Jaccard Index Prognostic Hallmark Genes
A Jaccard Index of the overlap between prognostic and hallmark genes for 17 cancer types across different mapping schemes. The impact of selecting different mapping schemes was assessed by pairwise comparisons where there were 5 or more shared genes.
SEEK ID: https://fairdomhub.org/assays/1393
Modelling Analysis
Projects: Consensus Hallmark Annotation
Investigation: Cancer Hallmark Consensus
Study: Prognostic and Hallmark Gene Networks
Assay position:
Biological problem addressed: Biological Network Analysis
Organisms: No organisms
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Created: 22nd Jan 2021 at 16:13
Last updated: 5th Mar 2021 at 10:05
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Projects: Consensus Hallmark Annotation, FAIR Functional Enrichment, The evolution of Gene Ontology
Institutions: University of Leiden, LIACS
https://orcid.org/0000-0002-1279-5133I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
Projects: Consensus Hallmark Annotation, The evolution of Gene Ontology
Web page: Not specified
Data and experimental methods to support the work in the following paper:
Establishing Consensus Annotation for the Hallmarks of Cancer, 2020, Yi Chen, F.J.Verbeek and K.Wolstencroft, in submission
Programme: Hallmarks of cancer
Public web page: Not specified
The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. In this investigation we compare cancer hallmark mapping strategies from different studies, based on Gene Ontology and biological pathway annotation. By analysing the semantic ...
Submitter: Katy Wolstencroft
Studies: Comparing Cancer Hallmark Descriptions, Evolution of Gene Ontology Terms, Prognostic and Hallmark Gene Networks
Assays: Analysing Changes to GO Biological Process, Annotation Consensus and GO Consensus, Hub genes of modules and enriched GO terms, Jaccard Index Prognostic Hallmark Genes, WGCNA Prognostic Hallmark Genes
This study examines how different hallmark gene datasets intersect with prognostic cancer genes
Submitter: Katy Wolstencroft
Investigation: Cancer Hallmark Consensus
Assays: Hub genes of modules and enriched GO terms, Jaccard Index Prognostic Hallmark Genes, WGCNA Prognostic Hallmark Genes
