Unknown

Dataset Information

0

Decoding of persistent multiscale structures in complex biological networks.

ABSTRACT: Networks of genes, proteins, and cells exhibit significant multiscale organization, with distinct communities appearing at different spatial resolutions. Here, we apply the concept of 'persistent homology' to identify network communities that persist within defined scale ranges, yielding a hierarchy of robust structures in data. Application to mouse single-cell transcriptomes significantly expands the catalog of cell types identified by current tools, while analysis of SARS-COV-2 networks suggests pro-viral hijacking of WNT.

SUBMITTER: Zheng F 

PROVIDER: S-EPMC7310637 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

Identifying persistent structures in multiscale 'omics data.

Zheng Fan F   Zhang She S   Churas Christopher C   Pratt Dexter D   Bahar Ivet I   Ideker Trey T  

bioRxiv : the preprint server for biology 20201003

In any 'omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here we use the concept of "persistent homology", drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell tr  ...[more]

Similar Datasets

Unknown Inferring dynamic topology for decoding spatiotemporal structures in complex heterogeneous networks.
| S-EPMC6140519 | biostudies-literature
Unknown HiDeF: identifying persistent structures in multiscale 'omics data.
| S-EPMC7789082 | biostudies-literature
Unknown Nonparametric sparsification of complex multiscale networks.
| S-EPMC3035633 | biostudies-literature
Unknown Multiscale representations of community structures in attractor neural networks.
| S-EPMC8412329 | biostudies-literature
Unknown Interactive, multiscale navigation of large and complicated biological networks.
| S-EPMC3072549 | biostudies-literature
Unknown Extracting the multiscale backbone of complex weighted networks.
| S-EPMC2672499 | biostudies-literature
Unknown Evolution of complex modular biological networks.
| S-EPMC2233666 | biostudies-literature
Unknown Epidemic spreading on complex networks with community structures.
| S-EPMC4954979 | biostudies-literature
Unknown Persistent homology of unweighted complex networks via discrete Morse theory.
| S-EPMC6761140 | biostudies-literature
Unknown Multiscale mixing patterns in networks.
| S-EPMC5910813 | biostudies-literature