BpLi: Circadian Genes Expression in Bipolar Disorder Patients
In SARP.compo: Network-Based Interpretation of Changes in Compositional Data

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These two datasets give the expression level of main circadian genes in lymphoblastoid cells from bipolar disorder patients, as determined by qRT-PCR. Results are expressed in cycle thresholds (CT) units.

1 2	data(BpLi_J2) data(BpLi_J4)

Each dataset is a data frame with 78 rows and 26 columns. Each row give the RNA quantification of circadian and control genes for lymphoblastoid cells of a given patient, either with or without lithium in the culture medium.

Phenotype	factor	Patient phenotype, either responding (R) or not (NR) to lithium
Patient	integer	Patient code
Li	factor	Is lithium present (Oui) or not (Non) in the culture medium of the cells

Other columns are the different circadian genes and reference genes expression levels, expressed as quantities in arbitrary units after quantitative reverse transcription PCR assays, using the Syber Green technology. Three sets of assays were done, using three different dilutions according to the explored gene: 1/20 (PER3, BHLHE41, NR1D1, DBP), 1/100 (GSK3b, RORA, PER1, PER2, CLOCK, ARNTL, CRY2, BHLHE40) and 1/200 (ARNTL2, TIMELESS, CRY1, CSNK1E). The numerical suffixe after the reference gene name (SDHA or HPRT) gives this dilution level – for instance, SDHA_20 is for the 1/20 dilution level, HRPT_100 for the 1/100 level...

Patients were classified as presenting a good response (R) or a lack of responce (NR) to lithium treatment based on the ALDA scale, see the original publication for details. Lymphoblastoid cells from each patients, obtained from blood samples, were cultivated for 2 (BpLi_J2) or 4 (BpLi_J4) days either with or without LiCl.

Data courtesy allowed to be included in the package, by Cynthia Marie-Claire.

Geoffrey, P. A., Curis E., Courtin, C., Moreira, J., Morvillers, T., Etain, B., Laplanche, J.-L., Bellivier, F. and Marie-Claire, C. (2017). Lithium response in bipolar disorders and core clock genes expression. World J Biol Psychiatry, doi: 10.1080/15622975.2017.1282174.

SARP.compo documentation built on May 16, 2021, 1:06 a.m.