Third, many prediction methods, including the two studies compared to here, consider only annotated proteins with at least one annotated interaction partner for their studies [ 16, 19, 26, 27, 62].
Novel exon skipping events were determined by identifying novel splice junctions that share are within annotated transcripts and span at least one annotated exon.
More specifically, we defined the interaction based on a measure of gene functional similarity introduced in [ 34] as follows: Two protein complexes are functionally interacted with each other if they share at least one annotating GO term, where annotating GO terms include direct annotating GO terms and their ancestors in the GO directed acyclic graph.
The "known" and "novel" contig clusters classification was based on Ensembl gene annotation (version 64) [ 20]: assembled contig clusters that overlapped with at least one annotated transcript by at least one nucleotide were classified as "known", the remaining contig clusters were classified as "novel".
They obtained a total of 679 differentially spliced genes, including 209 genes with at least one annotated alternative exon.
Besides a lower GC content, numerous predicted transposase genes are interspersed with the mam-like genes (at least 6 annotated transposase sequences were found between mamD-like and mamL-like).
We add a further constraint that, for each pair of TFs, at least one annotated binding site pair is within a cluster, i.e., sufficiently close to each other, as is typically the case in real promoters as well [76].
Only pathways that included at least 15 annotated genes were taken into consideration.
Exons, which were entirely coding in at least one annotated transcript, were labeled "CDS".
We took only the GO/pathway categories that had at least 10 annotated genes.
