Gene set enrichment analysis of SNP data in dairy and beef cattle with bovine respiratory disease

Animal Genetics
M NeupaneHolly L Neibergs

Abstract

Bovine respiratory disease (BRD) is a complex disease that is associated with infection by bacterial and viral pathogens when cattle fail to adequately respond to stress. The objective of this study was to use gene set enrichment analysis of SNP data (GSEA-SNP) and a network analysis (ingenuity pathway analysis) to identify gene sets, genes within gene sets (leading-edge genes) and upstream regulators associated with BRD in pre-weaned dairy calves and beef feedlot cattle. BRD cases and controls were diagnosed using the McGuirk health scoring system. Holstein calves were sampled from commercial calf-raising facilities in California (1003 cases and 1011 controls) and New Mexico (376 cases and 372 controls). Commercial feedlot cattle were sampled from Colorado (500 cases and 499 controls) and Washington (504 cases and 497 controls). There were 102 and 237 unique leading-edge genes identified in the dairy calf and beef cattle populations respectively. Six leading-edge genes (ADIPOQ, HTR2A, MIF, PDE6G, PRDX3 and SNCA) were associated with BRD in both dairy and beef cattle. Network analysis identified glucose as the most influential upstream regulator in dairy cattle, whereas in beef cattle, TNF was the most influential upstream regu...Continue Reading

References

Nov 14, 1998·Biochimica Et Biophysica Acta·R VeldhuizenF Possmayer
Dec 10, 1998·Nucleic Acids Research·H OgataM Kanehisa
Jan 12, 2000·Journal of Dairy Science·L BouchardP Lacasse
May 25, 2002·Science·Stacey B GabrielDavid Altshuler
Oct 12, 2002·American Journal of Physiology. Lung Cellular and Molecular Physiology·R SchmidtA Günther
Jul 5, 2003·Physiological Reviews·Dean Sheppard
Jul 26, 2003·Circulation Research·Andreas Friebe, Doris Koesling
Sep 4, 2003·Genome Research·Paul D ThomasApurva Narechania
Jan 18, 2005·Microbial Pathogenesis·Christopher J KuckleburgCharles J Czuprynski
Jan 19, 2005·BMC Immunology·Renji ReghunathanAlirio J Melendez
Jul 13, 2005·The Journal of Experimental Medicine·Stefan A MuljoKlaus Rajewsky
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Mar 23, 2006·Annual Review of Immunology·Ming O LiRichard A Flavell
Jul 18, 2006·The American Journal of Clinical Nutrition·Philip C Calder
Oct 13, 2006·Respiratory Research·Srirupa MukhopadhyayTapan K Mukherjee
Feb 10, 2007·Journal of Leukocyte Biology·Konstantin Salojin, Tamas Oravecz
Feb 22, 2007·The Journal of Immunology : Official Journal of the American Association of Immunologists·Niranjana A Nagarajan, Mitchell Kronenberg
Mar 27, 2007·Bioinformatics·Yurii S AulchenkoCornelia M van Duijn
Oct 30, 2007·American Journal of Human Genetics·Kai WangMaja Bucan
Feb 27, 2008·The Veterinary Clinics of North America. Food Animal Practice·Sheila M McGuirk
Dec 17, 2008·Journal of Perinatology : Official Journal of the California Perinatal Association·D J Askew, G A Silverman
Jul 1, 2009·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Robert W FultonAmy Reck
Jul 9, 2009·European Journal of Human Genetics : EJHG·Gang PengMomiao Xiong
Mar 9, 2010·The Journal of Biological Chemistry·Hayley A Craig-BarnesNades Palaniyar
Mar 10, 2010·Amino Acids·Jesse Goyette, Carolyn L Geczy
May 12, 2010·Cold Spring Harbor Perspectives in Biology·Toby Lawrence
Jul 14, 2010·The Veterinary Clinics of North America. Food Animal Practice·Mark R AckermannJames A Roth
Oct 12, 2010·Nature Medicine·Kong Chen, Jay K Kolls
Mar 26, 2011·Nature Reviews. Immunology·John W SempleJohn Freedman
Sep 13, 2012·Annals of the Rheumatic Diseases·Gabriela Franco SalinasDominique Baeten
Nov 9, 2012·International Journal of Biological Sciences·Mercedes Rincon, Charles G Irvin
Nov 29, 2012·The Journal of Clinical Investigation·Yael G AlevyMichael J Holtzman
Mar 20, 2013·Molecular Aspects of Medicine·Mike Mueckler, Bernard Thorens
Aug 24, 2013·Nature Reviews. Immunology·Rama KhokhaAshley Weiss
Sep 3, 2013·Antioxidants & Redox Signaling·Claudia N Paiva, Marcelo T Bozza
Sep 10, 2013·Pulmonary Circulation·Roberto Sessa, Akiko Hata
Nov 19, 2013·Nucleic Acids Research·David CroftPeter D'Eustachio
Dec 7, 2013·Endocrine Reviews·Monalisa F AzevedoConstantine A Stratakis
Dec 18, 2013·Bioinformatics·Andreas KrämerStuart Tugendreich
Jun 3, 2014·BMC Bioinformatics·Justin Andrew Christiaan Powell
Nov 28, 2014·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Dec 17, 2014·The Journal of Pathology·Purnima K WaghKathryn A Wikenheiser-Brokamp
Dec 17, 2014·Frontiers in Immunology·Nathan LawlessDavid J Lynn

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Citations

Dec 3, 2020·Animal Health Research Reviews·Holly Neibergs
Apr 25, 2020·The Veterinary Clinics of North America. Food Animal Practice·Jodi L McGill, Randy E Sacco
Dec 7, 2021·Frontiers in Veterinary Science·Jorge Luis Mazorra-CarrilloHugo Esquivel-Solís

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