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-...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2021-02-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/57116 |
| _version_ | 1811202950719078400 |
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| author | Kenichi Shimada John A Bachman Jeremy L Muhlich Timothy J Mitchison |
| author_facet | Kenichi Shimada John A Bachman Jeremy L Muhlich Timothy J Mitchison |
| author_sort | Kenichi Shimada |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T02:46:18Z |
| format | Article |
| id | doaj.art-7e72ff77e6a34087a230b2668f1f7acf |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T02:46:18Z |
| publishDate | 2021-02-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-7e72ff77e6a34087a230b2668f1f7acf2022-12-22T03:51:09ZengeLife Sciences Publications LtdeLife2050-084X2021-02-011010.7554/eLife.57116shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map dataKenichi Shimada0https://orcid.org/0000-0001-8540-9785John A Bachman1https://orcid.org/0000-0001-6095-2466Jeremy L Muhlich2https://orcid.org/0000-0002-0811-637XTimothy J Mitchison3https://orcid.org/0000-0001-7781-1897Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, United StatesLaboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, United StatesLaboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, United StatesLaboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, United StatesIndividual 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.https://elifesciences.org/articles/57116DepMapshinyDepMapprecision medicineessential genessynthetic lethalityselectivity |
| spellingShingle | Kenichi Shimada John A Bachman Jeremy L Muhlich Timothy J Mitchison shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data eLife DepMap shinyDepMap precision medicine essential genes synthetic lethality selectivity |
| title | shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data |
| title_full | shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data |
| title_fullStr | shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data |
| title_full_unstemmed | shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data |
| title_short | shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data |
| title_sort | shinydepmap a tool to identify targetable cancer genes and their functional connections from cancer dependency map data |
| topic | DepMap shinyDepMap precision medicine essential genes synthetic lethality selectivity |
| url | https://elifesciences.org/articles/57116 |
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