For example, Huang et al  used RNA-Seq technology to select differentially expressed genes
(DEGs) in the subcutaneous and intramuscular adipose tissues of Large White pigs and found that these genes were mainly involved in lipid metabolism, regulated adipocyte differentiation through the MAPK signaling pathway, and accordingly affected lipid accumulation in subcutaneous and intramuscular adipose tissues.
Furthermore, a comparison of gene profile of both strains has resulted insignificant difference in the number and level of expressed genes
in infected lung and spleen samples.
Among differentially expressed genes
, IL1B, IL17F, IL6R, CXCL2, CCL20 and CCL25 were selected based on their immunological functions and CD8B and CD81 may contribute to variations of blood T lymphocyte subsets.
Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to confirm the differentially expressed genes
(DEGs), and then treated the MC3T3-E1 cells with estrogen receptor (ER) inhibitors a and [sz], respectively, and then examined the expression of Tgfbr1 and Bmpr1a genes.
Identification of differentially expressed genes
and functional enrichment analysis
The largest effort in interrogating the transcriptome of endometrial cancer is from TCGA ; however both the initial comprehensive report from TCGA on endometrial cancer and the follow-up report by others who focused on the RNA-seq data of endometrial cancer in TCGA did not provide transcriptome-wide information on the differentially expressed genes
in the scenario of endometrial cancer versus normal endometrial tissue [7, 8].
While both had relatively few differentially expressed genes
after 2 h of imipenem exposure (Figure 1), BR21 had more than twice the number (1009) of differentially expressed genes
compared to BR7 (459) after 8 h of exposure.
Linear model-experience Bayesian statistics using the Limma package in R combined with t-tests were applied for nonspecific filtration of the expression profile data , and the differentially expressed genes
were screened out.
Analysis of Differentially Expressed Genes
. To determine the differentially expressed genes
(DEG) between PSC and ISC specimens, negative binomial distribution test (NB) was performed.
The expression levels of genes were analyzed to identify differentially expressed genes
([absolute value of log2 fold change] > 1.5; [P.sub.adj] < 0.01), because some genes with small fold changes could be statistically significant but may not be promising candidates for further investigation.
Enrichment Analysis and the Pathway of Differentially Expressed Genes
. Gene expression was analysed using the [DELTA][DELTA]CT method.