Download the full-sized PDF of Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella sheddingDownload the full-sized PDF



Permanent link (DOI):


Export to: EndNote  |  Zotero  |  Mendeley


This file is in the following communities:

Roy Berg Kinsella Research Ranch


This file is in the following collections:

Journal Articles (Kinsella Ranch)

Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding Open Access


Author or creator
Kommadath, A.
Bao, H.
Arantes, A. S.
Plastow, G. S.
Tuggle, C. K.
Bearson, S. M. D.
Guan, L. L.
Stothard, P.
Additional contributors
expression data
protein families
enterica serovar typhimurium
Type of item
Journal Article (Published)
Background Salmonella enterica serovar Typhimurium is a gram-negative bacterium that can colonise the gut of humans and several species of food producing farm animals to cause enteric or septicaemic salmonellosis. While many studies have looked into the host genetic response to Salmonella infection, relatively few have used correlation of shedding traits with gene expression patterns to identify genes whose variable expression among different individuals may be associated with differences in Salmonella clearance and resistance. Here, we aimed to identify porcine genes and gene co-expression networks that differentiate distinct responses to Salmonella challenge with respect to faecal Salmonella shedding. Results Peripheral blood transcriptome profiles from 16 pigs belonging to extremes of the trait of faecal Salmonella shedding counts recorded up to 20 days post-inoculation (low shedders (LS), n = 8; persistent shedders (PS), n = 8) were generated using RNA-sequencing from samples collected just before (day 0) and two days after (day 2) Salmonella inoculation. Weighted gene co-expression network analysis (WGCNA) of day 0 samples identified four modules of co-expressed genes significantly correlated with Salmonella shedding counts upon future challenge. Two of those modules consisted largely of innate immunity related genes, many of which were significantly up-regulated at day 2 post-inoculation. The connectivity at both days and the mean gene-wise expression levels at day 0 of the genes within these modules were higher in networks constructed using LS samples alone than those using PS alone. Genes within these modules include those previously reported to be involved in Salmonella resistance such as SLC11A1 (formerly NRAMP1), TLR4, CD14 and CCR1 and those for which an association with Salmonella is novel, for example, SIGLEC5, IGSF6 and TNFSF13B. Conclusions Our analysis integrates gene co-expression network analysis, gene-trait correlations and differential expression to provide new candidate regulators of Salmonella shedding in pigs. The comparatively higher expression (also confirmed in an independent dataset) and the significantly higher connectivity of genes within the Salmonella shedding associated modules in LS compared to PS even before Salmonella challenge may be factors that contribute to the decreased faecal Salmonella shedding observed in LS following challenge.
Date created
License information
Attribution 4.0 International

Citation for previous publication
Kommadath, A., Bao, H., Arantes, A.S., Plastow, G.S., Tuggle, C.K., Bearson, S.M.D., Guan, L.L., Stothard, P. (2014). Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding. BMC Genomics, 15(452)

Link to related item

File Details

Date Uploaded
Date Modified
Audit Status
Audits have not yet been run on this file.
File format: pdf (Portable Document Format)
Mime type: application/pdf
File size: 1677077
Last modified: 2016:06:24 18:08:23-06:00
Filename: BMC_GEN_15(542)
Original checksum: e46912ad23de3df5c344dccc050bbd8f
Copyright note: ??? 2014 Kommadath et al.; licensee BioMed Central Ltd.
Well formed: true
Valid: true
File title: Abstract
File title: Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
File author: Arun Kommadath
Page count: 15
Activity of users you follow
User Activity Date