The 30 most highly expressed transcripts identified here in HT-29 cells are shown in Table S1.
The most highly abundant lipoproteins identified were OspA, OspB, OspC, OspD, OppA (-I, -II, -III, and -IV), LA-7, DbpA, and BB0028.
The previously uncharacterized gene HSPC111 was among the most highly induced mRNAs identified in this analysis.
The most highly connected network identified represented a cluster of genes involved in glutamatergic synaptic transmission.
It should be noted that glial fibrillary acidic protein (GFAP) is one of the most highly correlated proteins identified in the curated list of proteins.
This lower-than-expected slope appeared to be caused by a single major outlier point representing a protein disulfide isomerase, the most highly expressed nontoxin identified for both species.
Examination of the most highly expressed transcripts identified enrichment of numerous functional pathways in SS-TAMs that were mainly associated with enhanced phagocytic capacity, elevated lipid metabolism, matrix remodeling, and wound healing.
Among the transcriptionally active transcripts, the top 500 most highly expressed were identified from the leaf sheath (Additional file 1) and roots (Additional file 2) under N-limited conditions.
One of the most highly upregulated genes identified was ADRB3; the protein encoded by this gene has been shown to have functions in carbohydrate metabolism, energy reserve metabolism, positive regulation of the MAPK cascade and regulation of apoptosis [ 39, 40].
The cysteine synthase a transcript was also the most highly abundant transcript identified previously with paper (cellulose) feeding [ 26], which was the control condition (with acetone) in the current study.
