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Volume 51 Issue 8
Aug.  2024
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Article Contents

DAIS: a method for identifying spatial domains based on density clustering of spatial omics data

doi: 10.1016/j.jgg.2024.04.002
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This work was supported by the National Key R&D Program of China (2021YFC2501900), the National Natural Science Foundation of China (32300514), and the Science, Technology and Innovation Commission of Shenzhen Municipality (LCYX20220620105200001).

  • Received Date: 2024-02-18
  • Accepted Date: 2024-04-02
  • Rev Recd Date: 2024-03-17
  • Available Online: 2025-06-06
  • Publish Date: 2024-04-08
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  • Aibar, S., Gonzalez-Blas, C.B., Moerman, T., Huynh-Thu, V.A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.C., Geurts, P., Aerts, J., et al., 2017. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083-1086.
    Akkiraju, N., Edelsbrunner, H., Facello, M., Fu, P., Mucke, E. and Varela, C., 1995. Alpha Shapes: Definition and Software, Proceedings of the 1st International Computational Geometry Software Workshop.
    Bressan, D., Battistoni, G. and Hannon, G.J., 2023. The dawn of spatial omics. Science 381, eabq4964.
    Chen, A., Liao, S., Cheng, M., Ma, K., Wu, L., Lai, Y., Qiu, X., Yang, J., Xu, J., Hao, S., et al., 2022. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 185, 1777-1792 e21.
    Ester, M., Kriegel, H.-P., Sander, J. and Xu, X., 1996. A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise, kdd. pp. 226-231.
    Hatton, I.A., Galbraith, E.D., Merleau, N.S.C., Miettinen, T.P., Smith, B.M. and Shander, J.A., 2023. The human cell count and size distribution. Proc. Natl. Acad. Sci. U.S.A. 120, e2303077120.
    Hu, J., Li, X., Coleman, K., Schroeder, A., Ma, N., Irwin, D.J., Lee, E.B., Shinohara, R.T. and Li, M., 2021. SpaGCN: integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network. Nat. Methods 18, 1342-1351.
    Li, S., Liu, M., Do, M.H., Chou, C., Stamatiades, E.G., Nixon, B.G., Shi, W., Zhang, X., Li, P., Gao, S., et al., 2020. Cancer immunotherapy via targeted TGF-beta signalling blockade in T(H) cells. Nature 587, 121-125.
    Liang, Y., Shi, G., Cai, R., Yuan, Y., Xie, Z., Yu, L., Huang, Y., Shi, Q., Wang, L., Li, J. and Tang, Z., 2024. PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomics. Nat. Commun. 15, 600.
    Liu, Y., Yang, M., Deng, Y., Su, G., Enninful, A., Guo, C.C., Tebaldi, T., Zhang, D., Kim, D., Bai, Z., et al., 2020. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665-1681 e18.
    Meylan, M., Petitprez, F., Becht, E., Bougouin, A., Pupier, G., Calvez, A., Giglioli, I., Verkarre, V., Lacroix, G., Verneau, J., et al., 2022. Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer. Immunity 55, 527-541 e5.
    O'Donnell, J.S., Massi, D., Teng, M.W.L. and Mandala, M., 2018. PI3K-AKT-mTOR inhibition in cancer immunotherapy, redux. Semin. Cancer Biol. 48, 91-103.
    Preparata, F.P., Shamos, M.I., Preparata, F.P. and Shamos, M.I., 1985. Convex hulls: basic algorithms. Comput. Geom.: An Introduction. 95-149.
    Schumacher, T.N. and Thommen, D.S., 2022. Tertiary lymphoid structures in cancer. Science 375, eabf9419.
    Tian, L., Chen, F. and Macosko, E.Z., 2023. The expanding vistas of spatial transcriptomics. Nat. Biotechnol. 41, 773-782.
    Wang, B., Luo, J., Liu, Y., Shi, W., Xiong, Z., Shen, C. and Long, Y., 2023. Spatial-MGCN: a novel multi-view graph convolutional network for identifying spatial domains with attention mechanism. Briefings Bioinf. 24.
    Wu, L., Yan, J., Bai, Y., Chen, F., Zou, X., Xu, J., Huang, A., Hou, L., Zhong, Y., Jing, Z., et al., 2023. An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte-tumor cell crosstalk, local immunosuppression and tumor progression. Cell Res. 33, 585-603.
    Wu, R., Guo, W., Qiu, X., Wang, S., Sui, C., Lian, Q., Wu, J., Shan, Y., Yang, Z., Yang, S., et al., 2021. Comprehensive analysis of spatial architecture in primary liver cancer. Sci. Adv. 7, eabg3750.
    Zhang, L., Chen, D., Song, D., Liu, X., Zhang, Y., Xu, X. and Wang, X., 2022. Clinical and translational values of spatial transcriptomics. Signal Transduct. Targeted Ther. 7, 111.
    Zhang, Y., Ma, Y., Huang, Y., Zhang, Y., Jiang, Q., Zhou, M. and Su, J., 2020. Benchmarking algorithms for pathway activity transformation of single-cell RNA-seq data. Comput. Struct. Biotechnol. J. 18, 2953-2961.
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