Given a GEO series ID, ChiBE retrieves the dataset and maps on the network, automatically.
We retrieved the dataset of their study numbered GSE16759 from GEO.
In this study, we retrieved the dataset of EC-genes from the CTD and explored their propensities to be miRNA targets.
Among the 12 non-participant investigators, seven did not reply to our invitation letter, three were not able to retrieve the original dataset and two were not interested in the project.
A harvesting process is executed to retrieve the standardized datasets, which consist of file packages, from IPT and Metacat and to extract and import their content into the integrated database for marine biodiversity.
In our context, when a scientist has more than one advisor, it is not clear which links should be cut to retrieve the original ancestors (our dataset prevents us from identifying the principal supervisor from the secondary one, if any).
The Ensembl Gene IDs were subsequently submitted to BioMart (Ensembl Genes 72, Mus musculus GRCm38.p1 dataset) to retrieve the corresponding 1,000-bp 1,000-bp flanks of the transcripts of the genes of interest from the genome annotation.
Concerning the murine Wnt5 genes, the analysed expression data were also retrieved from the dataset browser of GEO database, [ 57] from microarray experiment during mice pancreatic development, using the Affymetrix Murine Genome U74 Version 2 array [ 58].
The middle-ware written in Perl script simultaneously executes the bioinformatics pipelines from the query submitted by the end-user, and retrieves the archived CYP dataset.
First, we identified DEGs by retrieving the multiple gene microarray datasets from GEO (GSE27713).
