**IF stands for host-microbe interaction factor; CF stands for genes involved in core biological processes Colonization and survival in plants requires numerous factors including proteins involved with iron assimilation, protein secretion, exopolysaccharide synthesis, motility, and stress-resistance [ 23, 24].
These epigenetic mechanisms establish and maintain core biological processes, including genomic imprinting and entrainment of circadian rhythms.
These pathways resided in 9 of 21 core biological processes represented in Reactome, and included pathways relevant to extracellular matrix (ECM) integrity, innate immunity, axon guidance, and signaling by PDRF (platelet-derived growth factor), NOTCH, and the transforming growth factor-β/SMAD receptor complex.
This supports previous findings which suggest that several core biological processes involved in growth and metabolism are highly conserved across species.
A negative class label indicates the data point is not likely to be directly involved in host-microbe interaction, rather it is associated with core biological processes such as transcription and translation or central pathways of metabolism.
Protein-DNA interactions are fundamental to core biological processes, including transcription, DNA replication, and chromosomal organization.
Using this reciprocal BLAST approximation, the authors were able to determine that 40% of S. cerevisiae genes and 20% of C. elegans genes are orthologous and that these proteins carry out a set of core biological processes (intermediary metabolism, DNA/RNA metabolism, protein folding, trafficking, and degradation; Chervitz et al. 1998).
Gene products in this category are generally widely conserved across metazoans and many are involved in core biological processes.
Our data suggest that honey bees use CpG methylation of intragenic regions as an epigenetic mechanism to control the levels of activity of the genes that are broadly expressed and might be needed for conserved core biological processes in virtually every type of cell.
