ArticleProceedings of the National Academy of Sciences of the United States of America2013
Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Prognostic models for newly-diagnosed chronic lymphocytic leukaemia in adults: a systematic review and meta-analysis.The Cochrane database of systematic reviews · 2020Pooled it
- Quantitative characterization of immune cells by measuring cellular signal transduction pathway activity.Scientific reports · 2024Article
- Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling.PLoS computational biology · 2022Article
- Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia.Nature cancer · 2021Article
- selectBoost: a general algorithm to enhance the performance of variable selection methods.Bioinformatics (Oxford, England) · 2021Article
- Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia.Leukemia · 2021Article
- BCR-associated factors driving chronic lymphocytic leukemia cells proliferation ex vivo.Scientific reports · 2019Article
- Identification of key candidate genes and miRNA‑mRNA target pairs in chronic lymphocytic leukemia by integrated bioinformatics analysis.Molecular medicine reports · 2019Article
- Personalized Drug Analysis in B Cell Chronic Lymphocytic Leukemia Patients.Medical science monitor : international medical journal of experimental and clinical research · 2017Article
- Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia.Journal of Cancer · 2017Article
- Identifying causal networks linking cancer processes and anti-tumor immunity using Bayesian network inference and metagene constructs.Biotechnology progress · 2016Article
- Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data.BMC bioinformatics · 2015Article
- Rapid learning for precision oncology.Nature reviews. Clinical oncology · 2014Review
- Systems analysis of high-throughput data.Advances in experimental medicine and biology · 2014Review
Corrections and comments
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Authors and funding
10 authors.
Funding
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Abstract
Cellular behavior is sustained by genetic programs that are progressively disrupted in pathological conditions--notably, cancer. High-throughput gene expression profiling has been used to infer statistical models describing these cellular programs, and development is now needed to guide orientated modulation of these systems. Here we develop a regression-based model to reverse-engineer a temporal genetic program, based on relevant patterns of gene expression after cell stimulation. This method integrates the temporal dimension of biological rewiring of genetic programs and enables the prediction of the effect of targeted gene disruption at the system level. We tested the performance accuracy of this model on synthetic data before reverse-engineering the response of primary cancer cells to a proliferative (protumorigenic) stimulation in a multistate leukemia biological model (i.e., chronic lymphocytic leukemia). To validate the ability of our method to predict the effects of gene modulation on the global program, we performed an intervention experiment on a targeted gene. Comparison of the predicted and observed gene expression changes demonstrates the possibility of predicting the effects of a perturbation in a gene regulatory network, a first step toward an orientated intervention in a cancer cell genetic program.
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