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. 2015 Dec;9(11-12):1105-22.
doi: 10.1002/prca.201500006. Epub 2015 Sep 16.

Priorities and trends in the study of proteins in eye research, 1924-2014

Richard D Semba  1 , Maggie Lam  2 , Kai Sun  1 , Pingbo Zhang  1 , Debra A Schaumberg  3   4 , Luigi Ferrucci  5 , Peipei Ping  2 , Jennifer E Van Eyk  6
Affiliations

Priorities and trends in the study of proteins in eye research, 1924-2014

Richard D Semba et al. Proteomics Clin Appl. 2015 Dec.

Abstract

Purpose: To identify the proteins that are relevant to eye research and develop assays for the study of a set of these proteins.

Experimental design: We conducted a bibliometric analysis by merging gene lists for human and mouse from the National Center for Biotechnology Information FTP site and combining them with PubMed references that were retrieved with the search terms "eye" [MeSH Terms] OR "eye" [All Fields] OR "eyes" [All Fields].

Results: For human and mouse eye studies, respectively, the total number of publications was 13,525 and 23,895 and the total number of proteins was 4050 and 4717. For proteins in human and mouse eye studies, respectively, 88.7 and 81.7% had five or fewer citations. The top 50 most intensively studied proteins for human and mouse eye studies were generally in the areas of photoreceptors and phototransduction, inflammation, and angiogenesis, neurodevelopment, lens transparency, and cell-cycle and cellular processes. We proposed selected reaction monitoring assays that were developed in silico for the top fifty most intensively studied proteins in human and mouse eye research.

Conclusions and clinical relevance: We conclude that scientists engaged in eye research tend to focus on the same proteins. Newer resources and tools in proteomics can expand the investigations to lesser-known proteins of the eye.

Keywords: Biological processes; Eye; Human proteome project; MS; Mouse; Proteomics.

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Conflict of interest statement

The authors have declared no conflict of interest.

Figures

Figure 1
Figure 1
Pie diagram of protein functions in (a) human and (b) mouse eye research classified by PANTHER.
Figure 1
Figure 1
Pie diagram of protein functions in (a) human and (b) mouse eye research classified by PANTHER.
Figure 2
Figure 2
(a) Heat map of the fifty most studied proteins in human eye research, 1974–2014. The first publication associated with both a gene and eye for human research in PubMed appeared in 1974. (b) Heat map of the fifty most studied proteins in the mouse eye research, 1924–2014. The first publication associated with both a gene and eye for mouse research in PubMed appeared in 1924. The heat map does not represent a full year for 2014, but only what was published on PubMed by 10/20/14.
Figure 2
Figure 2
(a) Heat map of the fifty most studied proteins in human eye research, 1974–2014. The first publication associated with both a gene and eye for human research in PubMed appeared in 1974. (b) Heat map of the fifty most studied proteins in the mouse eye research, 1924–2014. The first publication associated with both a gene and eye for mouse research in PubMed appeared in 1924. The heat map does not represent a full year for 2014, but only what was published on PubMed by 10/20/14.
Figure 3
Figure 3
Functional protein networks among the top 50 most studied proteins for (a) human and (b) mouse eye.
Figure 3
Figure 3
Functional protein networks among the top 50 most studied proteins for (a) human and (b) mouse eye.
See this image and copyright information in PMC

References

    1. Semba RD, Enghild JJ, Venkatraman V, Dyrlund TF, Van Eyk JE. The Human Eye Proteome Project: perspectives on an emerging proteome. Proteomics. 2013;13:2500–2511. - PMC - PubMed
    1. Aebersold R, Bader GD, Edwards AM, Van Eyk JE, et al. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J Proteome Res. 2013;12:23–27. - PubMed
    1. Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ. The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics. 2012;12:1134–1141. - PMC - PubMed
    1. Kuzyk MA, Parker CE, Domanski D, Borchers CH. Development of MRM-based assays for the absolute quantitation of plasma proteins. Methods Mol Biol. 2013;1023:53–81. - PubMed
    1. Shaham O, Menuchin Y, Farhy C, Ashery-Padan R. Pax6: a multi-level regulator of ocular development. Prog Ret Eye Res. 2012;31:351–376. - PubMed

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