Metagenes [ 71] were isolated from our T47D microarray dataset representing each sample (PR-null, WT PR, KR PR; with or without R5020 treatment).
The procedure was used to integrate two microarray datasets representing the dynamic response of the E. coli MG1655 strain to acid exposure (pH = 5.5) and a gene KO experiment performed in the related strain E. coli BW 25113, representing the transcriptional state of strains mutated in the 26 most differentially expressed genes.
We further compared the actively transcribed gene groups FUS and Ac-H3K9, EWS and Ac-H3K9, and FUS, EWS, and Ac-H3K9, with microarray datasets representing HEK-293 cells with siRNA mediated depletion of FUS, EWS, or a combined FUS and EWS depletion (Fig. 4b-d) [ 47].
In addition to the accurate annotation of trout genes represented on the microarray, our dataset represents a valuable and solid base for further investigating the molecular mechanisms involved in testis differentiation and the onset of spermatogenesis in fish.
The input to this integrated program is a microarray gene expression dataset representing a number of clinical specimens, with annotations of phenotypic class for each sample.
To identify genes that are co-expressed with known PCW genes, we adopted a two-step bi-clustering approach to analyze the aforementioned microarray dataset, which is represented as a 21,031 × 351 matrix, a required format by the QUBIC program [ 21].
With the purpose of limiting the interference of stromal cell contaminants, we selected a dataset representing a microarray analysis of seven types of normal and tumour epithelial cells populations, purified by laser-capture micro-dissection (LCM) reported by Tomlins et al. [11].
Normalisation analysis has been performed on four distinct, publicly available, raw datasets, representing microarray time series measurements during the Yeast Saccharomyces Cerevisiae cell cycle.
However, given the paucity of CL tumors represented in our microarray dataset, this hypothesis warrants further investigation in larger sample populations.
The 'Number of genes' represent the number of genes representing that complex in each microarray dataset.
