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Canonical labels for protein spots of proteomics maps

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Abstract

We consider the problem of canonical labeling for a class of maps, which include proteomics maps, which consist of a set of vertices or protein spots. If this problem is solved and followed, different laboratories studying proteomics maps will arrive at the same numbering of spots, which would facilitate comparisons of data from different sources. In addition, the proposed canonical numberings of protein spots would allow compiling a catalog of proteomics maps just as canonical labeling allows making catalogs graphs, or molecules, and other canonically labeled systems, which would make search for similar sets of maps very efficient. We approach the problem by modifying the algorithm of Jeffrey for graphical representation of DNA based on the chaos game. Graphical representation of DNA as a chaos game map has an important property in that this representation allows one to assign sequential labels to spots in a DNA map. We have modified the approach for sequential labeling of chaos game map representations to graphical representation of any tabular data, such as listing of (x, y) coordinates of protein spots of proteomics maps.

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Acknowledgments

Rok Orel thanks for the financial support the European Union, European Social Fund. Milan Randić thanks the Laboratory for Chemometrics, National Institute of Chemistry, Ljubljana, Slovenia, for hospitality. This work has been supported in part by the Ministry of Science and Higher Education, of Republic of Slovenia under Research Grant P1017.

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  1. National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia

    Milan Randić

  2. XLAB, Pot za Brdom 100, Ljubljana, Slovenia

    Rok Orel

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  1. Milan Randić
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  2. Rok Orel
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Correspondence to Milan Randić.

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Randić, M., Orel, R. Canonical labels for protein spots of proteomics maps. J Math Chem 52, 198–212 (2014). https://doi.org/10.1007/s10910-013-0255-3

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