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Analysis of gene correlations across all data sets, independent of "cell of origin" class, demonstrates a consistent association with a hierarchy of immune-regulatory gene expression that places IDO1, LAG3 and FGL2 ahead of PD1-ligands CD274 and PDCD1LG2.
Second, when we mapped the genes on fosmid-cloned genome fragments as a function of their origin class (archaeal core, lineage-specific core, early HT-genes, late HT-genes, and others), both early and late HT-genes were scattered among typical archaeal genes from the other classes.
In general, synteny blocks (here broadly defined as arrays of contiguous genes of same origin class) were small for all gene classes but those including early and late HGT events had the shortest average lengths (supplementary fig. S6, Supplementary Material online), indicating that HT-genes were transferred mostly as single genes and/or that HT-genes interspersed after transfer into host genomes.
Synteny blocks in archaeal fosmids were defined as arrays of one of more contiguous genes of same origin class (archaeal core, lineage-specific core, early HT-genes, late HT-genes, and others, including the remaining predicted genes without homologs in the database).
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Overall differences were already seen at a very general level of functional classification in COG classes and KEGG superclasses between gene origin classes.
We have previously developed an applied gene expression-based classifier for the separation of DLBCL cases into so-called "cell of origin" classes in samples derived from FFPE material [ 33].
However, there were remarkable similarities in the functional patterns observed for the different gene origin classes between Thaumarchaeota and GII/III-Euryarchaeota (fig. 7), suggesting similar underlying processes and/or mechanisms of adaptation by gene acquisition.
We have demonstrated that, in contrast with their expression in cell lines of differing origins, class IA PI3K adaptor, p85, and class II PI3K enzymes display a specific and selective tissue distribution.
For S. cerevisiae, we assessed the localization of 264 GO terms and 17 other functional annotations, including centromeres, telomeres, retrotransposon long terminal repeats (LTRs), classes of non-coding RNAs, classes of replication origins, classes of DNA breakpoints, and classes of cell cycle -regulated genes (full list in Methods).
Interneurons with different origin form separate interneuron classes and display distinct cellular properties.
In the long run, native talent endowment and family of origin social class position run together for all members of society.
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