ArticleMolecular systems biology2020
CEN-tools: an integrative platform to identify the contexts of essential genes.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 29 citations in OpenAlex.
- Synthetic lethality in cancer drug discovery: challenges and opportunities.Nature reviews. Drug discovery · 2026Review
- Integrative multiomic and immune profiling of lung adenocarcinoma: molecular landscapes, gene expression, and treatment response insights.The oncologist · 2025Article
- Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins.NAR genomics and bioinformatics · 2025Article
- PRODE recovers essential and context-essential genes through neighborhood-informed scores.Genome biology · 2025Article
- HELP: A computational framework for labelling and predicting human common and context-specific essential genes.PLoS computational biology · 2024Article
- Lethal phenotypes in Mendelian disorders.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- Lethal phenotypes in Mendelian disorders.medRxiv : the preprint server for health sciences · 2024Article
- Untangling the Context-Specificity of Essential Genes by Means of Machine Learning: A Constructive Experience.Biomolecules · 2023Article
- Essential genes: a cross-species perspective.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Review
- Recovering false negatives in CRISPR fitness screens with JLOE.Nucleic acids research · 2023Article
- Dynamic rewiring of biological activity across genotype and lineage revealed by context-dependent functional interactions.Genome biology · 2022Article
- CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.BMC genomics · 2021Article
- Predicting and characterizing a cancer dependency map of tumors with deep learning.Science advances · 2021Article
- CEN-tools: an integrative platform to identify the contexts of essential genes.Molecular systems biology · 2020Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
An emerging theme from large-scale genetic screens that identify genes essential for cell fitness is that essentiality of a given gene is highly context-specific. Identification of such contexts could be the key to defining gene function and also to develop novel therapeutic interventions. Here, we present Context-specific Essentiality Network-tools (CEN-tools), a website and python package, in which users can interrogate the essentiality of a gene from large-scale genome-scale CRISPR screens in a number of biological contexts including tissue of origin, mutation profiles, expression levels and drug responses. We show that CEN-tools is suitable for the systematic identification of genetic dependencies and for more targeted queries. The associations between genes and a given context are represented as dependency networks (CENs), and we demonstrate the utility of these networks in elucidating novel gene functions. In addition, we integrate the dependency networks with existing protein-protein interaction networks to reveal context-dependent essential cellular pathways in cancer cells. Together, we demonstrate the applicability of CEN-tools in aiding the current efforts to define the human cellular dependency map.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.