Access information for the KLK15 gene and its protein product was downloaded from different databases as given in Additional file 1. Potential KLK15 alternative splice variants were identified through sequence alignment analysis of the splice variants and Expression Sequence Tags (ESTs) reported in publicly available databases including NCBI and Ensembl.
We assessed completeness of a hospital-based clinical register – the Obstetric Database – by linking data from all women registered in the Obstetric Database as having given birth in 2013 to the National Patient Register with coverage of all births in 2013.
Completeness was assessed by comparing data from all women registered in the Obstetric Database as having given birth in 2013 and linking to the National Patient Register which was considered a gold standard.
For example, KEGG LIGAND is a popular biochemical pathways database, but it is incomplete for many compounds found in human organs as given in the Human Metabolome database HMDB.
OsPP genes were mapped on chromosomes by identifying their positions as given in RGAP database.
The probability Pbias i, w) in Equation (1) is given by a binomial distribution: (2) where f x is the proportion of amino-acid type x as given by the database amino-acid composition.
In Figure 2 we decided to maintain the relative direction of the syntenic genes as given by Ensembl database (5-3 or 3-5), in order to help the reader understand the modules' position, and provide information concerning the conservation of the orientation of the genes in the investigated species.
Since our alignment method operates on individual reactions, independent of the existing pathways as given in current databases, we not only reconstruct known pathways (as presented by KEGG, e.g. Figure 5, 9a, 12b c), but also discover new pathway possibilities with the component reactions annotated in different maps and not linked with each other in the original database, e.g. Figure 9b and 12a.
(1979 ▶) as given in the CIF file of the Cambridge Structural Database refcode NAHYPL were used as input.
Although these AS databases give an insight into the level of alternative splicing, they do not provide any visual representation and classification of the types of alternative splicing events occurring [ 10].
