Unveiling Fine-scale Spatial Structures and Amplifying Gene Expression Signals in Ultra-Large ST slices with HERGAST

Unveiling Fine-scale Spatial Structures and Amplifying Gene Expression Signals in Ultra-Large ST slices with HERGAST | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Brief Communication Unveiling Fine-scale Spatial Structures and Amplifying Gene Expression Signals in Ultra-Large ST slices with HERGAST Zhangsheng Yu, Yuqiao Gong, Xin Yuan, Qiong Jiao This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4753162/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 28 Apr, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract We propose HERGAST, a system for spatial structure identification and signal amplification in ultra-large-scale and ultra-high-resolution spatial transcriptomics data. To handle ultra-large data, we devise a Divide-Iterate-Conque strategy and construct a heterogeneous graph network to incorporate both local and global spatial relationships. HERGAST's high-precision spatial clustering enabled finding SPP1+ macrophages intermingled in tumors in colorectal cancer, while the enhanced gene expression signal enabled discovering unique spatial expression pattern of key genes in breast cancer. Biological sciences/Computational biology and bioinformatics/Software Biological sciences/Computational biology and bioinformatics/Data mining Biological sciences/Biotechnology/Genomics/Transcriptomics Biological sciences/Cancer Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryTable2.xlsx supplementaryinformation.docx Cite Share Download PDF Status: Published Journal Publication published 28 Apr, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4753162","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Brief Communication","associatedPublications":[],"authors":[{"id":329146485,"identity":"ce4f4925-890a-4b62-a288-303616f1d803","order_by":0,"name":"Zhangsheng 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