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

Fortelny N, Yang S, Pavlidis P, Lange PF, Overall CM - Nucleic Acids Res. (2014)

Bottom Line: 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.Neo-termini are also linked to associated proteases.In re-capitulating the major findings originally performed manually, this validates the utility of these new resources.

View Article: PubMed Central - PubMed

Affiliation: 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.

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Input and output of TopFINDer. (A) Input mask within the TopFIND web interface. (B) Venn diagram showing the overlap of termini evidences retrieved from TopFIND for a list of proteins. Evidence is either UniProt annotated terminus (Curated Start), terminus of an isoform derived from alternative splicing (Alternatively Spliced), or from alternative translation (Alternatively Translated), from cleavage (Cleaved), or a terminus observed in a non-protease related terminomics experiment (Experimentally Observed). (C) Matrix of substrates and proteases indicating cleavage of substrates. Fields are red where there is cleavage and black where there is none known between the protease and the substrate at this position. The y-axis shows the protein identifier and the position of each terminus. (D) Barplot showing the number of cleavages of each protease in the list. Bars of proteases whose cleavages are enriched in the list are in red, others in blue. (E) IceLogo of the sequences in the list.
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Figure 2: Input and output of TopFINDer. (A) Input mask within the TopFIND web interface. (B) Venn diagram showing the overlap of termini evidences retrieved from TopFIND for a list of proteins. Evidence is either UniProt annotated terminus (Curated Start), terminus of an isoform derived from alternative splicing (Alternatively Spliced), or from alternative translation (Alternatively Translated), from cleavage (Cleaved), or a terminus observed in a non-protease related terminomics experiment (Experimentally Observed). (C) Matrix of substrates and proteases indicating cleavage of substrates. Fields are red where there is cleavage and black where there is none known between the protease and the substrate at this position. The y-axis shows the protein identifier and the position of each terminus. (D) Barplot showing the number of cleavages of each protease in the list. Bars of proteases whose cleavages are enriched in the list are in red, others in blue. (E) IceLogo of the sequences in the list.

Mentions: A frequently requested functionality is to facilitate information retrieval for lists of thousands of proteins commonly generated by proteomics experiments. Here, we extended TopFIND with such a powerful analysis tool we call TopFINDer. TopFINDer enables analysis and functional annotation of protein N- or C-termini sets based on TopFIND data. From a list of protein identifiers and their terminal amino acid sequences as input (Figure 2A) TopFINDer returns comprehensive protein and terminus related (position-specific) information and analyses based on TopFIND data. The results are sent by email and contain a table (in a EXCEL compatible tab delimited text file) with general annotation of each protein (e.g. Supplementary Table S1) and position-specific information: for each identified terminus, TopFINDer reports the position of the terminus relative to the genome encoded sequence as well as the sequence context surrounding the terminus and evidences for the terminus from TopFIND. Important new information is provided including evidences for their classification by their origin as (i) termini inferred from alternative splicing derived protein isoforms in Ensembl or UniProt, (ii) N-termini inferred from alternative translation, (iii) termini inferred from cleavage together with the associated proteases, (iv) status as UniProt annotated canonical protein termini and (v) termini observed experimentally but without a known protease responsible for the cleavage.


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

Fortelny N, Yang S, Pavlidis P, Lange PF, Overall CM - Nucleic Acids Res. (2014)

Input and output of TopFINDer. (A) Input mask within the TopFIND web interface. (B) Venn diagram showing the overlap of termini evidences retrieved from TopFIND for a list of proteins. Evidence is either UniProt annotated terminus (Curated Start), terminus of an isoform derived from alternative splicing (Alternatively Spliced), or from alternative translation (Alternatively Translated), from cleavage (Cleaved), or a terminus observed in a non-protease related terminomics experiment (Experimentally Observed). (C) Matrix of substrates and proteases indicating cleavage of substrates. Fields are red where there is cleavage and black where there is none known between the protease and the substrate at this position. The y-axis shows the protein identifier and the position of each terminus. (D) Barplot showing the number of cleavages of each protease in the list. Bars of proteases whose cleavages are enriched in the list are in red, others in blue. (E) IceLogo of the sequences in the list.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383881&req=5

Figure 2: Input and output of TopFINDer. (A) Input mask within the TopFIND web interface. (B) Venn diagram showing the overlap of termini evidences retrieved from TopFIND for a list of proteins. Evidence is either UniProt annotated terminus (Curated Start), terminus of an isoform derived from alternative splicing (Alternatively Spliced), or from alternative translation (Alternatively Translated), from cleavage (Cleaved), or a terminus observed in a non-protease related terminomics experiment (Experimentally Observed). (C) Matrix of substrates and proteases indicating cleavage of substrates. Fields are red where there is cleavage and black where there is none known between the protease and the substrate at this position. The y-axis shows the protein identifier and the position of each terminus. (D) Barplot showing the number of cleavages of each protease in the list. Bars of proteases whose cleavages are enriched in the list are in red, others in blue. (E) IceLogo of the sequences in the list.
Mentions: A frequently requested functionality is to facilitate information retrieval for lists of thousands of proteins commonly generated by proteomics experiments. Here, we extended TopFIND with such a powerful analysis tool we call TopFINDer. TopFINDer enables analysis and functional annotation of protein N- or C-termini sets based on TopFIND data. From a list of protein identifiers and their terminal amino acid sequences as input (Figure 2A) TopFINDer returns comprehensive protein and terminus related (position-specific) information and analyses based on TopFIND data. The results are sent by email and contain a table (in a EXCEL compatible tab delimited text file) with general annotation of each protein (e.g. Supplementary Table S1) and position-specific information: for each identified terminus, TopFINDer reports the position of the terminus relative to the genome encoded sequence as well as the sequence context surrounding the terminus and evidences for the terminus from TopFIND. Important new information is provided including evidences for their classification by their origin as (i) termini inferred from alternative splicing derived protein isoforms in Ensembl or UniProt, (ii) N-termini inferred from alternative translation, (iii) termini inferred from cleavage together with the associated proteases, (iv) status as UniProt annotated canonical protein termini and (v) termini observed experimentally but without a known protease responsible for the cleavage.

Bottom Line: 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.Neo-termini are also linked to associated proteases.In re-capitulating the major findings originally performed manually, this validates the utility of these new resources.

View Article: PubMed Central - PubMed

Affiliation: 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.

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