Skip to main content
main-content

01.12.2018 | Research article | Ausgabe 1/2018 Open Access

BMC Immunology 1/2018

Cattle infection response network and its functional modules

Zeitschrift:
BMC Immunology > Ausgabe 1/2018
Autoren:
Hamid Beiki, Abbas Pakdel, Ardeshir Nejati Javaremi, Ali Masoudi-Nejad, James M. Reecy
Wichtige Hinweise

Electronic supplementary material

The online version of this article (https://​doi.​org/​10.​1186/​s12865-017-0238-4) contains supplementary material, which is available to authorized users.

Abstract

Background

Weighted Gene Co-expression Network analysis, a powerful technique used to extract co-expressed gene pattern from mRNA expression data, was constructed to infer common immune strategies used by cattle in response to five different bacterial species (Escherichia coli, Mycobacterium avium, Mycobacterium bovis, Salmonella and Staphylococcus aureus) and a protozoa (Trypanosoma Congolense) using 604 publicly available gene expression microarrays from 12 cattle infection experiments.

Results

A total of 14,999 transcripts that were differentially expressed (DE) in at least three different infection experiments were consolidated into 15 modules that contained between 43 and 4441 transcripts. The high number of shared DE transcripts between the different types of infections indicated that there were potentially common immune strategies used in response to these infections. The number of transcripts in the identified modules varied in response to different infections. Fourteen modules showed a strong functional enrichment for specific GO/pathway terms related to “immune system process” (71%), “metabolic process” (71%), “growth and developmental process” (64%) and “signaling pathways” (50%), which demonstrated the close interconnection between these biological pathways in response to different infections. The largest module in the network had several over-represented GO/pathway terms related to different aspects of lipid metabolism and genes in this module were down-regulated for the most part during various infections. Significant negative correlations between this module’s eigengene values, three immune related modules in the network, and close interconnection between their hub genes, might indicate the potential co-regulation of these modules during different infections in bovine. In addition, the potential function of 93 genes with no functional annotation was inferred based on neighbor analysis and functional uniformity among associated genes. Several hypothetical genes were differentially expressed during experimental infections, which might indicate their important role in cattle response to different infections.

Conclusions

We identified several biological pathways involved in immune response to different infections in cattle. These findings provide rich information for experimental biologists to design experiments, interpret experimental results, and develop novel hypothesis on immune response to different infections in cattle.
Zusatzmaterial
Additional file 1: Table S1. Module membership, connectivity and expression pattern of 14,499 probe-sets used in this study. (XLSX 1290 kb)
12865_2017_238_MOESM1_ESM.xlsx
Additional file 2: Table S2. Over-represented GO/Pathway terms in the co-expressed modules. (XLSX 206 kb)
12865_2017_238_MOESM2_ESM.xlsx
Additional file 3: Figure S1. Functional analysis of the “saddle brown” module genes. Over-represented GO/pathway terms were grouped based on kappa statistics [ 62]. The size of each category within a pie chart represents the number of included terms. Only the most significant GO/ terms within groups were labeled. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories. (A) Representative biological processes interactions among module genes. (B) Representative Reactome analysis interactions among module genes. (PDF 1302 kb)
Additional file 4: Figure S2. Functional analysis of the “light yellow” module genes. Over-represented GO/pathway terms were grouped based on kappa statistics [ 62]. The size of each category within a pie chart represents the number of included terms. Only the most significant GO/ terms within groups were labeled. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories. (A) Representative biological processes interactions among module genes. (B) Representative molecular function interactions among module genes. (C) Representative Reactome analysis interactions among module genes. (PDF 1482 kb)
Additional file 5: Figure S3. Functional analysis of the “blue” module genes. Over-represented GO/pathway terms were grouped based on kappa statistics [ 62]. The size of each category within a pie chart represents the number of included terms. Only the most significant GO/ terms within groups were labeled. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories. (A) Representative biological processes interactions among module genes. (B) Representative molecular function interactions among module genes. (C) Representative Reactome analysis interactions among module genes. (PDF 2680 kb)
Additional file 6: Table S3. Over-represented GO/Pathway terms in the “green”, “saddle brown”, “light yellow” and “blue” module hub genes. (XLSX 43 kb)
12865_2017_238_MOESM6_ESM.xlsx
Additional file 7: Table S4. Functional enrichment analysis of close neighbors (TOM > 0. 1) of 85 un-annotated genes in the network. (XLSX 50 kb)
12865_2017_238_MOESM7_ESM.xlsx
Additional file 8: Figure S4. Frequency of TOM connectivity in the network. (PDF 262 kb)
12865_2017_238_MOESM8_ESM.pdf
Literatur
Über diesen Artikel

Weitere Artikel der Ausgabe 1/2018

BMC Immunology 1/2018 Zur Ausgabe

Neu im Fachgebiet Innere Medizin


 

Meistgelesene Bücher aus der Inneren Medizin

2017 | Buch

Rheumatologie aus der Praxis

Entzündliche Gelenkerkrankungen – mit Fallbeispielen

Dieses Fachbuch macht mit den wichtigsten chronisch entzündlichen Gelenk- und Wirbelsäulenerkrankungen vertraut. Anhand von über 40 instruktiven Fallbeispielen werden anschaulich diagnostisches Vorgehen, therapeutisches Ansprechen und der Verlauf …

Herausgeber:
Rudolf Puchner

2016 | Buch

Ambulant erworbene Pneumonie

Was, wann, warum – Dieses Buch bietet differenzierte Diagnostik und Therapie der ambulant erworbenen Pneumonie zur sofortigen sicheren Anwendung. Entsprechend der neuesten Studien und Leitlinien aller wichtigen Fachgesellschaften.

Herausgeber:
Santiago Ewig

Mail Icon II Newsletter

Bestellen Sie unseren kostenlosen Newsletter Update Innere Medizin und bleiben Sie gut informiert – ganz bequem per eMail.

© Springer Medizin 

Bildnachweise