PreP: gene expression data pre-processing.

TL;DR: Comparative genome hybridization led to the identification of gene loci in L. plantarum WCFS1 that modulate the immune response of DCs and Transcriptome analysis and qPCR data showed that transcript level of gtcA3, predicted to be involved in glycosylation of cell wall teichoic acids, was substantially increased in the lp_2991 deletion mutant.

TL;DR: Gel retardation experiments, Northern blotting, and enzyme assays showed that CcpA represses its own expression and activates the expression of the divergently oriented prolidase-encoding pepQ gene, which constitutes a link between regulation of carbon metabolism and regulation of nitrogen metabolism.

TL;DR: P pneumococcal CodY predominantly regulates genes involved in amino acid metabolism and contributes to the early stages of infection, i.e., colonization of the nasopharynx.

TL;DR: The direct role of CodY in the regulation of several target genes was demonstrated by gel retardation experiments, and a conserved 15 nt palindromic sequence, the so-called CodY-box, located in the vicinity of the -35 box of target promoter regions was identified.

TL;DR: Based on the other reported data on reproducibility, the fold difference, a criterion which discriminates differentially expressed genes from housekeeping genes, is g e n e r a l l y n o t a b o v e 2 n t h e r e l i a b l e c o n f i d e n c e i n t e r v a l s.

TL;DR: In this paper, a 2-fold difference was adopted to identify differentially expressed genes in the oral cancer cell using a suitable normalization method, to test the validation of normalization and eventually to identify genes that may involve in oral cancer.

TL;DR: Engene is a versatile, and platform-independent web tool for exploratory analysis of gene expression data that aims at storing, visualizing and processing large sets of geneexpression patterns.

TL;DR: By building a model of gene expression, which is based on a few fundamental assumptions, a method for correction was developed and is presented here and should substantially reduce measurement error.