NEW ANALYTICS TOOL RELEASED
oposSOM is a comprehensive data analysis software combining diversity analyses, biomarker selection, functional information mining, and visualization to the machine learning based ‘high-dimensional data portraying’.
The new oposSOM-Browser extends this toolkit and introduces the interactive browsing of single gene and function set profiles, of their mapping into the molecular ‘portrait landscape’, of phenotype diversity and associated survival differences, and of cellular signaling pathway activation patterns. Further, individual signature gene list can be mapped and evaluated regarding diagnostic quality.
Currently, oposSOM-Browser provides in-detail data analytics of five different data sets previously evaluated using oposSOM software, among them transcriptome of almost 1,000 lymphoma cases and healthy blood transcriptome of about 3,500 Leipzig inhabitants. Additional data sets and further functionalities are in the pipeline.
AVAILABLE DATA SETS FOR BROWSING
Loeffler-Wirth H, Reikowski J, Hakobyan S, Wagner J, Binder H. oposSOM-Browser: an interactive tool to explore omics data landscapes in health science. BMC Bioinformatics 2020 2020/10/19; 21(1): 465.
BULK TRANSCRIPTOMICS OF CANCER
LYMPHOMA DATA SET (873 tumor samples, MMML consortium, LHA id 7WEWFE12CK-4)
Loeffler-Wirth H, Kreuz M, Hopp L, Arakelyan A, Haake A, Cogliatti SB, et al. A modular transcriptome map of mature B cell lymphomas. Genome Medicine 2019 April 30; 11(1): 27.
MELANOMA DATA SET (80 tumor & nevi samples, Kunz et al., LHA id 7R4PDEM4HG-2)
Kunz M, Löffler-Wirth H, Dannemann M, Willscher E, Doose G, Kelso J, et al. RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas. Oncogene 2018 2018/11/01; 37(47): 6136-6151.
LOWGRADE GLIOMA DATA SET (137 tumor samples, GGN consortium, LHA id 7Q0CFRJKW4-7)
Binder H, Willscher E, Loeffler-Wirth H, Hopp L, Jones DTW, Pfister SM, et al. DNA methylation, transcriptome and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development. Acta Neuropathologica Communications 2019 April 25; 7(1): 59.
GLIOMA GRADE 1-4 DATA SET (tumor samples, GGN consortium)
BULK METHYLOMICS OF CANCER
METHYLOME OF LOW GRADE GLIOMA (122 tumor samples, GGN consortium, LHA id7YJY236M67-5)
BULK TRANSCRIPTOMICS OF DIVERSE DISEASES
COELIAC DISEASE (25 duodenal samples, Wolf et al., LHA id 86RMNYPQ1Q-0)
Wolf J, Willscher E, Loeffler-Wirth H, Schmidt M, Flemming G, Zurek M, et al. Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease Biopsies. International Journal of Molecular Sciences 2021; 22(5): 2551.
BULK TRANSCRIPTOMICS OF BLOOD
PNEUMONIA DATA SET (180 samples + 10 controls, Burnham et al., LHA id 7RU79AQTJD-9)
Hopp L, Loeffler-Wirth H, Nersisyan L, Arakelyan A, Binder H. Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome. Frontiers in Immunology 2018 2018-July-17; 9(1620).
HEALTHY BLOOD TRANSCRIPTOM LIFE DATA SET (3388 samples, Schmidt et al., LHA id xxxxxxxxxxx)
Schmidt M, Loeffler-Wirth H, Hopp L, Arakelyan A, Scholz M, Kirsten H, et al. Portrayal of the human blood transcriptome of 3,388 adults and its relation to ageing and health. preprint 2019; doi 10.21203/rs.2.19387/v1.
SINGLE CELL TRANSCRIPTOMICS
BLOOD SAMPLES FROM CAR-T CELL THERAPY (77 meta-cells, Sheih et al. NatCom 2020)
GENOMICS DATA
SNP ATLAS (1039 individuals, Nikoghosyan et al. 2019, LHA id 81Y29P017A-3)
Nikoghosyan M, Hakobyan S, Hovhannisyan A, Loeffler-Wirth H, Binder H, Arakelyan A. Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians – A Machine Learning Approach. Frontiers in Genetics 2019 2019-April-26; 10(394).
CORONA VIRUS VARIANTS (Publication in preparation)