Presentation on theme: "Swan River foreshore, Perth, Western Australia University of Western Australia Biomedical, Biomolecular and Chemical Sciences."— Presentation transcript:
Swan River foreshore, Perth, Western Australia University of Western Australia Biomedical, Biomolecular and Chemical Sciences
Ian SmallMurray BadgerDavid DayHarvey Millar Steve SmithBarry PogsonJim Whelan ARC Centre Plant Energy Biology
SUBA SUBcellular location database for Arabidopsis proteins Sandra Tanz and Ian Castleden 4 th March 2011
Why protein localisation? Contributes towards the understanding of protein function and of biological inter-relationships, i.e. only proteins in the same location can interact. Separate subcellular locations often represent distinct cellular environments: proteins share similar attributes and play roles in defining the function of a subcellular compartment. To build hypotheses or models: large-scale phenotyping screens, microarray experiments and protein-protein interaction assays rely on protein localisation info.
How to localise proteins? Prediction In vitro uptake (imports) In vivo (GFP) Enzyme activity measurements Western blot Immunogold labeling Subcellular proteomics (MS) Protein-protein interaction Images modified from Millar et al., 2009
SUBA: SUBcellular location database for Arabidopsis proteins
What does SUBA document? MS (6398)GFP (2135) SUBA II (2007)SUBA III (2011) Combined sub-location data 250’719 1’022’040 Calls by PPI Calls by experiments (GFP, MS)827319’528 Distinct proteins localised by GFP and/or MS Bioinformatic predictions by10 predictors24 predictors NEW!
Data mining Search of the NCBI PubMed (Medline) and Entrez (GenBank) databases using keywords Alert via
Data mining Search publication to extract localisation information = fully curated data
SUBA III interface
SUBA III interface
SUBA III flatfile
Analysis of SUBA III data – on the way… Do data become more or less consistent over time? Experimental data (MS vs GFP) How reliable are experimental localisation data? Has the overlap of data changed with increasing data sets?
How reliable are GFP localisation data? Total GFP localisations confirmed by MS Total GFP localisations disputed by MS MS (9016)GFP (2554) MS (74172)GFP (1844) 1386 neither confirmed or disputed
Analysis of SUBA III data – on the way… Do data become more or less consistent over time? Experimental data (MS vs GFP) How reliable are experimental localisation data? Has the overlap of data changed with increasing data sets? Does evidence for multiple locations mean the protein is dual targeted/dynamic or is it a false positive? Prediction vs experimental data How reliable are predictors today? PPI data What do PPI data tell us about sub-cellular location? Organellar proteome: Can we discover novel organellar proteins?
SUBA under the hood
SUBA Tables (predictors)
SUBA Tables (“original” sources)
Suba Tables (publications) etmode=xml&id=
SUBA Tables (automation)
SELECT suba3.suba3.*, suba3.src_ppi_1.* FROM suba3.suba3 LEFT OUTER JOIN suba3.src_ppi AS src_ppi_1 ON suba3.suba3.locus = src_ppi_1.`locusA` WHERE EXISTS (SELECT 1 FROM suba3.src_ppi WHERE suba3.suba3.locus = suba3.src_ppi.`locusA` AND suba3.src_ppi.`locusB` IN (‘AT3G ’)) “denormalisation” src_msms Suba2