Network Visualization and Analysis of Spatially Aware Gene Expression Data with InsituNet

Salamon, JohnSouth 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 (författare)

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.

Qian, XiaoyanUppsala 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(Swepub:su)xqian (författare)
Nilsson, MatsUppsala 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(Swepub:uu)matsnils (författare)
Lynn, David JohnSouth 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 (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, AustraliaInstitutionen för biokemi och biofysik (creator_code:org_t)

Av författaren/redakt...: Salamon, John; Qian, Xiaoyan; Nilsson, Mats; Lynn, David John

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