ICBO_2018_53: Visualization of gene expression and expression as a phenotype with the XPO, XAO and DO using a combination of experimental data sources

TitleICBO_2018_53: Visualization of gene expression and expression as a phenotype with the XPO, XAO and DO using a combination of experimental data sources
Publication TypeConference Paper
Year of Publication2018
AuthorsPells, T, Fisher, M, Segerdell, E, Fortriede, J, Burns, K, Chu, S, Chaturvedi, P, James-Zorn, C, Lotay, V, Nenni, M, Ponferrada, VG, Wang, DZhou, Wang, Y, Karimi, K, Vize, P, Zorn, A
Conference NameInternational Conference on Biomedical Ontology (ICBO 2018)
Date Published08/06/2018
PublisherInternational Conference on Biological Ontology
Keywordsbiocuration, gene expression, genomics, human disease modeling, model organism database, xenopus anatomy ontology, xenopus phenotype ontology
Abstract

Xenbase (www.xenbase.org) is a knowledge base for researchers and biomedical scientists that employ Xenopus (X. laevis and X. tropicalis) as a model organism in gaining a deeper understanding of developmental and disease processes. Through expert curation and automated data provisioning from various sources this MOD (model organism database) strives to integrate the Xenopus body of knowledge together with the visualization of biologically significant interactions. We present a vision for the usage of various ontologies that facilitate the visualization of gene expression from a combination of experimental data sources and the linking thereof back to human disease modeling. In keeping with the philosophy to foster greater insight through the use of visualization techniques that bring together data from different sources and show trends in the large body of experimental and curated data in Xenbase. The approach has been taken to represent key developmental stages and selected embryonic/adult tissue anatomy terms with a modified heat map rendering. This gives us the combined results from the in-situ gene expression summary as well as normalized TPM read counts (Sessions et al.) and UMI counts from the single cell experiment data (Peshkin et al.). Through the acquisition of RNA-seq and ChIP-seq Xenopus data from GEO and subsequent processing through a bioinformatics pipeline to obtain average TPM read counts and differential expression readings. This enables the subsequent construction and visualization of EaP (Expression as a Phenotype) in conjunction with the XPO (Xenopus Phenotype Ontology) and DO (Disease Ontoloty). This data manipulation has practical application in making the information accessible from gene pages and linking back to the source (eg:article/image). If you use Xenbase resources in your research please consider citing us, for example Nucleic Acids Res. 2018 46(D1):D861-D868.

URLhttp://icbo2018.cgrb.oregonstate.edu/