ArticleGenome biology2020
Convergent network effects along the axis of gene expression during prostate cancer progression.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- Article
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- Unannotated noncoding transcripts as a source of intratumor heterogeneity in malignant cell states.Science China. Life sciences · 2026Article
- Review
- Protein disulfide isomerases regulate androgen receptor stability and promote prostate cancer cell growth and survival.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrated proteogenomic characterization of localized prostate cancer identifies biological insights and subtype-specific therapeutic strategies.Nature communications · 2025Article
- Proteome-wide copy-number estimation from transcriptomics.Molecular systems biology · 2024Article
- Proteomic landscape profiling of primary prostate cancer reveals a 16-protein panel for prognosis prediction.Cell reports. Medicine · 2024Article
- Proteomic-based stratification of intermediate-risk prostate cancer patients.Life science alliance · 2024Article
- A pathway activity-based proteomic classifier stratifies prostate tumors into two subtypes.Clinical proteomics · 2023Article
- A neutrophil extracellular traps-related classification predicts prognosis and response to immunotherapy in colon cancer.Scientific reports · 2023Article
- Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.Scientific data · 2022Article
- From Omics to Multi-Omics Approaches for In-Depth Analysis of the Molecular Mechanisms of Prostate Cancer.International journal of molecular sciences · 2022Review
- Comparison of approaches to transcriptomic analysis in multi-sampled tumors.Briefings in bioinformatics · 2021Article
- Optimizing network propagation for multi-omics data integration.PLoS computational biology · 2021Article
- The Etiology and Pathophysiology Genesis of Benign Prostatic Hyperplasia and Prostate Cancer: A New Perspective.Medicines (Basel, Switzerland) · 2021Review
- Correlation of MRI-Lesion Targeted Biopsy vs. Systematic Biopsy Gleason Score with Final Pathological Gleason Score after Radical Prostatectomy.Diagnostics (Basel, Switzerland) · 2021Article
Corrections and comments
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Authors and funding
30 authors at 11 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTumor-specific genomic aberrations are routinely determined by high-throughput genomic measurements. It remains unclear how complex genome alterations affect molecular networks through changing protein levels and consequently biochemical states of tumor tissues.
resultsHere, we investigate the propagation of genomic effects along the axis of gene expression during prostate cancer progression. We quantify genomic, transcriptomic, and proteomic alterations based on 105 prostate samples, consisting of benign prostatic hyperplasia regions and malignant tumors, from 39 prostate cancer patients. Our analysis reveals the convergent effects of distinct copy number alterations impacting on common downstream proteins, which are important for establishing the tumor phenotype. We devise a network-based approach that integrates perturbations across different molecular layers, which identifies a sub-network consisting of nine genes whose joint activity positively correlates with increasingly aggressive tumor phenotypes and is predictive of recurrence-free survival. Further, our data reveal a wide spectrum of intra-patient network effects, ranging from similar to very distinct alterations on different molecular layers.
conclusionsThis study uncovers molecular networks with considerable convergent alterations across tumor sites and patients. It also exposes a diversity of network effects: we could not identify a single sub-network that is perturbed in all high-grade tumor regions.
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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 Socratic graph.