The reported filtering routine can capture the core cell-type-specific PPI network for any cell-type from time series gene expression datasets, and is not limited to well-known systems.
Moreover, the specific changes in the pathways that overlap between the two cell types vary considerably; pathways that form part of the strong core in one cell type may be only perturbation-specific in another cell type, suggesting different usage of the same pathways in response to different environmental stresses.
Protein Epitope matching table presents UniProt ID, protein type, origin information (organism, genotype, genome, chromosome and allele) and information of the epitope (cell type, core epitope, epitope name, sequence, the caused disease, antibody, MHC serotype and epitope position).
Figure 5 breaks the pathway responses into three categories: "strong core" responses in either cell type are significant for multiple individual conditions as well as all individual conditions together.
The expression profiles of the MS and PS genes were obtained for each of the four core eVOC ontologies (Anatomical System, Cell Type, Developmental Stage and Pathology).
Although most cells possess the basic RNAi core machinery, some cell types have the intriguing ability to naturally take up exogenous dsRNA and use it to initiate RNAi silencing [ 22, 23, 40- 42].
Conventionally, core TFs are selected to convert one cell type into another mostly based on literature and the experimental identification of genes that are differentially expressed in one cell type compared to the specific cell types.
In addition, DAGs (diacylglycerols), retinylesters [ 7– 9] and ether lipids have been reported to be components of the LD cores in different cell types [ 10, 11].
A key finding was that there exists a universal core of functionally associated host responses irrespective of immune cell type.
Both pathway-level and metabolite-level analyses helped to identify core metabolic responses to multiple perturbations common across both cell types, with three metabolites identified as a conserved core response module, responding to multiple environmental perturbations in each cell type.
We determined a substantial "core" set of promoters possessing each mark in every surveyed BTSC cell type, which largely overlapped the corresponding fNSC sets.
