oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
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BiBTeXBackground: oposSOM is a comprehensive, machine learning based open-source data analysis software combining functionalities such as diversity analyses, biomarker selection, function mining, and visualization. Results: These functionalities are now available as interactive web-browser application for a broader user audience interested in extracting detailed information from high-throughput omics data sets pre-processed by oposSOM. It enables interactive browsing of single-gene and gene set profiles, of molecular 'portrait landscapes', of associated phenotype diversity, and signalling pathway activation patterns. Conclusion: The oposSOM-Browser makes available interactive data browsing for five transcriptome data sets of cancer (melanomas, B-cell lymphomas, gliomas) and of peripheral blood (sepsis and healthy individuals) at www.izbi.uni-leipzig.de/opossom-browser .
DOI: 10.1186/s12859-020-03806-w
Projects: LHA - Leipzig Health Atlas, oBIG - omics Bioinformatics for Health
Publication type: Journal article
Journal: BMC Bioinformatics
Human Diseases: No Human Disease specified
Citation: BMC Bioinformatics 21(1),465
Date Published: 1st Dec 2020
Registered Mode: by DOI
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Created: 3rd Feb 2021 at 16:51
Last updated: 7th Dec 2021 at 17:58
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The Leipzig Health Atlas (LHA) is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research fields in which our team has scientific and clinical expertise.
Programme: i:DSem - Integrative Datensemantik in der Systemmedizin
Public web page: https://www.health-atlas.de
Start date: 1st Apr 2016
End date: 28th Feb 2021
The aim of oBIG is to establish modern genome bioinformatics in Armenia to investigate genesis and progression of complex diseases. Therefore we will extend the collaboration between the Interdisciplinary Center for Bioinformatics (IZBI) of Leipzig University and the Institute of Molecular Biology (IMB) in Yerevan, Armenia, to accomplish three main aspects of the project:Firstly, current research topics in systems biology of cancer, lung diseases and infections will be addressed by a joint team ...
Programme: Default Programme
Public web page: https://www.izbi.uni-leipzig.de/current-projects/obig/
oposSOM is a comprehensive, machine learning based open-source data analysis software combining functionalities such as diversity analyses, biomarker selection, function mining, and visualization. These functionalities are now available as interactive web-browser application for a broader user audience interested in extracting detailed information from high-throughput omics data sets pre-processed by oposSOM. It enables interactive browsing of single-gene and gene set profiles, of molecular ...
Creator: Henry Löffler-Wirth
Submitter: René Hänsel
Model type: Self-Organizing Map
Model format: R package
Environment: Shiny
Projects: Leipzig Melanoma Studies, CAPSys - Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome, CapSys - Systems Medicine of Community Acquired Pneumonia, e:Med, HNPCC-Sys - Genomic and transcriptomic heterogeneity of colorectal tumours arising in Lynch syndrome, oBIG - omics Bioinformatics for Health
Institutions: Interdisciplinary Center for Bioinformatics (IZBI)
https://orcid.org/0000-0002-2242-4678
Projects: Leipzig Melanoma Studies, GLA - German Lymphoma Alliance, MMML-MYC-SYS, GGN - German Glioma Network, LIFE Adult, LIFE - Leipzig Research Center for Civilization Diseases, Task Force COVID-19 Leipzig, NFDI4Health, LHA - Leipzig Health Atlas, Think different, imSAVAR - Immune safety avatar: nonclinical mimicking of the immune system effects of immunomodulatory therapies, oBIG - omics Bioinformatics for Health, Vine Bioinformatics - grape genomics for Innovative viticulture
Institutions: University of Leipzig, Interdisciplinary Center for Bioinformatics (IZBI)
https://orcid.org/0000-0001-8239-440X
Within the framework of the funding measure "i:DSem - Integrative Data Semantics in Systems Medicine", the Federal Ministry of Education and Research supports research projects that take up this approach. Interdisciplinary research projects are to create the basis so that in the future, for example, the attending physician will have application-oriented computer programmes at his or her disposal that will enable him or her to access all clinically relevant data. This should significantly support ...
Projects: LHA - Leipzig Health Atlas
This is the Programme users can request to have a Project created and associated with, without the need to create and manage their own.
Projects: SCALE-TORT, oBIG - omics Bioinformatics for Health, e:Med
Web page: Not specified
