shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data

Individual cancers rely on distinct essential genes for their survival. The Cancer Dependency Map (DepMap) is an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines. To make this drug discovery resource more accessible to the scientific community, we built an easy-to-...
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Gespeichert in:

Autor*in:	Kenichi Shimada [verfasserIn] John A Bachman [verfasserIn] Jeremy L Muhlich [verfasserIn] Timothy J Mitchison [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	DepMap shinyDepMap precision medicine essential genes synthetic lethality selectivity

Übergeordnetes Werk:	In: eLife - eLife Sciences Publications Ltd, 2013, 10(2021)
Übergeordnetes Werk:	volume:10 ; year:2021

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.7554/eLife.57116

Katalog-ID:	DOAJ00666511X

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callnumber-first	Q - Science
author	Kenichi Shimada
spellingShingle	Kenichi Shimada misc QH301-705.5 misc DepMap misc shinyDepMap misc precision medicine misc essential genes misc synthetic lethality misc selectivity misc Medicine misc R misc Science misc Q misc Biology (General) shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
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topic_title	QH301-705.5 shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data DepMap shinyDepMap precision medicine essential genes synthetic lethality selectivity
topic	misc QH301-705.5 misc DepMap misc shinyDepMap misc precision medicine misc essential genes misc synthetic lethality misc selectivity misc Medicine misc R misc Science misc Q misc Biology (General)
topic_unstemmed	misc QH301-705.5 misc DepMap misc shinyDepMap misc precision medicine misc essential genes misc synthetic lethality misc selectivity misc Medicine misc R misc Science misc Q misc Biology (General)
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title	shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
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title_auth	shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
abstract	Individual cancers rely on distinct essential genes for their survival. The Cancer Dependency Map (DepMap) is an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines. To make this drug discovery resource more accessible to the scientific community, we built an easy-to-use browser, shinyDepMap (https://labsyspharm.shinyapps.io/depmap). shinyDepMap combines CRISPR and shRNA data to determine, for each gene, the growth reduction caused by knockout/knockdown and the selectivity of this effect across cell lines. The tool also clusters genes with similar dependencies, revealing functional relationships. shinyDepMap can be used to (1) predict the efficacy and selectivity of drugs targeting particular genes; (2) identify maximally sensitive cell lines for testing a drug; (3) target hop, that is, navigate from an undruggable protein with the desired selectivity profile, such as an activated oncogene, to more druggable targets with a similar profile; and (4) identify novel pathways driving cancer cell growth and survival.
abstractGer	Individual cancers rely on distinct essential genes for their survival. The Cancer Dependency Map (DepMap) is an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines. To make this drug discovery resource more accessible to the scientific community, we built an easy-to-use browser, shinyDepMap (https://labsyspharm.shinyapps.io/depmap). shinyDepMap combines CRISPR and shRNA data to determine, for each gene, the growth reduction caused by knockout/knockdown and the selectivity of this effect across cell lines. The tool also clusters genes with similar dependencies, revealing functional relationships. shinyDepMap can be used to (1) predict the efficacy and selectivity of drugs targeting particular genes; (2) identify maximally sensitive cell lines for testing a drug; (3) target hop, that is, navigate from an undruggable protein with the desired selectivity profile, such as an activated oncogene, to more druggable targets with a similar profile; and (4) identify novel pathways driving cancer cell growth and survival.
abstract_unstemmed	Individual cancers rely on distinct essential genes for their survival. The Cancer Dependency Map (DepMap) is an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines. To make this drug discovery resource more accessible to the scientific community, we built an easy-to-use browser, shinyDepMap (https://labsyspharm.shinyapps.io/depmap). shinyDepMap combines CRISPR and shRNA data to determine, for each gene, the growth reduction caused by knockout/knockdown and the selectivity of this effect across cell lines. The tool also clusters genes with similar dependencies, revealing functional relationships. shinyDepMap can be used to (1) predict the efficacy and selectivity of drugs targeting particular genes; (2) identify maximally sensitive cell lines for testing a drug; (3) target hop, that is, navigate from an undruggable protein with the desired selectivity profile, such as an activated oncogene, to more druggable targets with a similar profile; and (4) identify novel pathways driving cancer cell growth and survival.
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title_short	shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
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