Niche-DE: phân tích biểu hiện gen khác biệt theo ngách trong dữ liệu transcriptomic không gian xác định tương tác tế bào phụ thuộc vào ngữ cảnh

Genome Biology - 2024
Kaishu Mason1, Anuja Sathe2, Paul R. Hess1, Jiazhen Rong3, Chi-Yun Wu4, Emma Furth5, Katalin Susztak6, Jonathan Levinsohn6, Hanlee P. Ji2, Nancy Zhang1
1Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, USA
2Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, USA
3Genomics and Computational Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
4The Gladstone Institute, San Francisco, USA
5Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
6Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA

Tóm tắt

Các phương pháp hiện có để phân tích dữ liệu transcriptomic không gian tập trung vào việc xác định sự biến đổi biểu hiện gen toàn cục của các loại tế bào trong mô, thay vì những thay đổi biểu hiện gen cục bộ do các tương tác tế bào-tế bào gây ra. Chúng tôi đề xuất một quy trình thống kê mới gọi là phân tích biểu hiện gen khác biệt theo ngách (niche-DE), nhằm xác định các gen liên quan đến ngách đặc hiệu của loại tế bào, được thể hiện khác biệt trong một loại tế bào cụ thể trong bối cảnh các ngách không gian xác định. Chúng tôi tiếp tục phát triển phương pháp niche-LR, một phương pháp nhằm làm sáng tỏ các cơ chế tín hiệu ligand-receptor tạo nền tảng cho các mô hình biểu hiện gen khác biệt theo ngách. Niche-DE và niche-LR có thể áp dụng cho dữ liệu transcriptomic không gian dựa trên điểm có độ phân giải thấp và dữ liệu có độ phân giải tế bào đơn hoặc dưới tế bào.

Từ khóa

#biểu hiện gen #ngách #transcriptomic không gian #tương tác tế bào #tín hiệu ligand-receptor

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