The 8 regions amplified in ≥3 cell lines (Additional file 1: Table S9) include 825 protein-coding genes with microarray expression information; 396 of them had a higher average expression in lines with gains/amplifications vs. those without them.
On the Gbrowse search result page, four tracks are shown, including a predicted gene model track, a RNA-Seq assembled transcript track (linked to the transcript sequence and its microarray expression information), a RNA-Seq coverage plot track and a microarray probe track.
These links were selected as they may in addition support automated correlation with additional genomic information such as multiple sequence information, microarray expression data, conserved domains, as well as information on a gene's function.
We therefore related our microarray expression data to information on TFBSs upstream of the transcription start site [ 14].
This software plots gene expression over the Medusa network (in a color scale) by overlapping functional input data (microarray expression data) with interaction information (NOTCH, WNT, AD, and apoptosis subnetworks) and distributes the microarray signal according to the coordinates of the nodes and its interactions in the network of interest.
The correlation signature projects heterogeneous microarray expression data onto a coherent information space where a gene is represented by the vector of its correlations against a series of landmark genes.
Microarray expression data and miRNA-target information data are used to identify reliable regulatory relationship between miRNAs and mRNA, and then cooperative microRNAs can be identified using hypergeometric test.
TRUNCATULIX is a relational, integrated database of sequence data, annotation information and microarray expression data, which is specially created to store data of the model legume Medicago truncatula.
First, in order to improve upon the limitations of microarray data, we now propose a method to combine microarray expression data with mRNA:microRNA binding information.
This finding suggested that the DE-based strategy can provide additional advantages in identifying promising candidates by fully exploiting the rich information from the microarray expression data.
This database include a variety of information, for instance, microarray expression data with 255 samples from 14 experiments, 30 mRNA-seq samples belonging to four experiments, other genomic data including coding and non-coding genes (miRNA), as well as a set of SNPs from 17 wild and 14 cultivated soybean sub-species [ 52].
