Analysis of the relationship between longitudinal gene expressions and ordered categorical event data

Natasa Rajicic; Dianne M. Finkelstein; David A. Schoenfeld; Henry V. Baker; Ulysses Balis; Paul Bankey; Timothy R. Billiar; Bernard H. Brownstein; Steven E. Calvano; David G. Camp; George Casella; Irshad H. Chaudry; J. Perren Cobb; Joseph Cuschieri; Ronald W. Davis; Asit K. De; Celeste C. Finnerty; Bradley Freeman; Richard L. Gamelli; Nicole S. Gibran; Brian G. Harbrecht; Douglas L. Hayden; Laura Hennessy; David N. Herndon; Jureta W. Horton; Marc G. Jeschke; Jeffrey Johnson; Matthew B. Klein; James A. Lederer; Stephen F. Lowry; Ronald V. Maier; John A. Mannick; Philip H. Mason; Grace P. McDonald-Smith; Carol L. Miller-Graziano; Michael N. Mindrinos; Joseph P. Minei; Lyle L. Moldawer; Ernest E. Moore; Avery B. Nathens; Grant E. O'Keefe; Laurence G. Rahme; Daniel G. Remick; Michael B. Shapiro; Geoffrey M. Silver; Richard D. Smith; John Storey; Robert Tibshirani; Ronald G. Tompkins; Mehmet Toner; H. Shaw Warren; Michael A. West; Wenzhong Xiao

doi:10.1002/sim.3665

Analysis of the relationship between longitudinal gene expressions and ordered categorical event data

Natasa Rajicic, Dianne M. Finkelstein, David A. Schoenfeld, Henry V. Baker, Ulysses Balis, Paul Bankey, Timothy R. Billiar, Bernard H. Brownstein, Steven E. Calvano, David G. Camp, George Casella, Irshad H. Chaudry, J. Perren Cobb, Joseph Cuschieri, Ronald W. Davis, Asit K. De, Celeste C. Finnerty, Bradley Freeman, Richard L. Gamelli, Nicole S. GibranBrian G. Harbrecht, Douglas L. Hayden, Laura Hennessy, David N. Herndon, Jureta W. Horton, Marc G. Jeschke, Jeffrey Johnson, Matthew B. Klein, James A. Lederer, Stephen F. Lowry, Ronald V. Maier, John A. Mannick, Philip H. Mason, Grace P. McDonald-Smith, Carol L. Miller-Graziano, Michael N. Mindrinos, Joseph P. Minei, Lyle L. Moldawer, Ernest E. Moore, Avery B. Nathens, Grant E. O'Keefe, Laurence G. Rahme, Daniel G. Remick, Michael B. Shapiro, Geoffrey M. Silver, Richard D. Smith, John Storey, Robert Tibshirani, Ronald G. Tompkins, Mehmet Toner, H. Shaw Warren, Michael A. West, Wenzhong Xiao

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Abstract

The NIH project 'Inflammatory and Host Response to Injury' (Glue) is being conducted to study the changes in the body over time in response to trauma and burn. Patients are monitored for changes in their clinical status, such as the onset of and recovery from organ failure. Blood samples are drawn over the first days and weeks after the injury to obtain gene expression levels over time. Our goal was to develop a method of selecting genes that differentially expressed in patients who either improved or experienced organ failure. For this, we needed a test for the association between longitudinal gene expressions and the time to the occurrence of ordered categorical outcomes indicating recovery, stable disease, and organ failure. We propose a test for which the relationship between the gene expression and the events is modeled using the cumulative proportional odds model that is a generalization of the pooling repeated observation method. Given the high-dimensionality of the microarray data, it was necessary to control for the multiplicity of the testing. To control for the false discovery rate (FDR), we applied both a permutational approach as well as Efron's empirical estimation method. We explore our method through simulations and provide the analysis of the multi-center, longitudinal study of immune response to inflammation and trauma (http://www.gluegrant.org).

Original language	English (US)
Pages (from-to)	2817-2832
Number of pages	16
Journal	Statistics in Medicine
Volume	28
Issue number	22
DOIs	https://doi.org/10.1002/sim.3665
State	Published - Sep 30 2009

Keywords

Microarray analysis
Multiple testing
Ordinal data
Permutation test
Score test

ASJC Scopus subject areas

Epidemiology
Statistics and Probability

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10.1002/sim.3665

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Rajicic, N., Finkelstein, D. M., Schoenfeld, D. A., Baker, H. V., Balis, U., Bankey, P., Billiar, T. R., Brownstein, B. H., Calvano, S. E., Camp, D. G., Casella, G., Chaudry, I. H., Cobb, J. P., Cuschieri, J., Davis, R. W., De, A. K., Finnerty, C. C., Freeman, B., Gamelli, R. L., ... Xiao, W. (2009). Analysis of the relationship between longitudinal gene expressions and ordered categorical event data. Statistics in Medicine, 28(22), 2817-2832. https://doi.org/10.1002/sim.3665

Rajicic, N, Finkelstein, DM, Schoenfeld, DA, Baker, HV, Balis, U, Bankey, P, Billiar, TR, Brownstein, BH, Calvano, SE, Camp, DG, Casella, G, Chaudry, IH, Cobb, JP, Cuschieri, J, Davis, RW, De, AK, Finnerty, CC, Freeman, B, Gamelli, RL, Gibran, NS, Harbrecht, BG, Hayden, DL, Hennessy, L, Herndon, DN, Horton, JW, Jeschke, MG, Johnson, J, Klein, MB, Lederer, JA, Lowry, SF, Maier, RV, Mannick, JA, Mason, PH, McDonald-Smith, GP, Miller-Graziano, CL, Mindrinos, MN, Minei, JP, Moldawer, LL, Moore, EE, Nathens, AB, O'Keefe, GE, Rahme, LG, Remick, DG, Shapiro, MB, Silver, GM, Smith, RD, Storey, J, Tibshirani, R, Tompkins, RG, Toner, M, Warren, HS, West, MA & Xiao, W 2009, 'Analysis of the relationship between longitudinal gene expressions and ordered categorical event data', Statistics in Medicine, vol. 28, no. 22, pp. 2817-2832. https://doi.org/10.1002/sim.3665

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abstract = "The NIH project 'Inflammatory and Host Response to Injury' (Glue) is being conducted to study the changes in the body over time in response to trauma and burn. Patients are monitored for changes in their clinical status, such as the onset of and recovery from organ failure. Blood samples are drawn over the first days and weeks after the injury to obtain gene expression levels over time. Our goal was to develop a method of selecting genes that differentially expressed in patients who either improved or experienced organ failure. For this, we needed a test for the association between longitudinal gene expressions and the time to the occurrence of ordered categorical outcomes indicating recovery, stable disease, and organ failure. We propose a test for which the relationship between the gene expression and the events is modeled using the cumulative proportional odds model that is a generalization of the pooling repeated observation method. Given the high-dimensionality of the microarray data, it was necessary to control for the multiplicity of the testing. To control for the false discovery rate (FDR), we applied both a permutational approach as well as Efron's empirical estimation method. We explore our method through simulations and provide the analysis of the multi-center, longitudinal study of immune response to inflammation and trauma (http://www.gluegrant.org).",

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author = "Natasa Rajicic and Finkelstein, {Dianne M.} and Schoenfeld, {David A.} and Baker, {Henry V.} and Ulysses Balis and Paul Bankey and Billiar, {Timothy R.} and Brownstein, {Bernard H.} and Calvano, {Steven E.} and Camp, {David G.} and George Casella and Chaudry, {Irshad H.} and Cobb, {J. Perren} and Joseph Cuschieri and Davis, {Ronald W.} and De, {Asit K.} and Finnerty, {Celeste C.} and Bradley Freeman and Gamelli, {Richard L.} and Gibran, {Nicole S.} and Harbrecht, {Brian G.} and Hayden, {Douglas L.} and Laura Hennessy and Herndon, {David N.} and Horton, {Jureta W.} and Jeschke, {Marc G.} and Jeffrey Johnson and Klein, {Matthew B.} and Lederer, {James A.} and Lowry, {Stephen F.} and Maier, {Ronald V.} and Mannick, {John A.} and Mason, {Philip H.} and McDonald-Smith, {Grace P.} and Miller-Graziano, {Carol L.} and Mindrinos, {Michael N.} and Minei, {Joseph P.} and Moldawer, {Lyle L.} and Moore, {Ernest E.} and Nathens, {Avery B.} and O'Keefe, {Grant E.} and Rahme, {Laurence G.} and Remick, {Daniel G.} and Shapiro, {Michael B.} and Silver, {Geoffrey M.} and Smith, {Richard D.} and John Storey and Robert Tibshirani and Tompkins, {Ronald G.} and Mehmet Toner and Warren, {H. Shaw} and West, {Michael A.} and Wenzhong Xiao",

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AU - Rajicic, Natasa

AU - Finkelstein, Dianne M.

AU - Schoenfeld, David A.

AU - Baker, Henry V.

AU - Balis, Ulysses

AU - Bankey, Paul

AU - Billiar, Timothy R.

AU - Brownstein, Bernard H.

AU - Calvano, Steven E.

AU - Camp, David G.

AU - Casella, George

AU - Chaudry, Irshad H.

AU - Cobb, J. Perren

AU - Cuschieri, Joseph

AU - Davis, Ronald W.

AU - De, Asit K.

AU - Finnerty, Celeste C.

AU - Freeman, Bradley

AU - Gamelli, Richard L.

AU - Gibran, Nicole S.

AU - Harbrecht, Brian G.

AU - Hayden, Douglas L.

AU - Hennessy, Laura

AU - Herndon, David N.

AU - Horton, Jureta W.

AU - Jeschke, Marc G.

AU - Johnson, Jeffrey

AU - Klein, Matthew B.

AU - Lederer, James A.

AU - Lowry, Stephen F.

AU - Maier, Ronald V.

AU - Mannick, John A.

AU - Mason, Philip H.

AU - McDonald-Smith, Grace P.

AU - Miller-Graziano, Carol L.

AU - Mindrinos, Michael N.

AU - Minei, Joseph P.

AU - Moldawer, Lyle L.

AU - Moore, Ernest E.

AU - Nathens, Avery B.

AU - O'Keefe, Grant E.

AU - Rahme, Laurence G.

AU - Remick, Daniel G.

AU - Shapiro, Michael B.

AU - Silver, Geoffrey M.

AU - Smith, Richard D.

AU - Storey, John

AU - Tibshirani, Robert

AU - Tompkins, Ronald G.

AU - Toner, Mehmet

AU - Warren, H. Shaw

AU - West, Michael A.

AU - Xiao, Wenzhong

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KW - Microarray analysis

KW - Multiple testing

KW - Ordinal data

KW - Permutation test

KW - Score test

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ER -

Analysis of the relationship between longitudinal gene expressions and ordered categorical event data

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Keywords

ASJC Scopus subject areas

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