Integration of machine learning and meta-analysis identifies the transcriptomic bio-signature of mastitis disease in cattle

PloS One
Somayeh SharifiEsmaeil Ebrahimie

Abstract

Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in dairy cattle. Rapid detection of this disease is so important in order to prevent transmission to other cows and helps to reduce inappropriate use of antibiotics. With the rapid progress in high-throughput technologies, and accumulation of various kinds of '-omics' data in public repositories, there is an opportunity to retrieve, integrate, and reanalyze these resources to improve the diagnosis and treatment of different diseases and to provide mechanistic insights into host resistance in an efficient way. Meta-analysis is a relatively inexpensive option with good potential to increase the statistical power and generalizability of single-study analysis. In the current meta-analysis research, six microarray-based studies that investigate the transcriptome profile of mammary gland tissue after induced mastitis by E. coli infection were used. This meta-analysis not only reinforced the findings in individual studies, but also several novel terms including responses to hypoxia, response to drug, anti-apoptosis and positive regulation of transcription from RNA polymerase II promot...Continue Reading

References

Aug 1, 1984·The Journal of Dairy Research·A J Bramley, F H Dodd
Jul 1, 1997·The Veterinary Journal·M A Kossaibati, R J Esslemont
Aug 17, 1999·Preventive Veterinary Medicine·P J Rajala-Schultz, Y T Gröhn
Jan 14, 2003·Annual Review of Immunology·Kiyoshi TakedaShizuo Akira
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Oct 11, 2003·Trends in Genetics : TIG·Yves MoreauMichal Dabrowski
Oct 15, 2003·Veterinary Research·Christian BurvenichLuc Duchateau
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
May 13, 2004·Clinical and Diagnostic Laboratory Immunology·Douglas D BannermanPascal Rainard
Sep 21, 2004·Journal of Dairy Science·Y T GröhnY H Schukken
Nov 1, 2005·Drug Discovery Today·Miles D HouslayKam Y J Zhang
Feb 24, 2006·Nature Reviews. Molecular Cell Biology·Andrew R Joyce, Bernhard Ø Palsson
Jul 19, 2006·Biochemical Pharmacology·Christoffer GebhardtJochen Hess
Sep 9, 2006·Journal of Dairy Science·K LauzonP Lacasse
Aug 19, 2007·IEEE Transactions on Systems, Man, and Cybernetics. Part B, Cybernetics : a Publication of the IEEE Systems, Man, and Cybernetics Society·Darren DanceyDavid McLean
Dec 7, 2007·The Journal of Immunology : Official Journal of the American Association of Immunologists·Umayal Lakshmanan, Alan G Porter
Jun 17, 2008·Animal Reproduction Science·A AhmadzadehM A McGuire
Jun 21, 2008·The Journal of Immunology : Official Journal of the American Association of Immunologists·Lone SkovJan G J van de Winkel
Sep 5, 2008·PLoS Medicine·Adaikalavan RamasamyDouglas G Altman
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 17, 2009·Molecular Diversity·Khac-Minh Thai, Gerhard F Ecker
Feb 2, 2010·Current Genomics·Aurelia BuscaAshok Kumar
Jan 29, 2011·BMC Medical Genomics·Azadeh MohammadiMansoor Salehi

❮ Previous
Next ❯

Citations

Jun 13, 2019·Journal of Applied Genetics·Somayeh SharifiJames M Reecy
Jun 27, 2019·Scientific Reports·Hamed Kharrati-KoopaeeAli Esmailizadeh
Mar 11, 2020·Scientific Reports·Robert M HydeMartin J Green
Feb 28, 2020·Scientific Reports·Taesic Lee, Hyunju Lee
Jan 4, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Devika Subramanian, Jeyakumar Natarajan
Mar 6, 2021·Veterinary and Animal Science·T C F Carvalho-SombraD C S Nunes-Pinheiro
Jul 10, 2021·The Journal of Dairy Research·Matheus DenizJoão Ricardo Dittrich

❮ Previous
Next ❯

Methods Mentioned

BETA
PCA

Software Mentioned

MetaDe
Google Scholar
R Affy package
R
DAVID
Dataset for Annotation , Visualization and Integrated Discover...
RapidMiner Studio
RapidMiner

Related Concepts

Related Feeds

Apoptosis

Apoptosis is a specific process that leads to programmed cell death through the activation of an evolutionary conserved intracellular pathway leading to pathognomic cellular changes distinct from cellular necrosis

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.

Apoptotic Caspases

Apoptotic caspases belong to the protease enzyme family and are known to play an essential role in inflammation and programmed cell death. Here is the latest research.

Anti-inflammatory Treatments

A drug or substance that reduces inflammation (redness, swelling, and pain) in the body. Anti-inflammatory agents block certain substances in the body that cause inflammation and swelling. Discover the latest research on anti-inflammatory treatments here

Caspases in Metabolic Diseases

Caspases, the family of cysteine proteases are involved in programmed cell death, but their role in metabolic diseases, inflammation and immunity has been of interested. Discover the latest research on caspases in metabolic diseases here.

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.