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Regardless, the microarray experiments did not confirm the differential expression of the frd operon, as detected by BACFA analysis and confirmed by qRT-PCR.
AR performed the microarray experiments, did the mice infections, prepared all Figures and Tables, and participated in the analysis of the data and the writing of the manuscript.
BS performed HR MAS MRS and microarray experiments, did the preprocessing of the HR MAS MRS data, contributed to analysis and interpretation of HR MAS MRS and microarray data and drafting of the manuscript.
Given the many caveats of the data at the time the Lee et al. ChIP-chip data were collected only in YPD and the microarray experiments did not contain all possible environmental perturbations this finding paints a relatively optimistic picture regarding the functionality of individual TF binding sites.
Functional profiling of the differentially expressed genes from microarray experiments didn't reveal any enrichment in gene ontology categories related to cell proliferation.
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This compares favourably to Affymetrix microarray experiments done with LNCaP, which typically find between two and eight thousand genes (Gene Expression Omibus (GEO); [ 22, 23]; January 16th , 2006.
TuberQ also provides information about gene essentiality information, as determined from whole cell based knockout experiments, and expression information obtained from microarray experiments done in different stress-related conditions.
The development of Liverome was initiated to compare our own gene signatures derived from microarray experiments done on a large HCC cohort in Korea (through "The 21C Frontier Functional Human Genome Project of Korea") with publicly reported gene signatures.
Interestingly, our microarray experiment did not show any increase in the levels of Nfkb1 (e.g. p105 or p50) and RelA, the major components of classical NF-κB pathway [47], [48].
Moreover, a significant upregulation of GADD45A gene was observed in both MCF-7 and MDA-MB-231 cell lines, although the microarray experiment did not show any significant upregulation in the latter cell line.
Two of the MS-HRM assays used in the microarray validation experiments did not confirm the microarray results.
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