Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

Swati Sinha; Birgit Eisenhaber; Lars Juhl Jensen; Bharata Kalbuaji; Frank Eisenhaber

doi:10.1002/pmic.201800093

Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

Swati Sinha, Birgit Eisenhaber, Lars Juhl Jensen, Bharata Kalbuaji, Frank Eisenhaber

Disease Systems Biology Program

3 Citationer (Scopus)

55 Downloads (Pure)

Abstract

The mentioning of gene names in the body of the scientific literature 1901–2017 and their fractional counting is used as a proxy to assess the level of biological function discovery. A literature score of one has been defined as full publication equivalent (FPE), the amount of literature necessary to achieve one publication solely dedicated to a gene. It has been found that less than 5000 human genes have each at least 100 FPEs in the available literature corpus. This group of elite genes (4817 protein-coding genes, 119 non-coding RNAs) attracts the overwhelming majority of the scientific literature about genes. Yet, thousands of proteins have never been mentioned at all, ≈2000 further proteins have not even one FPE of literature and, for ≈4600 additional proteins, the FPE count is below 10. The protein function discovery rate measured as numbers of proteins first mentioned or crossing a threshold of accumulated FPEs in a given year has grown until 2000 but is in decline thereafter. This drop is partially offset by function discoveries for non-coding RNAs. The full human genome sequencing does not boost the function discovery rate. Since 2000, the fastest growing group in the literature is that with at least 500 FPEs per gene.

Originalsprog	Engelsk
Artikelnummer	e1800093
Tidsskrift	Proteomics
Vol/bind	18
Udgave nummer	21-22
Sider (fra-til)	1-13
ISSN	1615-9853
DOI	https://doi.org/10.1002/pmic.201800093
Status	Udgivet - nov. 2018

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10.1002/pmic.201800093Licens: CC BY

Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000Forlagets udgivne version, 533 KBLicens: CC BY

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Darkness in the Human Gene and Protein Function Space : Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. / Sinha, Swati; Eisenhaber, Birgit; Jensen, Lars Juhl et al.

I: Proteomics, Bind 18, Nr. 21-22, e1800093, 11.2018, s. 1-13.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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abstract = "The mentioning of gene names in the body of the scientific literature 1901–2017 and their fractional counting is used as a proxy to assess the level of biological function discovery. A literature score of one has been defined as full publication equivalent (FPE), the amount of literature necessary to achieve one publication solely dedicated to a gene. It has been found that less than 5000 human genes have each at least 100 FPEs in the available literature corpus. This group of elite genes (4817 protein-coding genes, 119 non-coding RNAs) attracts the overwhelming majority of the scientific literature about genes. Yet, thousands of proteins have never been mentioned at all, ≈2000 further proteins have not even one FPE of literature and, for ≈4600 additional proteins, the FPE count is below 10. The protein function discovery rate measured as numbers of proteins first mentioned or crossing a threshold of accumulated FPEs in a given year has grown until 2000 but is in decline thereafter. This drop is partially offset by function discoveries for non-coding RNAs. The full human genome sequencing does not boost the function discovery rate. Since 2000, the fastest growing group in the literature is that with at least 500 FPEs per gene.",

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Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

Abstract

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