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XDeathDB: a visualization platform for cell death molecular interactions.
Gadepalli, Venkat Sundar; Kim, Hangil; Liu, Yueze; Han, Tao; Cheng, Lijun.
  • Gadepalli VS; Research Information Technology, College of Medicine, Ohio State University, 1585 Neil Ave, Columbus, OH, 43210, USA.
  • Kim H; 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA.
  • Liu Y; The Grainger College of Engineering, The University of Illinois-Urbana-Champaign, Urbana and Champaign, Champaign, IL, 61801, USA.
  • Han T; 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA.
  • Cheng L; 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA. lijun.cheng@osumc.edu.
Cell Death Dis ; 12(12): 1156, 2021 12 14.
Article in English | MEDLINE | ID: covidwho-1585874
ABSTRACT
Lots of cell death initiator and effector molecules, signalling pathways and subcellular sites have been identified as key mediators in both cell death processes in cancer. The XDeathDB visualization platform provides a comprehensive cell death and their crosstalk resource for deciphering the signaling network organization of interactions among different cell death modes associated with 1461 cancer types and COVID-19, with an aim to understand the molecular mechanisms of physiological cell death in disease and facilitate systems-oriented novel drug discovery in inducing cell deaths properly. Apoptosis, autosis, efferocytosis, ferroptosis, immunogenic cell death, intrinsic apoptosis, lysosomal cell death, mitotic cell death, mitochondrial permeability transition, necroptosis, parthanatos, and pyroptosis related to 12 cell deaths and their crosstalk can be observed systematically by the platform. Big data for cell death gene-disease associations, gene-cell death pathway associations, pathway-cell death mode associations, and cell death-cell death associations is collected by literature review articles and public database from iRefIndex, STRING, BioGRID, Reactom, Pathway's commons, DisGeNET, DrugBank, and Therapeutic Target Database (TTD). An interactive webtool, XDeathDB, is built by web applications with R-Shiny, JavaScript (JS) and Shiny Server Iso. With this platform, users can search specific interactions from vast interdependent networks that occur in the realm of cell death. A multilayer spectral graph clustering method that performs convex layer aggregation to identify crosstalk function among cell death modes for a specific cancer. 147 hallmark genes of cell death could be observed in detail in these networks. These potential druggable targets are displayed systematically and tailoring networks to visualize specified relations is available to fulfil user-specific needs. Users can access XDeathDB for free at https//pcm2019.shinyapps.io/XDeathDB/ .
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: Signal Transduction / Cell Death / Regulated Cell Death Type of study: Reviews Limits: Animals / Humans Language: English Journal: Cell Death Dis Year: 2021 Document Type: Article Affiliation country: S41419-021-04397-X

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Signal Transduction / Cell Death / Regulated Cell Death Type of study: Reviews Limits: Animals / Humans Language: English Journal: Cell Death Dis Year: 2021 Document Type: Article Affiliation country: S41419-021-04397-X