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We selected the top 500 genes that are differentially expressed between subclass A and subclass B. We calculated and compared relative average gene expression ratios between subclass A and subclass B in each species.
We used independent t-tests to select orthologous genes that had significant differences in expression between subclass A and subclass B in both species (P < 0.05 in both t-tests) and yielded 329 genes.
Gene expression patterns of HCCs from Myc, E2f1 and Myc E2f1 transgenic mice were most similar to those of the better survival group of human HCCs (subclass B), whereas the expression patterns of HCCs from Myc Tgfa transgenic mice and DENA-induced mouse HCCs were most similar to those of the poorer survival group of human HCCs (subclass A).
If the distance to template.A is smaller, a prediction of "subclass A" is assigned to sample S. A prediction of "subclass B" is similarly performed.
To model representative expression pattern of subclass A, i.e., over-expression of marker.A and under-expressed of marker.B, a value of 1 is assigned to each of the nA marker.A genes, and a value of −1 to each of the nB marker.B genes.
Considering the function diversity of subclass A, three Hsfs GhHsf39 (A2), GhHsf25 (and) and GhHsf34 (A4a) were also used as the representatives.
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Here we overview the key steps: For simplicity, suppose the case of prediction of 2 subclasses, A and B. The signature genes consist of nA (marker.A) and nB (marker.B) over-expressed marker genes in subclass A and B, respectively.
Suppose the case of prediction of 2 subclasses, A and B, and the signature to be tested includes nA and nB over-expressed marker genes in subclass A and B, respectively.
So far, eight structurally unrelated SR subclasses (A-H) [ 39] have been characterized of which subclasses A and B are thought to be the most relevant ones.
We define a class Father as a subclass of a class Ancestor and a class Son as a subclass of a class Descendent.
Such a subclass is a subset of a larger subclass of channels with very noisy unreliable links from the source to the relay.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com