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However, the expression correlations of the new cell lines with those predicted to share similar addiction patterns were significantly higher (Fig. 4B; P<0.004, empirical significance based on the permuted null distribution).
Since mutations in the MECP2, FOXG1 and CDKL5 genes result in overlapping neurological phenotypes, we additionally investigated the inter gene expression correlations of the three genes in the brain.
First, we computed pairwise expression correlations of the eight FFRPs across a compendium of 466 transcriptome profiles of H. salinarum NRC-1 from 35 different growth conditions (high temperature, copper, high H2O2, etc.; Additional file 11: Table S10) [ 20, 21, 28- 36].
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For example, nodes can be colored to indicate sub-cellular localizations of the proteins in the two-step network, the size of nodes and edges can be rendered to reflect metrics of interaction confidence values, the expression correlation of the mRNA transcripts associated with the proteins in the two-step network, or other network properties such as clustering coefficients (Figure 4B).
In this case the association between two genes was quantified as the gene expression correlation of the genes (Methods).
Finally, no clear expression correlation of the transcription factors to their respective transporters could be stated (data not shown).
The high expression correlation of the PSY-ECG50 is a strong indicator that these genes may function in common biological processes.
We compared this result with what could be found by only looking at gene expression correlation of the genes that are linked in our pathway.
Briefly, expression correlations of all the PCSK genes with all the other genes in the human genome (n = 17330) were analyzed in large number (n = 1869) of samples.
Although there is low reproducibility of differentially expressed genes between diverse data sources for the same kind of diseases, the expression correlation of those genes is high [ 46].
We also compared the expression correlations of different markers between ACC and normal looking tissues (Table 2).
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