Data driven linear algebraic methods for analysis of molecular pathways: Application to disease progression in shock/trauma

Journal of Biomedical Informatics

Volumn 45, Issue 2, 2012, Pages 372-387

  McGuire, Mary F ^a   Sriram Iyengar, M ^b   Mercer, David W ^c  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF TEXAS   (United States)

^c UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

Author keywords

Biomedical informatics; Hypothesis generation; Signaling pathways; Systems biology; Trauma

Indexed keywords

BIOMEDICAL INFORMATICS; HYPOTHESIS GENERATION; SIGNALING PATHWAYS; SYSTEMS BIOLOGY; TRAUMA;

ACTIVATION ANALYSIS; ALGEBRA; CROSSTALK; DISEASE CONTROL; JAVA PROGRAMMING LANGUAGE; MOLECULAR INTERACTIONS; MOLECULAR STRUCTURE; PATHOLOGY; SEMANTICS;

DIAGNOSIS;

ALGORITHM; ARTICLE; DISEASE COURSE; HUMAN; HYPOTHESIS; INJURY; MATHEMATICS; MOLECULAR INTERACTION; MULTIPLE ORGAN FAILURE; PATHWAY SEMANTICS ALGORITHM; PRIORITY JOURNAL; PROTEIN EXPRESSION; SEMANTICS; SHOCK; STATISTICAL ANALYSIS; TRANSCRIPTION REGULATION;

ALGORITHMS; DISEASE PROGRESSION; HUMANS; MULTIPLE ORGAN FAILURE; SEMANTICS; SHOCK, TRAUMATIC; SIGNAL TRANSDUCTION;

EID: 84858291334     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2011.12.002     Document Type: Article

References (82)

1. Kong X., Fang M., Fang F., Li P., Xu Y. PPAR-gamma enhances IFN-gamma-mediated transcription and rescues the TGf-beta antagonism by stimulating CIITA in vascular smooth muscle cells. J Mol Cell Cardiol 2009, 46:748-757. [PubMed: 19358337].
2. Tosi G., Bozzo L., Accolla R.S. The dual function of the MHC class II transactivator CIITA against HTLV retroviruses. Front Biosci 2009, 14:4149-4156. [PubMed: 19273341].
3. Santora R., Kozar R.A. Molecular mechanisms of pharmaconutrients. J Surg Res 2009, [PubMed20080249].
4. McQuiggan M., Kozar R., Sailors R.M., Ahn C., McKinley B., Moore F. Enteral glutamine during active shock resuscitation is safe and enhances tolerance of enteral feeding. JPEN J Parenter Enteral Nutr 2008, 32:28-35. [PubMed: 18165444].
5. Yamaoka T., Yan F., Cao H., Hobbs S.S., Dise R.S., Tong W., et al. Transactivation of EGF receptor and ErbB2 protects intestinal epithelial cells from TNF-induced apoptosis. Proc Natl Acad Sci USA 2008, 105:11772-11777. [PubMed: 18701712].
6. Clark J.A., Clark A.T., Hotchkiss R.S., Buchman T.G., Coopersmith C.M. Epidermal growth factor treatment decreases mortality and is associated with improved gut integrity in sepsis. Shock 2008, 30:36-42. [PubMed: 18004230].
7. Eitoku M., Sato L., Senda T., Horikoshi M. Histone chaperones: 30 years from isolation to elucidation of the mechanisms of nucleosome assembly and disassembly. Cell Mol Life Sci 2008, 65:414-444. [PubMed: 17955179].
8. Weng G., Bhalla U.S., Iyengar R. Complexity in biological signaling systems. Science 1999, 284:92-96. [PubMed: 10102825].
9. Serrano-Fernandez P., Moller S., Goertsches R., Fiedler H., Koczan D., Thiesen H.J., et al. Time course transcriptomics of IFNB1b drug therapy in multiple sclerosis. Autoimmunity 2009, [PubMed: 19883335].
10. Costanzo-Garvey D.L., Pfluger P.T., Dougherty M.K., Stock J.L., Boehm M., Chaika O., et al. KSR2 is an essential regulator of amp kinase, energy expenditure, and insulin sensitivity. Cell Metab 2009, 10:366-378. [PubMed: 19883615].
11. Hoofnagle A.N., Wener M.H. The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J Immunol Meth 2009, 347:3-11. [PubMed: 19538965].
12. Van Den Berghe G., Wouters P., Weekers F., Verwaest C., Bruyninckx F., Schetz M., et al. Intensive insulin therapy in the critically ill patients. N Eng J Med 2001, 345:1359-1367. [PubMed: 11794168].
13. Channavajhala P.L., Wu L., Cuozzo J.W., Hall J.P., Liu W., Lin L.L., et al. Identification of a novel human kinase supporter of Ras (hKSR-2) that functions as a negative regulator of Cot (Tpl2) signaling. J Biol Chem 2003, 278:47089-47097. [PubMed: 12975377].
14. Hall J.P., Kurdi Y., Hsu S., Cuozzo J., Liu J., Telliez J.B., et al. Pharmacologic inhibition of tpl2 blocks inflammatory responses in primary human monocytes, synoviocytes, and blood. J Biol Chem 2007, 282:33295-33304. [PubMed: 17848581].
15. Yoshikawa Y., Satoh T., Tamura T., Wei P., Bilasy S.E., Edamatsu H., et al. The M-Ras-RA-GEF-2-Rap1 pathway mediates tumor necrosis factor-alpha dependent regulation of integrin activation in splenocytes. Mol Biol Cell 2007, 18:2949-2959. [PubMed: 17538012].
16. Cartwright N., Murch O., McMaster S.K., Paul-Clark M.J., van Heel D.A., Ryffel B., et al. Selective NOD1 agonists cause shock and organ injury/dysfunction in vivo. Am J Respir Crit Care Med 2007, 175:595-603. [PubMed: 17234906].
17. Chen G.Y., Shaw M.H., Redondo G., Nunez G. Innate immune receptor nod1 protects the intestine from inflammation-induced tumorigenesis. Cancer Res 2008, 68:10060-10067. [PubMed: 19074871].
18. McGuire M.F., Iyengar M.S., Mercer D.W. Computational approaches for translational clinical research in disease progression. J Investig Med 2011, 59:893-903. [PubMed: 21712727].
19. Grubman A., Kaparakis M., Viala J., Allison C., Badea L., Karrar A., et al. The innate immune molecule, NOD1, regulates direct killing of Helicobacter pylori by antimicrobial peptides. Cell Microbiol 2009, [PubMed: 20039881].
20. Chuang H.Y., Lee E., Liu Y.T., Lee D., Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol 2007, 3:140. [PubMed: 17940530].
21. Chen G.Y., Nunez G. Gut immunity: a NOD to the commensals. Curr Biol 2009, 19. [PubMed: 19243695].
22. Subramanian A., Tamayo P., Mootha V., Mukherjee S., Ebert B., Gillette M., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102:15545-15550. [PubMed: 16199517].
23. Tamayo P., Steinhardt G., Liberzon A., Mesirov J.P. Gene set enrichment analysis made right. 2011, arXiv:1110. 4128v1.
24. McGuire M.F., Iyengar M.S. Software tools for biological pathway modeling. Symbolic systems biology: theory and methods 2010, 175-195. Jones & Bartlett Publishers, Sudbury. M.S. Iyengar (Ed.).
25. Li W.X. Canonical and non-canonical JAK-STAT signaling. Trends Cell Biol 2008, 18:545-551. [PubMed: 18848449].
26. Cho K.H., Shin S.Y., Lee H.W., Wolkenhauer O. Investigations into the analysis and modeling of the TNF alpha-mediated NF-kappa B-signaling pathway. Genome Res 2003, 13:2413-2422. [PubMed: 14559780].
27. Klahr D., Simon H.A. Studies of scientific discovery: complementary approaches and convergent findings. Psychol Bullet 1999, 125:524-543. [PubMed: NA].
28. Hsich G., Kenney K., Gibbs C.J., Lee K.H., Harrington M.G. The 14-3-3 brain protein in cerebrospinal fluid as a marker for transmissible spongiform encephalopathies. N Eng J Med 1996, 335:924-930. [PubMed: 8782499].
29. Haubitz M., Good D.M., Woywodt A., Haller H., Rupprecht H., Theodorescu D., et al. Identification and validation of urinary biomarkers for differential diagnosis and evaluation of therapeutic intervention in anti-neutrophil cytoplasmic antibody-associated vasculitis. Mol Cell Proteomics 2009, 8:2296-2307. [PubMed: 19564150].
30. Heuer RJ. Psychology of intelligence analysis history staff. Central Intelligence Agency: Center for the Study of Intelligence; 1999.
31. Schunn CD, Klahr D. A 4-space model of scientific discovery. In: Proceedings of the 17th annual conference of the cognitive science society; 1995.
32. Brown R.E. Morphogenomics and morphoproteomics: a role for anatomic pathology in personalized medicine. Arch Pathol Lab Med 2009, 133:568-579. [PubMed: 19391654].
33. Ingenuity S. IPA network generation algorithm whitepaper © 2005 Ingenuity Systems proprietary and confidential. In: Ingenuity Systems; 2005. p. 26.
34. Evans T.S., Lambiotte R. Line graphs, link partitions, and overlapping communities. Phys Rev E Stat Nonlin Soft Matter Phys 2009, 80:016105. [PubMed: 19658772].
35. Ahn Y.Y., Bagrow J.P., Lehmann S. Link communities reveal multiscale complexity in networks. Nature 2010, 466:761-764. [PubMed: 20562860].
36. Tononi G., Sporns O., Edelman G.M. Measures of degeneracy and redundancy in biological networks. Proc Natl Acad Sci USA 1999, 96:3257-3262. [PubMed: 10077671].
37. Edelman G.M., Gally J.A. Degeneracy and complexity in biological systems. Proc Natl Acad Sci USA 2001, 98:13763-13768. [PubMed: 11698650].
38. Macia J., Sole R.V. Distributed robustness in cellular networks: insights from synthetic evolved circuits. J R Soc Interf 2009, 6:393-400. [PubMed: 18796402].
39. Whitacre J.M. Degeneracy: a link between evolvability, robustness and complexity in biological systems. Theor Biol Med Model 2010, 7:6. [PubMed: 20167097].
40. Tieri P., Grignolio A., Zaikin A., Mishto M., Remondini D., Castellani G.C., et al. Network, degeneracy and bow tie integrating paradigms and architectures to grasp the complexity of the immune system. Theor Biol Med Model 2010, 7:32. [PubMed: 20701759].
41. Bruni L.E. Cellular semiotics and signal transduction. Introduction to biosemiotics: the new biological synthesis 2007, 365-408. Springer, Berlin. M. Barbieri (Ed.).
42. Ingenuity. Pathways knowledge [Accessed 04.13.10]. http://www.ingenuity.com/products/pathways_knowledge.html.
43. Bondy A., Murty U.S.R. Graph theory (Graduate Texts in Mathematics) 2008, Springer.
44. Brown R.E. Morphoproteomics: exposing protein circuitries in tumors to identify potential therapeutic targets in cancer patients. Expert Rev Proteomics 2005, 2:337-348. [PubMed: 16000081].
45. Birkhoff G., MacLane S. A survey of modern algebra 1953, AK Peters/CRC Press, New York, (February 6, 1998).
46. Heron M, Hoyert D, Xu J, Scott C, Tejada-Vera B. Deaths: preliminary data for 2006. In: Hyattsville MD, editor. National vital statistics reports, vol. 56(16). National Center for Health Statistics; 2008.
47. Stewart R.M. Injury prevention: why so important?. J Trauma 2007, 62:S47-S48. [PubMed: 17556969].
48. Watson GA, Sperry JL, Rosengart MR, Minei JP, Harbrecht BG, Moore EE, Cuschieri J, Maier RV, Billiar TR, Peitzman AB. Inflammation, host response to injury I. Fresh frozen plasma is independently associated with a higher risk of multiple organ failure and acute respiratory distress syndrome. J Trauma 2009;67:221-7; discussion 228-30 [PubMed: 19667872].
49. Deitch E.A. Multiple organ failure. Pathophysiology and potential future therapy. Ann Surg 1992, 216:117-134. [PubMed: 1503516].
50. Maier B., Lefering R., Lehnert M., Laurer H.L., Steudel W.I., Neugebauer E.A., et al. Early versus late onset of multiple organ failure is associated with differing patterns of plasma cytokine biomarker expression and outcome after severe trauma. Shock 2007, 28:668-674. [PubMed: 18092384].
51. Janeway C., Travers P., Walport M., Shlomchik M. Immunobiology 2004, Garland Science. 6th ed.
52. Vodovotz Y. Translational systems biology of inflammation and healing. Wound Repair Regen 2010, 18:3-7. [PubMed: 20082674].
53. Hranjec T., Swenson B.R., Dossett L.A., Metzger R., Flohr T.R., Popovsky K.A., et al. Diagnosis-dependent relationships between cytokine levels and survival in patients admitted for surgical critical care. J Am Coll Surg 2010, 210. 833-44, 845-6, [PubMed: 20421061].
54. Jastrow K.M., Gonzalez E.A., McGuire M.F., Suliburk J.W., Kozar R.A., et al. Early cytokine production risk stratifies trauma patients for multiple organ failure. J Am Coll Surg 2009, 209:320-331. [PubMed: 19717036].
55. Visser T., Pillay J., Koenderman L., Leenen L.P. Postinjury immune monitoring: can multiple organ failure be predicted?. Curr Opin Crit Care 2008, 14:666-672. [PubMed: 19005307].
56. Roumen R.M., Redl H., Schlag G., Zilow G., Sandtner W., Koller W., et al. Inflammatory mediators in relation to the development of multiple organ failure in patients after severe blunt trauma. Crit Care Med 1995, 23:474-480. [PubMed: 7874897].
57. McGuire M.F., Iyengar M.S., Mercer D.W. Measurement units may impact results of pathway analysis. J Crit Care 2007, 22:342-343. [PubMed: NA].
58. Castellheim A., Brekke O.L., Espevik T., Harboe M., Mollnes T.E. Innate immune responses to danger signals in systemic inflammatory response syndrome and sepsis. Scand J Immunol 2009, 69:479-491. [PubMed: 19439008].
59. Bianchi M.E. DAMPs, PAMPs and alarmins: all we need to know about danger. J Leuk Biol 2007, 81:1-5. [PubMed: 17032697].
60. Calderon T.M., Gertz S.D., Sarembock I.J., Berliner J.A., Fallon J.T., Taubman M.B., et al. Induction of IG9 monocyte adhesion molecule expression in smooth muscle and endothelial cells after balloon arterial injury in cholesterol-fed rabbits. Arterioscler Thromb Vasc Biol 2000, 20:1293-1300. [PubMed: 10807745].
61. Clark J.A., Coopersmith C.M. Intestinal crosstalk: a new paradigm for understanding the gut as the " motor" of critical illness. Shock 2007, 28:384-393. [PubMed: 17577136].
62. Hassoun H.T., Weisbrodt N.W., Mercer D.W., Kozar R.A., Moody F.G., Moore F.A. Inducible nitric oxide synthase mediates gut ischemia/reperfusion-induced ileus only after severe insults. J Surg Res 2001, 97:150-154. [PubMed: 11341791].
63. Li W, Xu M, Zhou XJ. Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets. J Biomed Inform 2010;43:550-9. [PubMed: 20083231].
64. Veliz-Cuba A., Jarrah A.S., Laubenbacher R. Polynomial algebra of discrete models in systems biology. Bioinformatics 2010, 26:1637-1643. [PubMed: 20448137].
65. Tipney H.J., Leach S.M., Feng W., Spritz R., Williams T., Hunter L. Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology. BMC Bioinform 2009, 10(Suppl. 2):S12. [PubMed: 19208187].
66. Ruths D.A., Nakhleh L., Iyengar M.S., Reddy S.A., Ram P.T. Hypothesis generation in signaling networks. J Comput Biol 2006, 13:1546-1557. [PubMed: 17147477].
67. Aristotelis T. Pattern discovery for hypothesis generation in biology. In: New York University; 2006. p. 167.
68. Sam L, Liu Y, Li J, Friedman C, Lussier YA. Discovery of protein interaction networks shared by diseases. Pac Symp Biocomput 2007;76-87. [PubMed: 17992746].
69. Sachs K., Gentles A.J., Youland R., Itani S., Irish J., Nolan G.P., et al. Characterization of patient specific signaling via augmentation of Bayesian networks with disease and patient state nodes. Conf Proc IEEE Eng Med Biol Soc 2009, 2009:6624-6627. [PubMed: 19963681].
70. Kanehisa M., Goto S., Furumichi M., Tanabe M., Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucl Acids Res 2010, 38:D355-D360. [PubMed: 19880382].
71. Brent R., Lok L. Cell biology. A fishing buddy for hypothesis generators. Science 2005, 308:504-506. [PubMed: 15845840].
72. Shahar Y. Dimensions of time in illness: an objective view. Ann Intern Med 2000, 132:45-53. [PubMed: 10627251].
73. Cobb JP, Buchman TG, Karl IE, Hotchkiss RS. Molecular biology of multiple organ dysfunction syndrome: injury, adaptation, and apoptosis. Surg Infect (Larchmt) 2000;1:207-13; discussion 214-5. [PubMed: 12594891].
74. Adib-Conquy M., Cavaillon J.M. Compensatory anti-inflammatory response syndrome. Thromb Haemost 2009, 101:36-47. [PubMed: 19132187].
75. Warren H.S., Elson C.M., Hayden D.L., Schoenfeld D.A., Cobb J.P., Maier R.V., et al. A genomic score prognostic of outcome in trauma patients. Mol Med 2009, 15:220-227. [PubMed: 19593405].
76. Boulon S., Westman B.J., Hutten S., Boisvert F.M., Lamond A.I. The nucleolus under stress. Mol Cell 2010, 40:216-227. [PubMed: 20965417].
77. Klahr D., Dunbar K. Dual space search during scientific reasoning. Cognit Sci 1988, 12:1-48. [PubMed: NA].
78. McGuire MF. Pathway semantics: an algebraic data driven algorithm to generate hypotheses about molecular patterns underlying disease progression. In: School of biomedical informatics Houston: University of Texas Health Science Center at Houston; 2011. p. 173.
79. Monnier M., Boehm F. Prufung der Leistungsfahigkeit des optischen Systems durch kombinierte Elektroretinographie und Elektroencephalographie beim Menschen. Helv Physiol Pharmacol Acta 1947, 5:33. C rend, [PubMed: 18932909].
80. Reddy S.A. Signaling pathways in pancreatic cancer. Cancer J 2001, 7:274-286. [PubMed: 11561604].
81. Lee E., Chuang H.Y., Kim J.W., Ideker T., Lee D. Inferring pathway activity toward precise disease classification. PLoS Comput Biol 2008, 4:e1000217. [PubMed: 18989396].
82. Wu Y., Zhang X., Yu J., Ouyang Q. Identification of a topological characteristic responsible for the biological robustness of regulatory networks. PLoS Comput Biol 2009, 5:e1000442. [PubMed: 19629157].