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Nucleic Acids Res. 2015 Jan;43(Database issue):D290-7. doi: 10.1093/nar/gku1012. Epub 2014 Oct 20.

Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events.

Author information

1
Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada.
2
Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada.
3
Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
4
Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.
5
Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada chris.overall@ubc.ca.

Abstract

The knowledgebase TopFIND is an analysis platform focussed on protein termini, their origin, modification and hence their role on protein structure and function. Here, we present a major update to TopFIND, version 3, which includes a 70% increase in the underlying data to now cover a 90,696 proteins, 165,044 N-termini, 130,182 C-termini, 14,382 cleavage sites and 33,209 substrate cleavages in H. sapiens, M. musculus, A. thaliana, S. cerevisiae and E. coli. New features include the mapping of protein termini and cleavage entries across protein isoforms and significantly, the mapping of protein termini originating from alternative transcription and alternative translation start sites. Furthermore, two analysis tools for complex data analysis based on the TopFIND resource are now available online: TopFINDer, the TopFIND ExploRer, characterizes and annotates proteomics-derived N- or C-termini sets for their origin, sequence context and implications for protein structure and function. Neo-termini are also linked to associated proteases. PathFINDer identifies indirect connections between a protease and list of substrates or termini thus supporting the evaluation of complex proteolytic processes in vivo. To demonstrate the utility of the tools, a recent N-terminomics data set of inflamed murine skin has been re-analyzed. In re-capitulating the major findings originally performed manually, this validates the utility of these new resources. The point of entry for the resource is http://clipserve.clip.ubc.ca/topfind from where the graphical interface, all application programming interfaces (API) and the analysis tools are freely accessible.

PMID:
25332401
PMCID:
PMC4383881
DOI:
10.1093/nar/gku1012
[Indexed for MEDLINE]
Free PMC Article

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