Supplemental functional annotation was inferred through the alignment of translated sequences against active sites in Pfam using the HMM-based tool provided by Pfam [68].
merlin's interface is particularly user friendly, providing "drop down boxes" (see Additional file 1: Figure S1 of the supplemental material) for the annotation of each gene.
The mean p-value for each cluster was determined and used to list the clusters in order of significance (additional file 2 – Supplemental Table S2: Functional annotation clustering of cigarette smoke signature genes).
(XLSM 1433 kb) Additional file 4: Supplemental Dataset 3. Gene Ontology annotations of representative transcripts.
A full list of the circRNAs identified is provided (Supplemental Table S1), including circRNA annotation, chromosomal coordinates, length, and accession number of the mRNA counterpart.
The subplot along with the annotation descriptions (see Supplemental Results) provide the genes associated with the cells surviving initial apoptotic events.
These examples demonstrate that the theoretical proteome of strain CBS1483 cannot be simply derived from the 10,172 protein sequences (Table 3; see also Table S4 in the supplemental material) predicted by genome annotation of the consensus sequence.
We also used annotations extracted from the supplemental data published by Johnston, et al., and added annotations for variants listed in ClinVar and locus-specific databases (LSDB) registered in the Leiden Open Variation Database (LOVD).
Raw and output data were exported along with TAIR10 annotations in the supplemental data (Additional files 2, 3 and 4: Table S1).
An example CSV annotation file from the supplemental material for [ 8] is shown in Figure 4.
