Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

BMC Genomics

Table 3 Gene cluster and proteome peptide identification results.

	Number of APS matches (to Gene clusters, Proteins, or Peptides)	i) "Best" filtered model consistent with peptide data	ii) Gene cluster does not contain a "Best" filtered model, but does have APS matches	iii) "Best" filtered model in cluster is inconsistent with peptide data
Gene Clusters	214	201	9	4
Protein identifications
Total	2872	2729	56	87
Single peptide	1791	1698	28	65
Multi-peptide	1081	1031	28	22
Peptide identifications
Unique	405	379	13	13
(single peptide hits)	(149)
(multi-peptide hits)	(256)

(Identified peptides validating exon/intron boundaries: 54 peptides covering 54 introns)
Of the 8709 gene model clusters generated only 214 contained individual gene models with significant APS scores. These 214 clusters were then classified into three distinct types; a). those where all peptide identifications were consistent with the filtered gene model selected as the best model for that particular genomic locus, b). those where the cluster did not include a "best" filtered model but still contained models with matching peptide identifications, and c). those clusters where the "best" filtered model either did not match or other models in the cluster were more parsimonious with the proteomics data suggesting that the filtered model was not the most likely model for that particular gene locus.

ISSN: 1471-2164