메뉴 건너뛰기




Volumn 45, Issue 1, 2017, Pages 1-10

Benchmarking Sepsis Gene Expression Diagnostics Using Public Data

Author keywords

diagnosis; gene expression; microarray; sepsis

Indexed keywords

AREA UNDER THE CURVE; ARTICLE; BENCHMARKING; CHRONIC OBSTRUCTIVE LUNG DISEASE; COHORT ANALYSIS; COMPARATIVE STUDY; CONTROLLED STUDY; FAS APOPTOTIC INHIBITORY MOLECULE 3 TO PLACENTA SPECIFIC 8 RATIO; GENE EXPRESSION; GENETIC ANALYSIS; GRAM NEGATIVE INFECTION; GRAM POSITIVE INFECTION; HUMAN; INFLAMMATION; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; PNEUMONIA; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SEPSIS; SEPSIS METASCORE; SEPTICYTE LAB; SHOCK; SYSTEMIC INFLAMMATORY RESPONSE SYNDROME; VIRUS INFECTION; CASE CONTROL STUDY; DIFFERENTIAL DIAGNOSIS; GENETICS; INFORMATION PROCESSING; SENSITIVITY AND SPECIFICITY;

EID: 84988954104     PISSN: 00903493     EISSN: 15300293     Source Type: Journal    
DOI: 10.1097/CCM.0000000000002021     Document Type: Article
Times cited : (71)

References (44)
  • 1
    • 84904734154 scopus 로고    scopus 로고
    • Empiric antibiotic treatment reduces mortality in severe sepsis and septic shock from the frst hour: Results from a guideline-based performance improvement program
    • Ferrer R, Martin-Loeches I, Phillips G, et al: Empiric antibiotic treatment reduces mortality in severe sepsis and septic shock from the frst hour: Results from a guideline-based performance improvement program. Crit Care Med 2014; 42:1749-1755
    • (2014) Crit Care Med , vol.42 , pp. 1749-1755
    • Ferrer, R.1    Martin-Loeches, I.2    Phillips, G.3
  • 2
    • 55449090398 scopus 로고    scopus 로고
    • Antibiotic-associated diarrhea: Epidemiology, trends and treatment
    • McFarland LV: Antibiotic-associated diarrhea: Epidemiology, trends and treatment. Future Microbiol 2008; 3:563-578
    • (2008) Future Microbiol , vol.3 , pp. 563-578
    • McFarland, L.V.1
  • 3
    • 77950218147 scopus 로고    scopus 로고
    • Impact of time to antibiotics on survival in patients with severe sepsis or septic shock in whom early goal-directed therapy was initiated in the emergency department
    • Gaieski DF, Mikkelsen ME, Band RA, et al: Impact of time to antibiotics on survival in patients with severe sepsis or septic shock in whom early goal-directed therapy was initiated in the emergency department. Crit Care Med 2010; 38:1045-1053
    • (2010) Crit Care Med , vol.38 , pp. 1045-1053
    • Gaieski, D.F.1    Mikkelsen, M.E.2    Band, R.A.3
  • 5
    • 49649083648 scopus 로고    scopus 로고
    • The balance of reproducibility sensitivity, and specifcity of lists of differentially expressed genes in microarray studies
    • Shi L, Jones WD, Jensen RV, et al: The balance of reproducibility sensitivity, and specifcity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics 2008; 9(Suppl 9):S10
    • (2008) BMC Bioinformatics , vol.9 , pp. S10
    • Shi, L.1    Jones, W.D.2    Jensen, R.V.3
  • 6
    • 0035179971 scopus 로고    scopus 로고
    • Replication validity of genetic association studies
    • Ioannidis JP, Ntzani EE, Trikalinos TA, et al: Replication validity of genetic association studies. Nat Genet 2001; 29:306-309
    • (2001) Nat Genet , vol.29 , pp. 306-309
    • Ioannidis, J.P.1    Ntzani, E.E.2    Trikalinos, T.A.3
  • 7
    • 84929629371 scopus 로고    scopus 로고
    • A comprehensive time-course-based multicohort analysis of sepsis and sterile infammation reveals a robust diagnostic gene set
    • Sweeney TE, Shidham A, Wong H R, et al: A comprehensive time-course-based multicohort analysis of sepsis and sterile infammation reveals a robust diagnostic gene set. Sci Transl Med 2015; 7:287ra71
    • (2015) Sci Transl Med , vol.7 , pp. 287ra71
    • Sweeney, T.E.1    Shidham, A.2    Wong, H.R.3
  • 8
    • 84943279884 scopus 로고    scopus 로고
    • A molecular biomarker to diagnose community-acquired pneumonia on intensive care unit admission
    • Scicluna BP, Klein Klouwenberg PM, van Vught LA, et al: A molecular biomarker to diagnose community-acquired pneumonia on intensive care unit admission. Am J Respir Crit Care Med 2015; 192:826-835
    • (2015) Am J Respir Crit Care Med , vol.192 , pp. 826-835
    • Scicluna, B.P.1    Klein Klouwenberg, P.M.2    Van Vught, L.A.3
  • 9
    • 84953790265 scopus 로고    scopus 로고
    • A molecular host response assay to discriminate between sepsis and infection-negative systemic infammation in critically ill patients: Discovery and validation in independent cohorts
    • McHugh L, Seldon TA, Brandon RA, et al: A molecular host response assay to discriminate between sepsis and infection-negative systemic infammation in critically ill patients: Discovery and validation in independent cohorts. PLoS Med 2015; 12:e1001916
    • (2015) PLoS Med , vol.12 , pp. e1001916
    • McHugh, L.1    Seldon, T.A.2    Brandon, R.A.3
  • 10
    • 53149135477 scopus 로고    scopus 로고
    • Key issues in conducting a meta-analysis of gene expression microarray datasets
    • Ramasamy A, Mondry A, Holmes CC, et al: Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med 2008; 5:e184
    • (2008) PLoS Med , vol.5 , pp. e184
    • Ramasamy, A.1    Mondry, A.2    Holmes, C.C.3
  • 11
    • 84910658471 scopus 로고    scopus 로고
    • OptimalCutpoints: An R Package for Selecting Optimal Cutpoints in Diagnostic Tests
    • Available at: Accessed September 20, 2016
    • Lopez-Raton M, Rodriguez-Alvarez MX, Suarez CC, et al: OptimalCutpoints: An R Package for Selecting Optimal Cutpoints in Diagnostic Tests. J Stat Soft 2014; 61:1-36. Available at: http:// www.jstatsoft.org/v61/i08/. Accessed September 20, 2016
    • (2014) J Stat Soft , vol.61 , pp. 1-36
    • Lopez-Raton, M.1    Rodriguez-Alvarez, M.X.2    Suarez, C.C.3
  • 12
    • 10844290766 scopus 로고    scopus 로고
    • A model-based background adjustment for oligonucleotide expression arrays
    • Wu Z, Irizarry R, Gentleman R, et al: A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 2004; 99:909-917
    • (2004) J Am Stat Assoc , vol.99 , pp. 909-917
    • Wu, Z.1    Irizarry, R.2    Gentleman, R.3
  • 13
    • 79958809160 scopus 로고    scopus 로고
    • Development and validation of a novel molecular biomarker diagnostic test for the early detection of sepsis
    • Sutherland A, Thomas M, Brandon RA, et al: Development and validation of a novel molecular biomarker diagnostic test for the early detection of sepsis. Crit Care 2011; 15:R149
    • (2011) Crit Care , vol.15 , pp. R149
    • Sutherland, A.1    Thomas, M.2    Brandon, R.A.3
  • 14
    • 84861785677 scopus 로고    scopus 로고
    • Infammasome-regulated cytokines are critical mediators of acute lung injury
    • Dolinay T, Kim YS, Howrylak J, et al: Infammasome-regulated cytokines are critical mediators of acute lung injury. Am J Respir Crit Care Med 2012; 185:1225-1234
    • (2012) Am J Respir Crit Care Med , vol.185 , pp. 1225-1234
    • Dolinay, T.1    Kim, Y.S.2    Howrylak, J.3
  • 15
    • 84864910724 scopus 로고    scopus 로고
    • A distinct infuenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia
    • Parnell GP, McLean AS, Booth DR, et al: A distinct infuenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia. Crit Care 2012; 16:R157
    • (2012) Crit Care , vol.16 , pp. R157
    • Parnell, G.P.1    McLean, A.S.2    Booth, D.R.3
  • 16
    • 34547470882 scopus 로고    scopus 로고
    • Genome-level expression profles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome
    • Wong HR, Shanley TP, Sakthivel B, et al; Genomics of Pediatric SIRS/Septic Shock Investigators: Genome-level expression profles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome. Physiol Genomics 2007; 30:146-155
    • (2007) Physiol Genomics , vol.30 , pp. 146-155
    • Wong, H.R.1    Shanley, T.P.2    Sakthivel, B.3
  • 17
    • 82855164062 scopus 로고    scopus 로고
    • The infuence of developmental age on the early transcriptomic response of children with septic shock
    • Wynn JL, Cvijanovich NZ, Allen GL, et al: The infuence of developmental age on the early transcriptomic response of children with septic shock. Mol Med 2011; 17:1146-1156
    • (2011) Mol Med , vol.17 , pp. 1146-1156
    • Wynn, J.L.1    Cvijanovich, N.Z.2    Allen, G.L.3
  • 18
    • 67650470273 scopus 로고    scopus 로고
    • Genomic expression profling across the pediatric systemic infammatory response syndrome, sepsis, and septic shock spectrum
    • Wong HR, Cvijanovich N, Allen GL, et al; Genomics of Pediatric SIRS/ Septic Shock Investigators: Genomic expression profling across the pediatric systemic infammatory response syndrome, sepsis, and septic shock spectrum. Crit Care Med 2009; 37:1558-1566
    • (2009) Crit Care Med , vol.37 , pp. 1558-1566
    • Wong, H.R.1    Cvijanovich, N.2    Allen, G.L.3
  • 19
    • 35348925444 scopus 로고    scopus 로고
    • Genome-level longitudinal expression of signaling pathways and gene networks in pediatric septic shock
    • Shanley TP, Cvijanovich N, Lin R, et al: Genome-level longitudinal expression of signaling pathways and gene networks in pediatric septic shock. Mol Med 2007; 13:495-508
    • (2007) Mol Med , vol.13 , pp. 495-508
    • Shanley, T.P.1    Cvijanovich, N.2    Lin, R.3
  • 20
    • 47249122242 scopus 로고    scopus 로고
    • Validating the genomic signature of pediatric septic shock
    • Cvijanovich N, Shanley TP, Lin R, et al; Genomics of Pediatric SIRS/ Septic Shock Investigators: Validating the genomic signature of pediatric septic shock. Physiol Genomics 2008; 34:127-134
    • (2008) Physiol Genomics , vol.34 , pp. 127-134
    • Cvijanovich, N.1    Shanley, T.P.2    Lin, R.3
  • 21
    • 84864446365 scopus 로고    scopus 로고
    • Critical COPD respiratory illness is linked to increased transcriptomic activity of neutrophil proteases genes
    • Almansa R, Socias L, Sanchez-Garcia M, et al: Critical COPD respiratory illness is linked to increased transcriptomic activity of neutrophil proteases genes. BMC Res Notes 2012; 5:401
    • (2012) BMC Res Notes , vol.5 , pp. 401
    • Almansa, R.1    Socias, L.2    Sanchez-Garcia, M.3
  • 22
    • 84860500036 scopus 로고    scopus 로고
    • Novel biomarker combination improves the diagnosis of serious bacterial infections in Malawian children
    • Irwin AD, Marriage F, Mankhambo LA, et al; IPD Group Study: Novel biomarker combination improves the diagnosis of serious bacterial infections in Malawian children. BMC Med Genomics 2012; 5:13
    • (2012) BMC Med Genomics , vol.5 , pp. 13
    • Irwin, A.D.1    Marriage, F.2    Mankhambo, L.A.3
  • 23
    • 84928821718 scopus 로고    scopus 로고
    • Time since onset of disease and individual clinical markers associate with transcriptional changes in uncomplicated dengue
    • van de Weg CA, van den Ham HJ, Bijl MA, et al: Time since onset of disease and individual clinical markers associate with transcriptional changes in uncomplicated dengue. PLoS Negl Trop Dis 2015; 9:e0003522
    • (2015) PLoS Negl Trop Dis , vol.9 , pp. e0003522
    • Van De Weg, C.A.1    Van Den Ham, H.J.2    Bijl, M.A.3
  • 25
    • 76249091272 scopus 로고    scopus 로고
    • Genomic transcriptional profling identifes a candidate blood biomarker signature for the diagnosis of septicemic melioidosis
    • Pankla R, Buddhisa S, Berry M, et al: Genomic transcriptional profling identifes a candidate blood biomarker signature for the diagnosis of septicemic melioidosis. Genome Biol 2009; 10:R127
    • (2009) Genome Biol , vol.10 , pp. R127
    • Pankla, R.1    Buddhisa, S.2    Berry, M.3
  • 26
    • 69949148793 scopus 로고    scopus 로고
    • Gene expression signatures diagnose infuenza and other symptomatic respiratory viral infections in humans
    • Zaas AK, Chen M, Varkey J, et al: Gene expression signatures diagnose infuenza and other symptomatic respiratory viral infections in humans. Cell Host Microbe 2009; 6:207-217
    • (2009) Cell Host Microbe , vol.6 , pp. 207-217
    • Zaas, A.K.1    Chen, M.2    Varkey, J.3
  • 27
    • 79952395259 scopus 로고    scopus 로고
    • Aberrant cell cycle and apoptotic changes characterise severe infuenza A infection-a meta-analysis of genomic signatures in circulating leukocytes
    • Parnell G, McLean A, Booth D, et al: Aberrant cell cycle and apoptotic changes characterise severe infuenza A infection-a meta-analysis of genomic signatures in circulating leukocytes. PLoS One 2011; 6:e17186
    • (2011) PLoS One , vol.6 , pp. e17186
    • Parnell, G.1    McLean, A.2    Booth, D.3
  • 28
    • 77956486528 scopus 로고    scopus 로고
    • Host adaptive immunity defciency in severe pandemic infuenza
    • Bermejo-Martin JF, Martin-Loeches I, Rello J, et al: Host adaptive immunity defciency in severe pandemic infuenza. Crit Care 2010; 14:R167
    • (2010) Crit Care , vol.14 , pp. R167
    • Bermejo-Martin, J.F.1    Martin-Loeches, I.2    Rello, J.3
  • 29
    • 77955894773 scopus 로고    scopus 로고
    • An interferon-inducible neu-trophil-driven blood transcriptional signature in human tuberculosis
    • Berry MP, Graham CM, McNab FW, et al: An interferon-inducible neu-trophil-driven blood transcriptional signature in human tuberculosis. Nature 2010; 466:973-977
    • (2010) Nature , vol.466 , pp. 973-977
    • Berry, M.P.1    Graham, C.M.2    McNab, F.W.3
  • 30
    • 84907320442 scopus 로고    scopus 로고
    • Identifcation of a human neonatal immune-metabolic network associated with bacterial infection
    • Smith CL, Dickinson P, Forster T, et al: Identifcation of a human neonatal immune-metabolic network associated with bacterial infection. Nat Commun 2014; 5:4649
    • (2014) Nat Commun , vol.5 , pp. 4649
    • Smith, C.L.1    Dickinson, P.2    Forster, T.3
  • 31
    • 80052957457 scopus 로고    scopus 로고
    • Excessive innate immune response and mutant D222G/N in severe A (H1N1) pandemic infuenza
    • Berdal JE, Mollnes TE, Washre T, et al: Excessive innate immune response and mutant D222G/N in severe A (H1N1) pandemic infuenza. J Infect 2011; 63:308-316
    • (2011) J Infect , vol.63 , pp. 308-316
    • Berdal, J.E.1    Mollnes, T.E.2    Washre, T.3
  • 32
    • 84872175208 scopus 로고    scopus 로고
    • Gene expression-based classifers identify Staphylococcus aureus infection in mice and humans
    • Ahn SH, Tsalik EL, Cyr DD, et al: Gene expression-based classifers identify Staphylococcus aureus infection in mice and humans. PLoS One 2013; 8:e48979
    • (2013) PLoS One , vol.8 , pp. e48979
    • Ahn, S.H.1    Tsalik, E.L.2    Cyr, D.D.3
  • 33
    • 84888990746 scopus 로고    scopus 로고
    • Whole blood gene expression profles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection
    • Mejias A, Dimo B, Suarez NM, et al: Whole blood gene expression profles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection. PLoS Med 2013; 10:e1001549
    • (2013) PLoS Med , vol.10 , pp. e1001549
    • Mejias, A.1    Dimo, B.2    Suarez, N.M.3
  • 34
    • 84881086889 scopus 로고    scopus 로고
    • Gene expression profles in febrile children with defned viral and bacterial infection
    • Hu X, Yu J, Crosby SD, et al: Gene expression profles in febrile children with defned viral and bacterial infection. Proc Natl Acad Sci U S A 2013; 110:12792-12797
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 12792-12797
    • Hu, X.1    Yu, J.2    Crosby, S.D.3
  • 35
    • 84888618702 scopus 로고    scopus 로고
    • Transcriptomic profling in childhood H1N1/09 infuenza reveals reduced expression of protein synthesis genes
    • Herberg JA, Kaforou M, Gormley S, et al: Transcriptomic profling in childhood H1N1/09 infuenza reveals reduced expression of protein synthesis genes. J Infect Dis 2013; 208:1664-1668
    • (2013) J Infect Dis , vol.208 , pp. 1664-1668
    • Herberg, J.A.1    Kaforou, M.2    Gormley, S.3
  • 36
    • 84904161011 scopus 로고    scopus 로고
    • Dengue virus infection induces expansion of a CD14(+)CD16(+) monocyte population that stimulates plasmablast differentiation
    • Kwissa M, Nakaya HI, Onlamoon N, et al: Dengue virus infection induces expansion of a CD14(+)CD16(+) monocyte population that stimulates plasmablast differentiation. Cell Host Microbe 2014; 16:115-127
    • (2014) Cell Host Microbe , vol.16 , pp. 115-127
    • Kwissa, M.1    Nakaya, H.I.2    Onlamoon, N.3
  • 37
    • 84962951085 scopus 로고    scopus 로고
    • Early and dynamic changes in gene expression in septic shock patients: A genome-wide approach
    • Cazalis MA, Lepape A, Venet F, et al: Early and dynamic changes in gene expression in septic shock patients: A genome-wide approach. Intensive Care Med Exp 2014; 2:20
    • (2014) Intensive Care Med Exp , vol.2 , pp. 20
    • Cazalis, M.A.1    Lepape, A.2    Venet, F.3
  • 38
    • 84930090652 scopus 로고    scopus 로고
    • Superiority of transcriptional profling over procalcitonin for distinguishing bacterial from viral lower respiratory tract infections in hospitalized adults
    • Suarez NM, Bunsow E, Falsey AR, et al: Superiority of transcriptional profling over procalcitonin for distinguishing bacterial from viral lower respiratory tract infections in hospitalized adults. J Infect Dis 2015; 212:213-222
    • (2015) J Infect Dis , vol.212 , pp. 213-222
    • Suarez, N.M.1    Bunsow, E.2    Falsey, A.R.3
  • 39
    • 84936802478 scopus 로고    scopus 로고
    • Host transcriptional response to infuenza and other acute respiratory viral infections-A prospective cohort study
    • Zhai Y, Franco LM, Atmar RL, et al: Host transcriptional response to infuenza and other acute respiratory viral infections-A prospective cohort study. PLoS Pathog 2015; 11:e1004869
    • (2015) PLoS Pathog , vol.11 , pp. e1004869
    • Zhai, Y.1    Franco, L.M.2    Atmar, R.L.3
  • 40
    • 84942475224 scopus 로고    scopus 로고
    • The blood transcriptome of experimental melioidosis refects disease severity and shows considerable similarity with the human disease
    • Conejero L, Potempa K, Graham CM, et al: The blood transcriptome of experimental melioidosis refects disease severity and shows considerable similarity with the human disease. J Immunol 2015; 195:3248-3261
    • (2015) J Immunol , vol.195 , pp. 3248-3261
    • Conejero, L.1    Potempa, K.2    Graham, C.M.3
  • 41
    • 84862908403 scopus 로고    scopus 로고
    • A genomic storm in critically injured humans
    • Infammation and Host Response to Injury Large-Scale Collaborative Research Program
    • Xiao W, Mindrinos MN, Seok J, et al; Infammation and Host Response to Injury Large-Scale Collaborative Research Program: A genomic storm in critically injured humans. J Exp Med 2011; 208:2581-2590
    • (2011) J Exp Med , vol.208 , pp. 2581-2590
    • Xiao, W.1    Mindrinos, M.N.2    Seok, J.3
  • 42
    • 67650508418 scopus 로고    scopus 로고
    • A genomic score prognostic of outcome in trauma patients
    • Infammation and Host Response to Injury Large Scale Collaborative Research Program
    • Warren HS, Elson CM, Hayden DL, et al; Infammation and Host Response to Injury Large Scale Collaborative Research Program: A genomic score prognostic of outcome in trauma patients. Mol Med 2009; 15:220-227
    • (2009) Mol Med , vol.15 , pp. 220-227
    • Warren, H.S.1    Elson, C.M.2    Hayden, D.L.3
  • 43
    • 84948952180 scopus 로고    scopus 로고
    • Reply: Comprehensive validation of the FAIM3:PLAC8 ratio in time-matched public gene expression data
    • all the authors
    • Scicluna BP, Klein Klouwenberg PM, van der Poll T; all the authors: Reply: Comprehensive validation of the FAIM3:PLAC8 ratio in time-matched public gene expression data. Am J Respir Crit Care Med 2015; 192:1261-1262
    • (2015) Am J Respir Crit Care Med , vol.192 , pp. 1261-1262
    • Scicluna, B.P.1    Klein Klouwenberg, P.M.2    Van Der Poll, T.3
  • 44
    • 84983096128 scopus 로고    scopus 로고
    • Comprehensive validation of the FAIM3:PLAC8 ratio in time-matched public gene expression data
    • Sweeney TE, Khatri P: Comprehensive validation of the FAIM3:PLAC8 ratio in time-matched public gene expression data. Am J Respir Crit Care Med 2015; 192:1260-1261
    • (2015) Am J Respir Crit Care Med , vol.192 , pp. 1260-1261
    • Sweeney, T.E.1    Khatri, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.