DataVXAdvanced SciencePaper
journal article·2023-07Open access

Spatial Reconstruction of Oligo and Single Cells by De Novo Coalescent Embedding of Transcriptomic Networks

Yuxuan Zhao, Shiqiang Zhang, Jian Xu, Yangyang Yu, Guangdun Peng, Carlo Vittorio Cannistraci, Jing‐Dong J. Han

Advanced Science· Volume 10· Issue 20
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Source abstract

Abstract

Abstract Single cell RNA‐seq (scRNA‐seq) profiles conceal temporal and spatial tissue developmental information. De novo reconstruction of single cell temporal trajectory has been fairly addressed, but reverse engineering single cell 3D spatial tissue organization is hitherto landmark based, and de novo spatial reconstruction is a compelling computational open problem. Here it is shown that a proposed algorithm for de novo coalescent embedding (D‐CE) of oligo/single cell transcriptomic networks can help to address this problem. Relying on the spatial information encoded in the expression patterns of genes, it is found that D‐CE of cell–cell association transcriptomic networks, by preserving mesoscale network organization, captures spatial domains, identifies spatially expressed genes, reconstructs cell samples’ 3D spatial distribution, and uncovers spatial domains and markers necessary for understanding the design principles on spatial organization and pattern formation. Comparison to the novoSpaRC and CSOmap (the only available de novo 3D spatial reconstruction methods) on 14 datasets and 497 reconstructions, reveals a significantly superior performance of D‐CE.
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Research context

OpenAlex topics: Single-cell and spatial transcriptomics · Cell Image Analysis Techniques · Advanced Fluorescence Microscopy Techniques

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Peking‐Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Center for Quantitative Biology (CQB) Peking University Beijing 100871 P. R. China

CAS Key Laboratory of Computational Biology Shanghai Institute of Nutrition and Health Chinese Academy of Sciences 320 Yue Yang Road Shanghai 200031 P. R. China

Center for Cell Lineage and Development CAS Key Laboratory of Regenerative Biology Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou 510530 P. R. China

Center for Cell Lineage and Atlas Bioland Laboratory Guangzhou 510530 P. R. China

Biomedical Cybernetics Group, Biotechnology Center (BIOTEC) Center for Molecular and Cellular Bioengineering (CMCB) Technische Universität Dresden Tatzberg 47–49 01307 Dresden Germany

Center for Complex Network Intelligence (CCNI) Tsinghua Laboratory of Brain and Intelligence (THBI) Department of Physics, Department of Computer Science Department of Biomedical Engineering Tsinghua University 60 Chengfu Road Beijing 100084 P. R. China

Center for Systems Biology Dresden (CSBD) Pfotenhauerstr 108, 01307 Dresden Germany

Funding

National Natural Science Foundation of China

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