Open Access Research article

Identification of proprotein convertase substrates using genome-wide expression correlation analysis

Hannu Turpeinen12, Sampo Kukkurainen23, Kati Pulkkinen12, Timo Kauppila123, Kalle Ojala4, Vesa P Hytönen23 and Marko Pesu125*

Author Affiliations

1 Immunoregulation, Institute of Biomedical Technology, FI-33014 University of Tampere, Finland

2 BioMediTech, Tampere, Finland

3 Protein Dynamics, Institute of Biomedical Technology, University of Tampere, Finland

4 Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland

5 Centre for Laboratory Medicine, Tampere University Hospital, Finland

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BMC Genomics 2011, 12:618  doi:10.1186/1471-2164-12-618

Published: 20 December 2011

Additional files

Additional file 1:

PCSK sequences used for Figure 1. Altogether 152 PCSK sequences were used.

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Additional file 2:

Whole genome expression correlations for PCSK1-7 genes. Non-logarithmic and logarithmic correlations as well as p values and common data points are listed. Genes in blue are bottom 5% genes that fulfill the inclusion criteria of signal peptide and PCSK recognition site. Red ones are the corresponding genes for top 5%.

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Additional file 3:

Mutual expression correlation between the PCSK gene pairs over the whole spectrum of healthy tissues.

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Additional file 4:

Mutual expression correlation between the PCSK gene pairs specified in different anatomical structures.

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Additional file 5:

Uniqueness expression correlation values of putative PCSK targets. The uniqueness values for putative targets were counted as follows: First, the correlating genes were sorted descending by correlation values with specific PCSK gene and ordinals were recorded. Then, the same was done ascending, one by one, for all the other PCSK genes. Finally, the ordinal numbers for each of the correlating putative targets were summed up. The lower the summed value the more unique the expression correlation is for the specific PCSK gene.

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Additional file 6:

Chromosomal clustering of putative PCSK targets.

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Additional file 7:

MultiDisp figures of potential PCSK target sequences. The sequences were predicted from the group of top-correlated gene translations using the general PC prediction and signal peptide prediction methods on the ProP 1.0 server (http://www.cbs.dtu.dk/services/ProP/ webcite). Potential target peptides from signal peptide-containing sequences were restricted to ten residues upstream (P10-P1) and downstream (P1'-P10') of the predicted cleavage site. Amino acid compositions at each site in the groups of potential targets for each PCSK were plotted using MultiDisp (http://bioinf.uta.fi/cgi-bin/MultiDisp.cgi webcite) that scales the character heights based on amino acid frequency. Scissors and dotted line mark the predicted cleavage site.

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Additional file 8:

Amino acid occurrence of putative target molecules for PCSK5. Twenty residues (P10 - P10', marked with numbers 10 - 10') around the PCSK cleavage sites of highly correlating genes have been plotted for PCSK5. Top (t) and bottom (b) groups are shown for each amino acid type. Blue color indicates increased occurrence of a particular amino acid residue type in certain position of the putative substrate when all PCSKs are considered, whereas red colors mean low occurrence of a specific amino acid. White indicates an average occurrence frequency of a specific amino acid. The increase or decrease in occurrence is shown as a scale of percentages and a combined data containing all PCSKs has been used as a comparison point. The scaling (-6 percentage to +6 percentage) is shown as a color gradient below the figure. The potentially scissile bond P1-P1' is marked with scissors and dashed line.

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