Oxygen and nutrient diffusion limitations through the collagen I matrix as well as competition for available nutrients resulted in growing levels of intra-cellular hypoxia, quantified by a statistically significant (p < 0.01) upregulation of HIF-1α gene expression.
To account for relatedness, the variance/covariance matrix was estimated from the genomic kinship matrix, as pedigree information was not available.
Also included, as available, are relevant supporting documents – the summary results matrix (Matrix), the United Nations Development Assistance Framework (UNDAF) and the consolidated results reports (Consolidated results) of the previous programme cycle.
In theory, KBAC can incorporate a covariate matrix as well, although this functionality is not yet available in the KBAC public release.
For such matrix, signed network adjacency was calculated implementing the Adjacency function as available in R WGCNA package (version 1.46) [ 107].
The dataset is available at http://bcb.cs.tufts.edu/athmm/scop/data/ We used the BLOSUM62 matrix as our simple model of evolutionary mutations (Eddy, 2004).
The variance matrix of ĝ, which we denote by V, is available via the prediction error variance matrix, and the underlying spline variance matrix as outlined [ 23].
We do not see the matrix as a fixed entity, but an entity to be developed and updated, when more knowledge becomes available.
We refer to this matrix as the MoLFunC Matrix.
In fact, the procedure may declare two matrices as "unrelated" when many data are available and there is great power to detect differences, even if these differences are trivial from a biological point of view [ 26, 27].
