Table 1 Terminology used in the present study.
Term | Definition |
|---|---|
Sample | One column in the expression matrix corresponding to a specific experimental condition in which the expression of all transcript is measured |
Subset | A down-sampled expression matrix |
Down-sampling | Extracting part of all samples contained in a full expression matrix to create a subset. |
Project | A group of samples from a same study |
Network | A list of the strongest links (=edges = associations) connecting transcripts (nodes). In individual networks, a lower HRR value indicates a stronger link. |
HRR | Highest Reciprocal Ranking: A ranking procedure of Pearson’s Correlation Coefficients |
PLC | Pathway Level Coexpression: a subnetwork containing a set of guide genes and their associated genes. |
Performance | Network and PLC performance is evaluated by their predictability regarding GO term annotations. It is quantitatively measured by the GO AUROC. It is quantitatively measured by the GO AUROC. |
GO AUROC | An absolute measurement of network performance in associating gene pairs into known GO associations. |
GG | Guide Gene: gene from a specific pathway used to extract other genes that are best co-expressed with it in a PLC. |
Aggregate | A superposition of several networks. Overlapping edges may be combined according to their HRR value or their number of occurrences. |
