Processed Data Sets for Consensus CSD Network for Bipolar Disorder

The aim of my master's thesis is to develop and generate a consensus CSD network for bipolar disorder (BP). This has relied on six data sets for BP and control samples, as well as a data set from skin for method development and CSD data from basal ganglia for comparison purposes. The processed versions of these data sets are available here. The Cytoscape file for BP, as well as the link lists for the CSD networks based on weighted untransformed and Fisher's Z transformed averages of correlation coefficients, are also provided. <br> The skin data set, used for the method development of the consensus CSD approach, originates from the GTEx Portal and is called ”Skin - Not Sun Exposed (Suprapubic)”. This data set has been converted to an appropriate format for CSD analysis. In addition, Gencode IDs have been translated to gene names, gene expressions have been averaged if some Gencode IDs correspond to the same gene names and the number of genes has been reduced to 1000. <br> The original data sets used for CSD analysis of bipolar disorder may be found at GEO with the following accession numbers: GSE80655, GSE92538, GSE53987, GSE5388, GSE12649 and GSE120340. The processed versions of these data sets have been normalized (if required), BP and control samples have been extracted, probe IDs have been converted to gene names and ambiguous and zero expression probes/genes as well as non-universally represented genes have been omitted. <br> The CSD data set from basal ganglia originates from Almaas Lab. The processed version of this data set includes the same gene pairs as the CSD network for BP and has been used to investigate a potential shift in correlations in the dorsolateral prefrontal cortex of BP patients towards basal ganglia.