Emergent statistical laws in single-cell transcriptomic data

被引:3
|
作者
Lazzardi, Silvia [1 ,2 ]
Valle, Filippo [1 ,2 ]
Mazzolini, Andrea [3 ,4 ]
Scialdone, Antonio [5 ,6 ,7 ]
Caselle, Michele [1 ,2 ]
Osella, Matteo [1 ,2 ]
机构
[1] Univ Turin, Dept Phys, Via P Giuria 1, I-10125 Turin, Italy
[2] INFN, Via P Giuria 1, I-10125 Turin, Italy
[3] Sorbonne Univ, PSL Univ, CNRS, Lab Phys,Ecole Normale Super, F-75005 Paris, France
[4] Univ Paris, F-75005 Paris, France
[5] Helmholtz Zentrum Munchen, Inst Epigenet & Stem Cells, Feodor Lynen Str 21, D-81377 Munich, Germany
[6] Helmholtz Zentrum Munchen, Inst Funct Epigenet, Ingolstadter Landstr 1, D-85764 Neuherberg, Germany
[7] Helmholtz Zentrum Munchen, Inst Computat Biol, Ingolstadter Landstr 1, D-85764 Neuherberg, Germany
关键词
GENE-EXPRESSION; RNA-SEQ; DISTRIBUTIONS; FEATURES; REVEALS; ORIGINS; SYSTEMS; GROWTH;
D O I
10.1103/PhysRevE.107.044403
中图分类号
O35 [流体力学]; O53 [等离子体物理学];
学科分类号
070204 ; 080103 ; 080704 ;
摘要
Large-scale data on single-cell gene expression have the potential to unravel the specific transcriptional programs of different cell types. The structure of these expression datasets suggests a similarity with several other complex systems that can be analogously described through the statistics of their basic building blocks. Transcriptomes of single cells are collections of messenger RNA abundances transcribed from a common set of genes just as books are different collections of words from a shared vocabulary, genomes of different species are specific compositions of genes belonging to evolutionary families, and ecological niches can be described by their species abundances. Following this analogy, we identify several emergent statistical laws in single-cell transcriptomic data closely similar to regularities found in linguistics, ecology, or genomics. A simple mathematical framework can be used to analyze the relations between different laws and the possible mechanisms behind their ubiquity. Importantly, treatable statistical models can be useful tools in transcriptomics to disentangle the actual biological variability from general statistical effects present in most component systems and from the consequences of the sampling process inherent to the experimental technique.
引用
收藏
页数:17
相关论文
共 50 条
  • [21] Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision
    Jones, Matthew G.
    Rosen, Yanay
    Yosef, Nir
    CELL REPORTS METHODS, 2022, 2 (04):
  • [22] Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
    Lohoff, T.
    Ghazanfar, S.
    Missarova, A.
    Koulena, N.
    Pierson, N.
    Griffiths, J. A.
    Bardot, E. S.
    Eng, C. -H. L.
    Tyser, R. C. V.
    Argelaguet, R.
    Guibentif, C.
    Srinivas, S.
    Briscoe, J.
    Simons, B. D.
    Hadjantonakis, A. -K.
    Gottgens, B.
    Reik, W.
    Nichols, J.
    Cai, L.
    Marioni, J. C.
    NATURE BIOTECHNOLOGY, 2022, 40 (01) : 74 - +
  • [23] Reconstructing gene regulatory networks in single-cell transcriptomic data analysis
    Dai, Hao
    Jin, Qi-Qi
    Li, Lin
    Chen, Luo-Nan
    ZOOLOGICAL RESEARCH, 2020, 41 (06) : 599 - 604
  • [24] A review of computational strategies for denoising and imputation of single-cell transcriptomic data
    Patruno, Lucrezia
    Maspero, Davide
    Craighero, Francesco
    Angaroni, Fabrizio
    Antoniotti, Marco
    Graudenzi, Alex
    BRIEFINGS IN BIOINFORMATICS, 2021, 22 (04)
  • [25] scPlant: A versatile framework for single-cell transcriptomic data analysis in plants
    Cao, Shanni
    He, Zhaohui
    Chen, Ruidong
    Luo, Yuting
    Fu, Liang-Yu
    Zhou, Xinkai
    He, Chao
    Yan, Wenhao
    Zhang, Chen -Yu
    Chen, Dijun
    PLANT COMMUNICATIONS, 2023, 4 (05)
  • [26] Bayesian Joint Modeling of Single-Cell Expression Data and Bulk Spatial Transcriptomic Data
    Yu, Jinge
    Wu, Qiuyu
    Luo, Xiangyu
    STATISTICS IN BIOSCIENCES, 2023, 15 (03) : 719 - 733
  • [27] Bayesian Joint Modeling of Single-Cell Expression Data and Bulk Spatial Transcriptomic Data
    Jinge Yu
    Qiuyu Wu
    Xiangyu Luo
    Statistics in Biosciences, 2023, 15 : 719 - 733
  • [28] Revealing Dynamic Mechanisms of Cell Fate Decisions From Single-Cell Transcriptomic Data
    Zhang, Jiajun
    Nie, Qing
    Zhou, Tianshou
    FRONTIERS IN GENETICS, 2019, 10
  • [29] MAGNETO: Cell type marker panel generator from single-cell transcriptomic data
    Tangherloni, Andrea
    Riva, Simone G.
    Myers, Brynelle
    Buffa, Francesca M.
    Cazzaniga, Paolo
    JOURNAL OF BIOMEDICAL INFORMATICS, 2023, 147
  • [30] CellDART: cell type inference by domain adaptation of single-cell and spatial transcriptomic data
    Bae, Sungwoo
    Na, Kwon Joong
    Koh, Jaemoon
    Lee, Dong Soo
    Choi, Hongyoon
    Kim, Young Tae
    NUCLEIC ACIDS RESEARCH, 2022, 50 (10) : E57