Data for: Glucocorticoids, genes and brain function

Published: 7 December 2017| Version 2 | DOI: 10.17632/zy9rbrnrg6.2
Contributors:
Grzegorz Juszczak,
Adrian Stankiewicz

Description

A search of the PubMed database revealed 17 transcriptomic studies that investigated the effects of cortisol, corticosterone or dexamethasone (synthetic glucocorticoid) on gene transcription in the brain or in cells derived from the central nervous system (Table 1). Transcriptomic data retrieved from papers and supplementary data were standardized using the bioDBnet/dbFind tool (https://biodbnet-abcc.ncifcrf.gov/db/dbFind.php). The original gene identifiers (input data) were converted into standardized gene names for the species used in the experiments. If available, Affymetrix or Illumina probe IDs were used as the input data for standardization, which allowed us to obtain the most up-to-date annotation for a given probe. If the probe ID was not available in the original data set or if the query using the probe ID as an input did not return data, the gene name was used as an input instead, followed by any other identifier that was provided by the authors of a given study. If by this point no standardized gene name was acquired, the output was obtained in one of three ways. If the Affymetrix probe ID was available, it was analyzed in the Affymetrix proprietary database (NetAffx™ Analysis Center, https://www.affymetrix.com/analysis/index.affx). In a few cases, where an ambiguous description of a gene was provided, the standardized gene name was recovered manually. Finally, if we were unable to obtain a standardized gene symbol, the original gene name was used. The obtained list of genes was sorted according to the frequency and consistency of transcriptional responses (up- or down-regulation reported in separate papers) using a proprietary R script. The resulting lists of genes were corrected in cases where the corresponding genes (orthologs) in mice, rats or humans have different names (Mt2/Mt2a and Il6r/Il6ra).

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Systems Neuroscience

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