In short, differential gene expression was calculated using FPKM values for every gene while incorporating expression level variances during significance testing.
The basic model could also incorporate expression of the α6 subunit, assuming that additional gene-specific factors contribute to produce a different tissue-specific expression profile.
To visualize the relationships among these TB- and LTBI-specific molecular signatures, a potential interaction network incorporating expression information was built with Cytoscape v3.1.0 [ 34].
Before taking promising effector candidates to experimental validation, one can incorporate expression data of in planta infection such as microarray or RNAseq data.
MutSigCV corrects for variation by using patient-specific mutation frequency and spectrum and gene-specific background mutation rates, incorporating expression levels and replication time.
This indicates that the importance of expression variability in complex trait regulation is not limited to genetic model systems and that it may be possible for GWASs and QTL mapping studies to improve their track record by incorporating expression data.
The Global Contrast, incorporating expression information for all probesets in all groups, identified 4282 significantly regulated probesets (P < 0.05) (Fig. 2), representing genes that from an inferential perspective are differentially regulated by WY between the two mouse strains.
For the DREM 2.0 analysis the following options were not set to default values: (i) genes in the time course were discarded if "Minimum Absolute Expression Change" was smaller than 0.5, (ii) "incorporate expression in regulator data" was activated for transcription factors with "Expression scaling weight" set to 1.
The model incorporates RBM47 expression as a continuous variable, estrogen receptor (ER) expression, progesterone receptor (PR) expression and Her2 expression.
Endeavour (Tranchevent et al., 2008) incorporates gene expression data from 79 normal human tissues found in Gene Expression Atlas, comparing gene expression between candidate and user-supplied seed genes across tissues.
