Quantifying Gene Essentiality Based on the Context of Cellular Components

Different genes have their protein products localized in various subcellular compartments. The diversity in protein localization may serve as a gene characteristic, revealing gene essentiality from a subcellular perspective. To measure this diversity, we introduced a Subcellular Diversity Index (SDI...
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Autor*in:	Kaiwen Jia [verfasserIn] Yuan Zhou [verfasserIn] Qinghua Cui [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2020

Schlagwörter:	cellular components localization diversity gene characteristic gene essentiality drug target

Übergeordnetes Werk:	In: Frontiers in Genetics - Frontiers Media S.A., 2011, 10(2020)
Übergeordnetes Werk:	volume:10 ; year:2020

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fgene.2019.01342

Katalog-ID:	DOAJ077273990

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allfieldsSound	10.3389/fgene.2019.01342 doi (DE-627)DOAJ077273990 (DE-599)DOAJ6c20d0d2989c40e698dabb4b98c3e853 DE-627 ger DE-627 rakwb eng QH426-470 Kaiwen Jia verfasserin aut Quantifying Gene Essentiality Based on the Context of Cellular Components 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Different genes have their protein products localized in various subcellular compartments. The diversity in protein localization may serve as a gene characteristic, revealing gene essentiality from a subcellular perspective. To measure this diversity, we introduced a Subcellular Diversity Index (SDI) based on the Gene Ontology-Cellular Component Ontology (GO-CCO) and a semantic similarity measure of GO terms. Analyses revealed that SDI of human genes was well correlated with some known measures of gene essentiality, including protein–protein interaction (PPI) network topology measurements, dN/dS ratio, homologous gene number, expression level and tissue specificity. In addition, SDI had a good performance in predicting human essential genes (AUC = 0.702) and drug target genes (AUC = 0.704), and drug targets with higher SDI scores tended to cause more side-effects. The results suggest that SDI could be used to identify novel drug targets and to guide the filtering of drug targets with fewer potential side effects. Finally, we developed a user-friendly online database for querying SDI score for genes across eight species, and the predicted probabilities of human drug target based on SDI. The online database of SDI is available at: http://www.cuilab.cn/sdi. cellular components localization diversity gene characteristic gene essentiality drug target Genetics Yuan Zhou verfasserin aut Qinghua Cui verfasserin aut In Frontiers in Genetics Frontiers Media S.A., 2011 10(2020) (DE-627)65799829X (DE-600)2606823-0 16648021 nnns volume:10 year:2020 https://doi.org/10.3389/fgene.2019.01342 kostenfrei https://doaj.org/article/6c20d0d2989c40e698dabb4b98c3e853 kostenfrei https://www.frontiersin.org/article/10.3389/fgene.2019.01342/full kostenfrei https://doaj.org/toc/1664-8021 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2020
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authorswithroles_txt_mv	Kaiwen Jia @@aut@@ Yuan Zhou @@aut@@ Qinghua Cui @@aut@@
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callnumber-first	Q - Science
author	Kaiwen Jia
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topic_title	QH426-470 Quantifying Gene Essentiality Based on the Context of Cellular Components cellular components localization diversity gene characteristic gene essentiality drug target
topic	misc QH426-470 misc cellular components misc localization diversity misc gene characteristic misc gene essentiality misc drug target misc Genetics
topic_unstemmed	misc QH426-470 misc cellular components misc localization diversity misc gene characteristic misc gene essentiality misc drug target misc Genetics
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title	Quantifying Gene Essentiality Based on the Context of Cellular Components
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title_full	Quantifying Gene Essentiality Based on the Context of Cellular Components
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title_sort	quantifying gene essentiality based on the context of cellular components
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title_auth	Quantifying Gene Essentiality Based on the Context of Cellular Components
abstract	Different genes have their protein products localized in various subcellular compartments. The diversity in protein localization may serve as a gene characteristic, revealing gene essentiality from a subcellular perspective. To measure this diversity, we introduced a Subcellular Diversity Index (SDI) based on the Gene Ontology-Cellular Component Ontology (GO-CCO) and a semantic similarity measure of GO terms. Analyses revealed that SDI of human genes was well correlated with some known measures of gene essentiality, including protein–protein interaction (PPI) network topology measurements, dN/dS ratio, homologous gene number, expression level and tissue specificity. In addition, SDI had a good performance in predicting human essential genes (AUC = 0.702) and drug target genes (AUC = 0.704), and drug targets with higher SDI scores tended to cause more side-effects. The results suggest that SDI could be used to identify novel drug targets and to guide the filtering of drug targets with fewer potential side effects. Finally, we developed a user-friendly online database for querying SDI score for genes across eight species, and the predicted probabilities of human drug target based on SDI. The online database of SDI is available at: http://www.cuilab.cn/sdi.
abstractGer	Different genes have their protein products localized in various subcellular compartments. The diversity in protein localization may serve as a gene characteristic, revealing gene essentiality from a subcellular perspective. To measure this diversity, we introduced a Subcellular Diversity Index (SDI) based on the Gene Ontology-Cellular Component Ontology (GO-CCO) and a semantic similarity measure of GO terms. Analyses revealed that SDI of human genes was well correlated with some known measures of gene essentiality, including protein–protein interaction (PPI) network topology measurements, dN/dS ratio, homologous gene number, expression level and tissue specificity. In addition, SDI had a good performance in predicting human essential genes (AUC = 0.702) and drug target genes (AUC = 0.704), and drug targets with higher SDI scores tended to cause more side-effects. The results suggest that SDI could be used to identify novel drug targets and to guide the filtering of drug targets with fewer potential side effects. Finally, we developed a user-friendly online database for querying SDI score for genes across eight species, and the predicted probabilities of human drug target based on SDI. The online database of SDI is available at: http://www.cuilab.cn/sdi.
abstract_unstemmed	Different genes have their protein products localized in various subcellular compartments. The diversity in protein localization may serve as a gene characteristic, revealing gene essentiality from a subcellular perspective. To measure this diversity, we introduced a Subcellular Diversity Index (SDI) based on the Gene Ontology-Cellular Component Ontology (GO-CCO) and a semantic similarity measure of GO terms. Analyses revealed that SDI of human genes was well correlated with some known measures of gene essentiality, including protein–protein interaction (PPI) network topology measurements, dN/dS ratio, homologous gene number, expression level and tissue specificity. In addition, SDI had a good performance in predicting human essential genes (AUC = 0.702) and drug target genes (AUC = 0.704), and drug targets with higher SDI scores tended to cause more side-effects. The results suggest that SDI could be used to identify novel drug targets and to guide the filtering of drug targets with fewer potential side effects. Finally, we developed a user-friendly online database for querying SDI score for genes across eight species, and the predicted probabilities of human drug target based on SDI. The online database of SDI is available at: http://www.cuilab.cn/sdi.
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title_short	Quantifying Gene Essentiality Based on the Context of Cellular Components
url	https://doi.org/10.3389/fgene.2019.01342 https://doaj.org/article/6c20d0d2989c40e698dabb4b98c3e853 https://www.frontiersin.org/article/10.3389/fgene.2019.01342/full https://doaj.org/toc/1664-8021
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