Introduction

Protein-protein interaction is a very important aspect of function genomics analysis. When elucidating protein functions with high through-put interaction data, localization information is always another factor need to take into account. The advancing of large scale protein subcellular localization detection and prediction has paved the road forconsidering proteins’ roles on their more specific environment, the cellular compartments’ level. In order to improve the usage and quality of interaction data, here, we present the SPPI database, integrating subcellular localization annotations to protein interaction data. The initial release contains about 22,500 subcellular localization-annotated interactions, over 80% of which are more reliable intra-subcellular ones. In addition, a currently largest high quality protein localization annotation dataset is also provided for new interaction filtration and other localization related usages.

Furthermore, database protein entries with filtered interactions have been grouped into five fully referenced subdatasets (animal, plant, virus, bacteria and eukaryote) based on their taxonomy class, and are further classified into eleven main categories according to respective subcellular localizations for easier search by experimentalists either with their special purpose, and confirm or at least partly help filtering their primary high throughput protein-protein interaction data. Based on sequence alignment, non-redundant subsets are also built, which may provide useful information for subcellular localization prediction. Besides, full and non-redundant subsets without repetitive sequences and short sequences of <20 amino acids which have standard machine readable sublocation information (such as extracellular, plasmic membrane et.al.)