ArticleScientific reports2016
A pathway-centric view of spatial proximity in the 3D nucleome across cell lines.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- KNeXT: a NetworkX-based topologically relevant KEGG parser.Frontiers in genetics · 2024Article
- Transcription factors organize into functional groups on the linear genome and in 3D chromatin.Heliyon · 2023Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Single-cell systems biology: probing the basic unit of information flow.Current opinion in systems biology · 2018Article
- seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.Frontiers in immunology · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
In various contexts, spatially proximal genes have been shown to be functionally related. However, the extent to which spatial proximity of genes in a pathway contributes to the pathway's context-specific activity is not known. Leveraging Hi-C data in six human cell-lines, we show that spatial proximity of genes in a pathway is highly correlated with the pathway's context-specific expression and function. Furthermore, spatial proximity of pathway genes correlates with interactions of their protein products, and the specific pathway genes that are proximal to one another tend to occupy higher levels in the regulatory hierarchy. In addition to intra-pathway proximity, related pathways are spatially proximal to one another and housekeeping-genes tend to be proximal to several other pathways suggesting their coordinating role. Substantially extending previous works, our study reveals a pathway-centric organization of 3D-nucleome, whereby, functionally related interacting driver genes tend to be in spatial-proximity in a context-specific manner.
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Registered trials
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