-1749. 10.1002/stem.99, 2789116, 19544434.
36. Lu SJ, Hipp JA, Feng Q, Hipp JD, Lanza R, Atala A. GeneChip analysis of human embryonic stem cell differentiation into hemangioblasts: an in silico dissection of mixed phenotypes. Genome Biol 2007, 8(11):R240. 10.1186/gb-2007-8-11-r240, 2258184, 17999768.
37. Pollard SM, Yoshikawa K, Clarke ID, Danovi D, Stricker S, Russell R, Bayani J, Head R, Lee M, Bernstein M, Squire JA, Smith A, Dirks P. Glioma stem cell lines expanded in adherent culture have tumor-specific phenotypes and are suitable for chemical and genetic screens. Cell Stem Cell 2009, 4(6):568-580. 10.1016/j.stem.2009.03.014, 19497285.
38. Hever A, Roth RB, Hevezi P, Marin ME, Acosta JA, Acosta H, Rojas J, Herrera R, Grigoriadis D, White E, Conlon PJ, Maki RA, Zlotnik A. Human endometriosis is associated with plasma cells and overexpression of B lymphocyte stimulator. Proc Natl Acad Sci USA 2007, 104(30):12451-12456. 10.1073/pnas.0703451104, 1941489, 17640886.
39. Hong Y, Ho KS, Eu KW, Cheah PY. A susceptibility gene set for early onset colorectal cancer that integrates diverse signaling pathways: implication for tumorigenesis. Clin Cancer Res 2007, 13(4):1107-1114. 10.1158/1078-0432.CCR-06-1633, 17317818.
40. Turashvili G, Bouchal J, Baumforth K, Wei W, Dziechciarkova M, Ehrmann J, Klein J, Fridman E, Skarda J, Srovnal J, Hajduch M, Murray P, Kolar Z. Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis. BMC Cancer 2007, 7:55. 10.1186/1471-2407-7-55, 1852112, 17389037.