LOCATE: a mouse protein subcellular localization database

Abstract

We present here LOCATE, a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing >1700 peer-reviewed publications. LOCATE represents the first effort to catalogue the experimentally verified subcellular location and membrane organization of mammalian proteins using a high-throughput approach and provides localization data for approximately 40% of the mouse proteome. It is available at http://locate.imb.uq.edu.au.

Figure 1

Visualization of MemO- and Pfam- and SCOP-predicted motif data. (a) Plots the number of computational methods (from 0 to 5) that predict whether a residue in the protein sequence participates in a helical transmembrane domain. Five independent methods are used in the TMD prediction; we assign a residue to a TMD if at least three of the five methods have a positive prediction at that position in the sequence and the range of the predicted TMD fulfils a set of rules defined in the MemO pipeline (M. J. Davis, F. Clark, J. L. Fink, Z. Yuan, F. Zhang, T. Kasukawa, Y. Hayashizaki, P. Carnici and R. D. Teasdale, manuscript in preparation). (b) A schematic diagram of a protein sequence with predicted domains mapped onto it. In this particular diagram, the transmembrane domains predicted by MemO are shown at the top of the figure and the domains predicted by Pfam or SCOP are shown in the bottom of the figure. The schematics are vertically aligned to show the positional relationships of the predicted TMDs and other domains.

Figure 2

Splicing graph. This graph shows the observed exons and splice junctions for the transcriptional unit 101566 and the splice isoforms of the transcripts that arise from this transcriptional unit. The light gray color represents soluble, cytoplasmic proteins (PA101566.2 and PA101566.4); light orange represents a Type II membrane protein (PA101566.1); black represents all observed exons. The green and red bars represent the observed start and stop codons, respectively. The teal rectangle represents the position and range of the MemO-predicted transmembrane domain; note that the transmembrane domain occurs in the exon that only appears in the Type II membrane protein and not in the soluble, cytoplasmic proteins. This is a clear example of how alternate splicing of these transcripts may change the proteins' membrane organization.