From this analysis pipeline, we defined "predicted causal interactions" as those miRNA-mRNA interactions between putative TDP-43-regulated miRNAs and target mRNA transcripts with annotations in the processes discovered by FatiGO.
The list of "tissue-specific" transcripts, with annotations, is provided in Additional file 11.
In the Additional file 10 we report the 81 Torvum transcripts with annotations referring to candidate R genes analogs (RGAs).
Transcripts may also be looked up by biological function using a keyword search tool that returns lists of transcripts with annotations matching a keyword or a phrase.
We interrogated the vgDbESTs for other transcripts with annotations related to lysosomal processes and singleton transcripts were identified in multiple species (data not shown).
In this way we listed those 20 transcripts with annotations that were most up- or most downregulated in light-induced plasmodia, based on the statistical significance of their differential expression (P < 0.05; Tables 2 and 3).
A total of 19,529 transcripts with annotations from Pfam (10,122) [ 24], PANTHER (8,905) [ 25], NCBI eukaryotic orthologous groups (KOG) (5,623) [ 26], KEGG (2,724 KEGG ortholog), and Arabidopsis homologous genes (9,106) were obtained.
Putative protein-coding genes and exons were obtained by overlapping the 368 transcript contigs with annotations from the four non-human genomes.
An analysis of the DE transcripts was performed using only the top DE transcripts with annotation derived from primary annotation sources rather than passaged secondary annotations (Table 3).
Putative maternal-sibling care transcripts were largely unannotated, but among transcripts with annotation (Additional file 2: Table S2) was odorant binding protein 1 precursor (obp 1; pheromone binding).
