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The same selection process was also run after random assignment of expression data as described above.
The philosophy adopted in this study regarding the assignment of expression status was conservative, as our focus was on building a high-quality resource.
To generate a null data set, we permuted the assignment of expression values in the human RH data, created a new correlation matrix, subtracted the matrix from the SymAtlas matrix and recomputed the Frobenius norm 10,000 times.
BN scores were directly converted to q-values - the false discovery rate [ 30] analogue of p-values, by comparing each feature's score on the original data to the distribution of scores from 1000 BN analyses on permuted data - each following an independent random permutation and assignment of expression values to the genes' putative cis-regulatory regions.
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Assignments of expression values to known genes were extracted from the UCSC table browser.
A more detailed assignment of CK1δ expression to specific differentiation steps and hematopoietic lineages could not be achieved on the CK1δ stained immunosections.
The assignment of prominence expression changes to particular GO, InterPro, KEGG or MGI Phenotype categories identified some tissue-specific differences, but these were relatively limited compared with the commonalities in cell metabolism, cell growth, and differentiation.
It enables the assignment of gene expression metrics and any comprehensive data to each network element.
A crucial issue when using supervised classification methods is that there must be solid evidence for the initial assignment of gene expression profiles to each category.
The assignment of gene expression data to individual metabolic reactions is complicated by the fact that there is not a one-to-one mapping between gene and reaction.
Other than total cohort median-based separation of patients, we also examined the relation of JMJD6 levels and prognosis by quartile assignment of JMJD6 expression in each subtype independently.
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