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Author:

Huo, Y. (Huo, Y..) | Guo, Y. (Guo, Y..) | Wang, J. (Wang, J..) | Xue, H. (Xue, H..) | Feng, Y. (Feng, Y..) | Chen, W. (Chen, W..) | Li, X. (Li, X..)

Indexed by:

Scopus SCIE

Abstract:

Recent advances in spatially resolved transcriptomic technologies have enabled unprecedented opportunities to elucidate tissue architecture and function in situ. Spatial transcriptomics can provide multimodal and complementary information simultaneously, including gene expression profiles, spatial locations, and histology images. However, most existing methods have limitations in efficiently utilizing spatial information and matched high-resolution histology images. To fully leverage the multi-modal information, we proposed a SPAtially embedded Deep Attentional graph Clustering (SpaDAC) method to identify spatial domains while reconstructing denoised gene expression profiles. This method can efficiently learn the low-dimensional embeddings for spatial transcriptomics data by constructing multi-view graph modules to capture both spatial location connectives and morphological connectives. Benchmark results demonstrate that SpaDAC outperforms other algorithms on several recent spatial transcriptomics datasets. SpaDAC is a valuable tool for spatial domain detection, facilitating the comprehension of tissue architecture and cellular microenvironment. The source code of SpaDAC is freely available at Github (https://github.com/huoyuying/SpaDAC.git). © 2023 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China

Keyword:

Spatial domain detection Spatial transcriptomics Multi-modal integration Graph attention network

Author Community:

  • [ 1 ] [Huo Y.]School of Software Engineering, Beijing Jiaotong University, Beijing, 100044, China
  • [ 2 ] [Guo Y.]School of Software Engineering, Beijing Jiaotong University, Beijing, 100044, China
  • [ 3 ] [Wang J.]School of Software Engineering, Beijing Jiaotong University, Beijing, 100044, China
  • [ 4 ] [Xue H.]School of Software Engineering, Beijing Jiaotong University, Beijing, 100044, China
  • [ 5 ] [Feng Y.]School of Software Engineering, Beijing University of Technology, Beijing, 100124, China
  • [ 6 ] [Chen W.]Baidu Inc., Beijing, 100193, China
  • [ 7 ] [Li X.]School of Software Engineering, Beijing Jiaotong University, Beijing, 100044, China

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Source :

Journal of Genetics and Genomics

ISSN: 1673-8527

Year: 2023

Issue: 9

Volume: 50

Page: 720-733

ESI Discipline: MOLECULAR BIOLOGY & GENETICS;

ESI HC Threshold:23

Cited Count:

WoS CC Cited Count:

SCOPUS Cited Count: 10

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 6

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