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Network Visualizati...
Network Visualization and Analysis of Spatially Aware Gene Expression Data with InsituNet
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- Salamon, John (författare)
- South Australian Hlth & Med Res Inst, EMBL Australia Grp, Infect & Immun Theme, North Terrace, Adelaide, SA 5000, Australia;Flinders Univ S Australia, Sch Med, Bedford Pk, SA 5042, Australia
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- Qian, Xiaoyan (författare)
- Uppsala universitet,Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Uppsala University, Sweden,Science for Life Laboratory, SciLifeLab,Institutionen för immunologi, genetik och patologi,Stockholm Univ, Dept Biophys & Biochem, Sci Life Lab, Box 1031, S-17121 Solna, Sweden
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- Nilsson, Mats (författare)
- Uppsala universitet,Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Uppsala University, Sweden,Molekylära verktyg,Science for Life Laboratory, SciLifeLab,Stockholm Univ, Dept Biophys & Biochem, Sci Life Lab, Box 1031, S-17121 Solna, Sweden
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- Lynn, David John (författare)
- South Australian Hlth & Med Res Inst, EMBL Australia Grp, Infect & Immun Theme, North Terrace, Adelaide, SA 5000, Australia;Flinders Univ S Australia, Sch Med, Bedford Pk, SA 5042, Australia
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(creator_code:org_t)
- Elsevier BV, 2018
- 2018
- Engelska.
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Ingår i: Cell Systems. - : Elsevier BV. - 2405-4712. ; 6:5, s. 626-630
- Relaterad länk:
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http://www.cell.com/...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- In situ sequencing methods generate spatially resolved RNA localization and expression data at an almost single-cell resolution. Few methods, however, currently exist to analyze and visualize the complex data that is produced, which can encode the localization and expression of a million or more individual transcripts in a tissue section. Here, we present InsituNet, an application that converts in situ sequencing data into interactive network-based visualizations, where each unique transcript is a node in the network and edges represent the spatial co-expression relationships between transcripts. InsituNet is available as an app for the Cytoscape platform at http://apps.cytoscape.org/apps/insitunet. InsituNet enables the analysis of the relationships that exist between these transcripts and can uncover how spatial co-expression profiles change in different regions of the tissue or across different tissue sections.
Ämnesord
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
Nyckelord
- network biology
- data visualization
- in situ sequencing
- gene expression
- Cytoscape
- spatial transcriptomics
- spatial co-expression
- Biochemistry
- biokemi
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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