ArticleProceedings of the National Academy of Sciences of the United States of America2010
Information-theoretic analysis of phenotype changes in early stages of carcinogenesis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Trial
- Signalling Entropy Across Measurement Scales: A Compositional Dilution Lemma and Cross-Modality Invariance for Information-Theoretic Analysis of Cancer Transcriptomes.Entropy (Basel, Switzerland) · 2026Article
- Sequential transcriptional waves and NF-κB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer.Nature communications · 2026Article
- The ubiquitin ligase KLHL6 drives resistance to CD8Nature · 2026Article
- The responses of HNSCC patients to immunotherapy are shown by two novel co-expression patterns.NPJ precision oncology · 2025Article
- SurprisalAnalysis: an open-source software for information-theoretic analysis of gene expression.Bioinformatics advances · 2025Article
- Kinetic Trajectories of Glucose Uptake in Single Cancer Cells Reveal a Drug-Induced Cell-State Change Within Hours of Drug Treatment.The journal of physical chemistry. B · 2024Article
- Detecting tipping points of complex diseases by network information entropy.Briefings in bioinformatics · 2024Article
- Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia.NPJ systems biology and applications · 2024Article
- Patient-specific signaling signatures predict optimal therapeutic combinations for triple negative breast cancer.Molecular cancer · 2024Article
- The essence of phase transitions in condensed matter by an information theoretic approach.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- SCA: recovering single-cell heterogeneity through information-based dimensionality reduction.Genome biology · 2023Article
- Overexpressed kinetochore genes are used by cancer cells as genome destabilizers and transformation catalysts.Translational oncology · 2023Article
- A quantum information processing machine for computing by observables.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Density Matrix via Few Dominant Observables for the Ultrafast Non-Radiative Decay in Pyrazine.Journal of chemical theory and computation · 2023Article
- The immunogenic radiation and new players in immunotherapy and targeted therapy for head and neck cancer.Frontiers in oral health · 2023Review
- Computational quantification and characterization of independently evolving cellular subpopulations within tumors is critical to inhibit anti-cancer therapy resistance.Genome medicine · 2022Article
- Maximum Entropy Technique and Regularization Functional for Determining the Pharmacokinetic Parameters in DCE-MRI.Journal of digital imaging · 2022Article
- Information theory: A foundation for complexity science.Proceedings of the National Academy of Sciences of the United States of America · 2022Review
- Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii.Communications biology · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cancer is a multistep process characterized by altered signal transduction, cell growth, and metabolism. To identify such processes in early carcinogenesis we use an information theoretic approach to characterize gene expression quantified as mRNA levels in primary keratinocytes (K) and human papillomavirus 16 (HPV16)-transformed keratinocytes (HF1 cells) from early (E) and late (L) passages and from benzo(a)pyrene-treated (BP) L cells. Our starting point is that biological signaling processes are subjected to the same quantitative laws as inanimate, nonequilibrium chemical systems. Environmental and genomic constraints thereby limit the maximal thermodynamic entropy that the biological system can reach. The procedure uncovers the changes in gene expression patterns in different networks and defines the significance of each altered network in the establishment of a particular phenotype. The development of transformed HF1 cells is shown to be represented by one major transcription pattern that is important at all times. Two minor transcription patterns are also identified, one that contributes at early times and a distinguishably different pattern that contributes at later times. All three transcription patterns defined by our analysis were validated by gene expression values and biochemical means. The major transcription pattern includes reduced transcripts participating in the apoptotic network and enhanced transcripts participating in cell cycle, glycolysis, and oxidative phosphorylation. The two minor patterns identify genes that are mainly involved in lipid or carbohydrate metabolism.
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Registered trials
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