ArticleCommunications biology2023
ALAN is a computational approach that interprets genomic findings in the context of tumor ecosystems.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Novel therapeutic strategies for metastatic castration‑resistant prostate cancer: Beyond androgen receptor pathway inhibition (Review).International journal of oncology · 2026Review
- Plasma extracellular vesicle proteomics nominates candidate biomarkers ofCell reports. Medicine · 2026Article
- CREB5 regulates stem cell-like transcriptional programs to enhance tumor progression in prostate cancer.Oncotarget · 2026Article
- CREB5 promotes tumorigenicity and upregulates druggable cell surface modalities in basal-like breast cancer.NPJ precision oncology · 2025Article
- Dissecting the functional differences and clinical features of R-spondin family members in metastatic prostate cancer.Oncotarget · 2025Article
- SOX2 utilizes FOXA1 as a heteromeric transcriptional partner to drive proliferation in therapy-resistant prostate cancer.bioRxiv : the preprint server for biology · 2025Article
- Androgen production, uptake, and conversion (APUC) genes define prostate cancer patients with distinct clinical outcomes.JCI insight · 2024Article
- Computational Approaches: A New Frontier in Cancer Research.Combinatorial chemistry & high throughput screening · 2024Review
- Unique Spectrum of Activating BRAF Alterations in Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Article
- ALAN is a computational approach that interprets genomic findings in the context of tumor ecosystems.Communications biology · 2023Article
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
Gene behavior is governed by activity of other genes in an ecosystem as well as context-specific cues including cell type, microenvironment, and prior exposure to therapy. Here, we developed the Algorithm for Linking Activity Networks (ALAN) to compare gene behavior purely based on patient -omic data. The types of gene behaviors identifiable by ALAN include co-regulators of a signaling pathway, protein-protein interactions, or any set of genes that function similarly. ALAN identified direct protein-protein interactions in prostate cancer (AR, HOXB13, and FOXA1). We found differential and complex ALAN networks associated with the proto-oncogene MYC as prostate tumors develop and become metastatic, between different cancer types, and within cancer subtypes. We discovered that resistant genes in prostate cancer shared an ALAN ecosystem and activated similar oncogenic signaling pathways. Altogether, ALAN represents an informatics approach for developing gene signatures, identifying gene targets, and interpreting mechanisms of progression or therapy resistance.
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What OpenQuestion holds
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.