ArticleFrontiers in genetics2018
Embedding of Genes Using Cancer Gene Expression Data: Biological Relevance and Potential Application on Biomarker Discovery.
Article in Frontiers in genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- A network medicine framework for multi-modal data integration in therapeutic target discovery.Communications chemistry · 2026Article
- Chloride Intracellular Channel 2 Can Function as a Malignant Factor in Head and Neck Squamous Cell Carcinoma.Head & neck · 2026Article
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- An effective encoding of human medical conditions in disease space provides a versatile framework for deciphering disease associations.Quantitative biology (Beijing, China) · 2025Article
- Overall survival of recurrent/metastatic head & neck squamous cell carcinoma patients progressing after ≥ 1 line of systemic therapy, treated with MVX-ONCO-1, a novel, first in class cell encapsulation-based immunotherapy: results of SAKK 11/16, a phase IIa trial.Experimental hematology & oncology · 2025Article
- Joint effects of environmental and neighborhood socioeconomic factors on cognitive function in the Heinz Nixdorf Recall Study.Environmental research · 2025Article
- Novel cancer subtyping method guided by tumor-normal sample in latent space of transcriptomic variational autoencoder.Scientific reports · 2025Article
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- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- Untangling the Context-Specificity of Essential Genes by Means of Machine Learning: A Constructive Experience.Biomolecules · 2023Article
- Molecular data representation based on gene embeddings for cancer drug response prediction.Scientific reports · 2023Article
- Biology-aware mutation-based deep learning for outcome prediction of cancer immunotherapy with immune checkpoint inhibitors.NPJ precision oncology · 2023Article
- Domain-PFP allows protein function prediction using function-aware domain embedding representations.Communications biology · 2023Article
- Auxiliary Diagnosis and Prognostic Value of Dehydrogenase/Reductase 2 (DHRS2) in Various Tumors.Iranian journal of public health · 2023Article
- Review
- Tbc1d10c is a selective, constitutive suppressor of the CD8 T-cell anti-tumor response.Oncoimmunology · 2022Article
- Immune Infiltration-Related ceRNA Network Revealing Potential Biomarkers for Prognosis of Head and Neck Squamous Cell Carcinoma.Disease markers · 2022Article
- DNA damage repair-related gene signature predicts prognosis and indicates immune cell infiltration landscape in skin cutaneous melanoma.Frontiers in endocrinology · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Artificial neural networks (ANNs) have been utilized for classification and prediction task with remarkable accuracy. However, its implications for unsupervised data mining using molecular data is under-explored. We found that embedding can extract biologically relevant information from The Cancer Genome Atlas (TCGA) gene expression dataset by learning a vector representation through gene co-occurrence. Ground truth relationship, such as cancer types of the input sample and semantic meaning of genes, were showed to retain in the resulting entity matrices. We also demonstrated the interpretability and usage of these matrices in shortlisting candidates from a long gene list as in the case of immunotherapy response. 73 related genes are singled out while the relatedness of 55 genes with immune checkpoint proteins (PD-1, PD-L1, and CTLA-4) are supported by literature. 16 novel genes (
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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 OpenQuestion graph.