SiCmiR Atlas: Single-Cell miRNA Landscapes Reveals Hub-miRNA and Network Signatures in Human Cancers

[2508.05692] SiCmiR Atlas: Single-Cell miRNA Landscapes Reveals Hub-miRNA and Network Signatures in Human Cancers Skip to main content Search Submit Donate Log in Search arXiv Press Enter to search · Advanced search Quantitative Biology > Genomics arXiv:2508.05692 (q-bio) [Submitted on 6 Aug 2025] Title: SiCmiR Atlas: Single-Cell miRNA Landscapes Reveals Hub-miRNA and Network Signatures in Human Cancers Authors: Xiao-Xuan Cai , Jing-Shan Liao , Jia-Jun Ma , Yu-Xuan Pang , Yi-Gang Chen , Yang-Chi-Dung Lin , Yi-Dan Chen , Xin Cao , Yi-Cheng Zhang , Tao-Sheng Xu , Tzong-Yi Lee , Hsi-Yuan Huang , Hsien-Da Huang View a PDF of the paper titled SiCmiR Atlas: Single-Cell miRNA Landscapes Reveals Hub-miRNA and Network Signatures in Human Cancers, by Xiao-Xuan Cai and 12 other authors View PDF Abstract: microRNA are pivotal post-transcriptional regulators whose single-cell behavior has remained largely inaccessible owing to technical barriers in single-cell small-RNA profiling. We present SiCmiR, a two-layer neural network that predicts miRNA expression profile from only 977 LINCS L1000 landmark genes reducing sensitivity to dropout of single-cell RNA-seq data. Proof-of-concept analyses illustrate how SiCmiR can uncover candidate hub-miRNAs in bulk-seq cell lines and hepatocellular carcinoma, scRNA-seq pancreatic ductal carcinoma and ACTH-secreting pituitary adenoma and extracellular-vesicle-mediated crosstalk in glioblastoma. Trained on 6462 TCGA paired miRNA-mRNA samples, SiCmiR attains state-of-the-art accuracy on held-out cancers and generalizes to unseen cancer types, drug perturbations and scRNA-seq. We next constructed SiCmiR-Atlas, containing 632 public datasets, 9.36 million cells, 726 cell types, which is the first dedicated database of single-cell mature miRNA expression--providing interactive visualization, biomarker identification and cell-type-resolved miRNA-target networks. SiCmiR transforms bulk-derived statistical power into a single-cell view of miRNA biology and provides a community resource SiCmiR Atlas for biomarker discovery. SiCmiR Atlas is avilable at this https URL . Subjects: Genomics (q-bio.GN) Cite as: arXiv:2508.05692 [q-bio.GN] (or arXiv:2508.05692v1 [q-bio.GN] for this version) https://doi.org/10.48550/arXiv.2508.05692 Focus to learn more arXiv-issued DOI via DataCite Related DOI : https://doi.org/10.1002/advs.202514446 Focus to learn more DOI(s) linking to related resources Submission history From: Xiao-Xuan Cai [ view email ] [v1] Wed, 6 Aug 2025 12:23:08 UTC (3,457 KB) Full-text links: Access Paper: View a PDF of the paper titled SiCmiR Atlas: Single-Cell miRNA Landscapes Reveals Hub-miRNA and Network Signatures in Human Cancers, by Xiao-Xuan Cai and 12 other authors View PDF view license Current browse context: q-bio.GN < prev | next > new | recent | 2025-08 Change to browse by: q-bio References & Citations NASA ADS Google Scholar Semantic Scholar export BibTeX citation Loading... BibTeX formatted citation × loading... Data provided by: Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer ( What is the Explorer? ) Connected Papers Toggle Connected Papers ( What is Connected Papers? ) Litmaps Toggle Litmaps ( What is Litmaps? ) scite.ai Toggle scite Smart Citations ( What are Smart Citations? ) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv ( What is alphaXiv? ) Links to Code Toggle CatalyzeX Code Finder for Papers ( What is CatalyzeX? ) DagsHub Toggle DagsHub ( What is DagsHub? ) GotitPub Toggle Gotit.pub ( What is GotitPub? ) Huggingface Toggle Hugging Face ( What is Huggingface? ) ScienceCast Toggle ScienceCast ( What is ScienceCast? ) Demos Demos Replicate Toggle Replicate ( What is Replicate? ) Spaces Toggle Hugging Face Spaces ( What is Spaces? ) Spaces Toggle TXYZ.AI ( What is TXYZ.AI? ) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower ( What are Influence Flowers? ) Core recommender toggle CORE Recommender ( What is CORE? ) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs . Which authors of this paper are endorsers? | Disable MathJax ( What is MathJax? ) We gratefully acknowledge support from our major funders , member institutions , , and all contributors. About · Help · Contact · Subscribe · Copyright · Privacy · Accessibility · Operational Status (opens in new tab) Major funding support from

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