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2015 ; 13
(2
): 1550010
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Analytical workflow profiling gene expression in murine macrophages
#MMPMID25708305
Nixon SE
; González-Peña D
; Lawson MA
; McCusker RH
; Hernandez AG
; O'Connor JC
; Dantzer R
; Kelley KW
; Rodriguez-Zas SL
J Bioinform Comput Biol
2015[Apr]; 13
(2
): 1550010
PMID25708305
show ga
Comprehensive and simultaneous analysis of all genes in a biological sample is a
capability of RNA-Seq technology. Analysis of the entire transcriptome benefits
from summarization of genes at the functional level. As a cellular response of
interest not previously explored with RNA-Seq, peritoneal macrophages from mice
under two conditions (control and immunologically challenged) were analyzed for
gene expression differences. Quantification of individual transcripts modeled
RNA-Seq read distribution and uncertainty (using a Beta Negative Binomial
distribution), then tested for differential transcript expression (False
Discovery Rate-adjusted p-value < 0.05). Enrichment of functional categories
utilized the list of differentially expressed genes. A total of 2079
differentially expressed transcripts representing 1884 genes were detected.
Enrichment of 92 categories from Gene Ontology Biological Processes and Molecular
Functions, and KEGG pathways were grouped into 6 clusters. Clusters included
defense and inflammatory response (Enrichment Score = 11.24) and ribosomal
activity (Enrichment Score = 17.89). Our work provides a context to the fine
detail of individual gene expression differences in murine peritoneal macrophages
during immunological challenge with high throughput RNA-Seq.
|Animals
[MESH]
|Computational Biology
[MESH]
|Gene Expression Profiling/*statistics & numerical data
[MESH]