Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes

Dmitry N. Grigoryev, Dilyara I. Cheranova, Daniel P. Heruth, Peixin Huang, Li Q. Zhang, Hamid Rabb, Shui Q. Ye

Research output: Contribution to journalArticle

Abstract

Background: Accumulated to-date microarray data on ischemia reperfusion injury (IRI) of kidney represent a powerful source for identifying new targets and mechanisms of kidney IRI. In this study, we conducted a meta-analysis of gene expression profiles of kidney IRI in human, pig, rat, and mouse models, using a new scoring method to correct for the bias of overrepresented species. The gene expression profiles were obtained from the public repositories for 24 different models. After filtering against inclusion criteria 21 experimental settings were selected for meta-analysis and were represented by 11 rat models, 6 mouse models, and 2 models each for pig and human, with a total of 150 samples. Meta-analysis was conducted using expression-based genome-wide association study (eGWAS). The eGWAS results were corrected for a rodent species bias using a new weighted scoring algorithm, which favors genes with unidirectional change in expression in all tested species. Results: Our meta-analysis corrected for a species bias, identified 46 upregulated and 1 downregulated genes, of which 26 (55%) were known to be associated with kidney IRI or kidney transplantation, including LCN2, CCL2, CXCL1, HMOX1, ICAM1, ANXA1, and TIMP1, which justified our approach. Pathway analysis of our candidates identified "Acute renal failure panel" as the most implicated pathway, which further validates our new method. Among new IRI candidates were 10 novel (

Original languageEnglish (US)
Article number231
JournalBMC Nephrology
Volume14
Issue number1
DOIs
StatePublished - 2013

Fingerprint

Genetic Association Studies
Reperfusion Injury
Meta-Analysis
Kidney
Genome-Wide Association Study
Transcriptome
Swine
Acute Kidney Injury
Kidney Transplantation
Genes
Rodentia
Research Design
Down-Regulation

Keywords

  • Bioinformatics
  • Ischemia reperfusion injury
  • Kidney
  • Meta-analysis

ASJC Scopus subject areas

  • Nephrology

Cite this

Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes. / Grigoryev, Dmitry N.; Cheranova, Dilyara I.; Heruth, Daniel P.; Huang, Peixin; Zhang, Li Q.; Rabb, Hamid; Ye, Shui Q.

In: BMC Nephrology, Vol. 14, No. 1, 231, 2013.

Research output: Contribution to journalArticle

Grigoryev, Dmitry N. ; Cheranova, Dilyara I. ; Heruth, Daniel P. ; Huang, Peixin ; Zhang, Li Q. ; Rabb, Hamid ; Ye, Shui Q. / Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes. In: BMC Nephrology. 2013 ; Vol. 14, No. 1.
@article{52694791a48249a3b22aa8ef0663e28c,
title = "Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes",
abstract = "Background: Accumulated to-date microarray data on ischemia reperfusion injury (IRI) of kidney represent a powerful source for identifying new targets and mechanisms of kidney IRI. In this study, we conducted a meta-analysis of gene expression profiles of kidney IRI in human, pig, rat, and mouse models, using a new scoring method to correct for the bias of overrepresented species. The gene expression profiles were obtained from the public repositories for 24 different models. After filtering against inclusion criteria 21 experimental settings were selected for meta-analysis and were represented by 11 rat models, 6 mouse models, and 2 models each for pig and human, with a total of 150 samples. Meta-analysis was conducted using expression-based genome-wide association study (eGWAS). The eGWAS results were corrected for a rodent species bias using a new weighted scoring algorithm, which favors genes with unidirectional change in expression in all tested species. Results: Our meta-analysis corrected for a species bias, identified 46 upregulated and 1 downregulated genes, of which 26 (55{\%}) were known to be associated with kidney IRI or kidney transplantation, including LCN2, CCL2, CXCL1, HMOX1, ICAM1, ANXA1, and TIMP1, which justified our approach. Pathway analysis of our candidates identified {"}Acute renal failure panel{"} as the most implicated pathway, which further validates our new method. Among new IRI candidates were 10 novel (",
keywords = "Bioinformatics, Ischemia reperfusion injury, Kidney, Meta-analysis",
author = "Grigoryev, {Dmitry N.} and Cheranova, {Dilyara I.} and Heruth, {Daniel P.} and Peixin Huang and Zhang, {Li Q.} and Hamid Rabb and Ye, {Shui Q.}",
year = "2013",
doi = "10.1186/1471-2369-14-231",
language = "English (US)",
volume = "14",
journal = "BMC Nephrology",
issn = "1471-2369",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes

AU - Grigoryev, Dmitry N.

AU - Cheranova, Dilyara I.

AU - Heruth, Daniel P.

AU - Huang, Peixin

AU - Zhang, Li Q.

AU - Rabb, Hamid

AU - Ye, Shui Q.

PY - 2013

Y1 - 2013

N2 - Background: Accumulated to-date microarray data on ischemia reperfusion injury (IRI) of kidney represent a powerful source for identifying new targets and mechanisms of kidney IRI. In this study, we conducted a meta-analysis of gene expression profiles of kidney IRI in human, pig, rat, and mouse models, using a new scoring method to correct for the bias of overrepresented species. The gene expression profiles were obtained from the public repositories for 24 different models. After filtering against inclusion criteria 21 experimental settings were selected for meta-analysis and were represented by 11 rat models, 6 mouse models, and 2 models each for pig and human, with a total of 150 samples. Meta-analysis was conducted using expression-based genome-wide association study (eGWAS). The eGWAS results were corrected for a rodent species bias using a new weighted scoring algorithm, which favors genes with unidirectional change in expression in all tested species. Results: Our meta-analysis corrected for a species bias, identified 46 upregulated and 1 downregulated genes, of which 26 (55%) were known to be associated with kidney IRI or kidney transplantation, including LCN2, CCL2, CXCL1, HMOX1, ICAM1, ANXA1, and TIMP1, which justified our approach. Pathway analysis of our candidates identified "Acute renal failure panel" as the most implicated pathway, which further validates our new method. Among new IRI candidates were 10 novel (

AB - Background: Accumulated to-date microarray data on ischemia reperfusion injury (IRI) of kidney represent a powerful source for identifying new targets and mechanisms of kidney IRI. In this study, we conducted a meta-analysis of gene expression profiles of kidney IRI in human, pig, rat, and mouse models, using a new scoring method to correct for the bias of overrepresented species. The gene expression profiles were obtained from the public repositories for 24 different models. After filtering against inclusion criteria 21 experimental settings were selected for meta-analysis and were represented by 11 rat models, 6 mouse models, and 2 models each for pig and human, with a total of 150 samples. Meta-analysis was conducted using expression-based genome-wide association study (eGWAS). The eGWAS results were corrected for a rodent species bias using a new weighted scoring algorithm, which favors genes with unidirectional change in expression in all tested species. Results: Our meta-analysis corrected for a species bias, identified 46 upregulated and 1 downregulated genes, of which 26 (55%) were known to be associated with kidney IRI or kidney transplantation, including LCN2, CCL2, CXCL1, HMOX1, ICAM1, ANXA1, and TIMP1, which justified our approach. Pathway analysis of our candidates identified "Acute renal failure panel" as the most implicated pathway, which further validates our new method. Among new IRI candidates were 10 novel (

KW - Bioinformatics

KW - Ischemia reperfusion injury

KW - Kidney

KW - Meta-analysis

UR - http://www.scopus.com/inward/record.url?scp=84886024037&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84886024037&partnerID=8YFLogxK

U2 - 10.1186/1471-2369-14-231

DO - 10.1186/1471-2369-14-231

M3 - Article

VL - 14

JO - BMC Nephrology

JF - BMC Nephrology

SN - 1471-2369

IS - 1

M1 - 231

ER -