Version 1
: Received: 5 March 2021 / Approved: 5 March 2021 / Online: 5 March 2021 (21:21:59 CET)
How to cite:
Zhao, Y.; Zhang, S.; Cannistraci, C.V.; Han, J.J. De Novo Spatial Reconstruction of Single Cells by Developmental Coalescent Embedding of Transcriptomic Networks. Preprints2021, 2021030196. https://doi.org/10.20944/preprints202103.0196.v1
Zhao, Y.; Zhang, S.; Cannistraci, C.V.; Han, J.J. De Novo Spatial Reconstruction of Single Cells by Developmental Coalescent Embedding of Transcriptomic Networks. Preprints 2021, 2021030196. https://doi.org/10.20944/preprints202103.0196.v1
Zhao, Y.; Zhang, S.; Cannistraci, C.V.; Han, J.J. De Novo Spatial Reconstruction of Single Cells by Developmental Coalescent Embedding of Transcriptomic Networks. Preprints2021, 2021030196. https://doi.org/10.20944/preprints202103.0196.v1
APA Style
Zhao, Y., Zhang, S., Cannistraci, C.V., & Han, J.J. (2021). <em><i>De Novo</i></em> Spatial Reconstruction of Single Cells by Developmental Coalescent Embedding of Transcriptomic Networks. Preprints. https://doi.org/10.20944/preprints202103.0196.v1
Chicago/Turabian Style
Zhao, Y., Carlo Vittorio Cannistraci and Jing-Dong J. Han. 2021 "<em><i>De Novo</i></em> Spatial Reconstruction of Single Cells by Developmental Coalescent Embedding of Transcriptomic Networks" Preprints. https://doi.org/10.20944/preprints202103.0196.v1
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 localization is hitherto landmark based, and de novo spatial reconstruction is a compelling computational open problem. Here we show that a new algorithm - named D-CE - for coalescent embedding of single cell transcriptomic networks can address this open problem. We rely merely on the spatial information encoded in the expression patterns of developmental signal transcription factor (DST) genes, and we find that D-CE of cell-cell association DST-transcriptomic networks reliably reconstructs the Geo-seq or single cell samples’ 3D spatial tissue distribution. Comparison to the novoSpaRC and CSOmap (recent and only available de novo 3D spatial reconstruction methods) on 16 datasets and 681 reconstructions, reveals a significantly distinctive superior performance of D-CE.
Single cell RNA-seq; spatial reconstruction; development; coalescent embedding
Subject
Biology and Life Sciences, Anatomy and Physiology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
