Xenbase: deep integration of GEO &amp; SRA RNA-seq and ChIP-seq data in a model organism database

Fortriede, Joshua D.; Pells, Troy J.; Chu, Stanley; Chaturvedi, Praneet; Wang, DongZhuo; Fisher, Malcom E; James-Zorn, Christina; Wang, Ying; Nenni, Mardi J.; Burns, Kevin A.; Lotay, Vaneet; Ponferrada, Virgilio G.; Karimi, Kamran; Zorn, Aaron M.; Vize, Peter D.

doi:10.1093/nar/gkz933

Cited by 60 publications

(66 citation statements)

References 15 publications

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“…With time, more sophisticated data interfaces allowed the accumulation of high quality expert curated content and more complex data representations such as gene pages, gene expression data support, and disease support ( 15 ). In recent years Xenbase has led the MOD community by developing powerful integrated support for RNA-seq and ChIP-seq content ( 16 ) plus phenotype and ‘gene expression as a phenotype’ features unique to the field. Once again, these also represent techniques widely used in modern echinoderm research.…”

Section: Introductionmentioning

confidence: 99%

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

Arshinoff

Cary

Karimi

et al. 2021

Nucleic Acids Research

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Echinobase (www.echinobase.org) is a third generation web resource supporting genomic research on echinoderms. The new version was built by cloning the mature Xenopus model organism knowledgebase, Xenbase, refactoring data ingestion pipelines and modifying the user interface to adapt to multispecies echinoderm content. This approach leveraged over 15 years of previous database and web application development to generate a new fully featured informatics resource in a single year. In addition to the software stack, Echinobase uses the private cloud and physical hosts that support Xenbase. Echinobase currently supports six echinoderm species, focused on those used for genomics, developmental biology and gene regulatory network analyses. Over 38 000 gene pages, 18 000 publications, new improved genome assemblies, JBrowse genome browser and BLAST + services are available and supported by the development of a new echinoderm anatomical ontology, uniformly applied formal gene nomenclature, and consistent orthology predictions. A novel feature of Echinobase is integrating support for multiple, disparate species. New genomes from the diverse echinoderm phylum will be added and supported as data becomes available. The common code development design of the integrated knowledgebases ensures parallel improvements as each resource evolves. This approach is widely applicable for developing new model organism informatics resources.

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Section: Introductionmentioning

confidence: 99%

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

Arshinoff

Cary

Karimi

et al. 2021

Nucleic Acids Research

Self Cite

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“…As an integral component of the larger Mouse Genome Informatics (MGI) resource ( 1–3 ), GXD combines expression data with genetic, functional, phenotypic and disease-oriented data, thereby enabling unique and powerful search capabilities that foster insights into the molecular mechanisms of human development, differentiation, and disease. In addition, GXD maintains links to external expression resources, including gene-based links to expression data from other vertebrate model organisms that are highly relevant for developmental research: zebrafish (ZFIN; 4 ), Xenopus (Xenbase; 5 ) and chicken (GEISHA; 6 ). For many years, GXD has collected RNA and protein expression information from RNA in situ hybridization, immunohistochemistry, in situ reporter (knock in), RT-PCR, northern blot, and western blot experiments.…”

Section: Introductionmentioning

confidence: 99%

The mouse Gene Expression Database (GXD): 2021 update

Baldarelli

Smith

Finger

et al. 2020

Nucleic Acids Research

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The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded GXD to include RNA-Seq data. Uniformly processed RNA-Seq data are imported from the EBI Expression Atlas and then integrated with the other types of expression data in GXD, and with the genetic, functional, phenotypic and disease-related information in Mouse Genome Informatics (MGI). This integration has made the RNA-Seq data accessible via GXD’s enhanced searching and filtering capabilities. Further, we have embedded the Morpheus heat map utility into the GXD user interface to provide additional tools for display and analysis of RNA-Seq data, including heat map visualization, sorting, filtering, hierarchical clustering, nearest neighbors analysis and visual enrichment.

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“…We logged into the GEO database [ 12 ], downloaded GSE86436 (lncRNA) and GSE59856 (miR) chips, synthesized matrix files, analyzed the data using the Limma package, and extracted LINC01320. miR-324-3p and miR-496 expression data were used to draw pictures.…”

Section: Methodsmentioning

confidence: 99%

Effects of lncRNA LINC01320 on Proliferation and Migration of Pancreatic Cancer Cells through Targeted Regulation of miR-324-3p

Meng

Guo

Zhang

2021

Journal of Healthcare Engineering

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Objective. LINC01320 is a new oncogenic gene. Nevertheless, the effect of LINC01320 on pancreatic cancer (PC) is still unclear. This research aimed to seek the influence of LINC01320 on PC and its possible mechanism. Methods. RT-qPCR is used to test the LINC01320 in tissues and cells. Cell viability, apoptosis, migration, and invasiveness are detected to explore the role of LINC01320 in PC, and target genes are predicted by bioinformatics methods. The mechanism of action was further explored by transfection of specific siRNA, miRNA mimetics, or miRNA inhibitors. In order to verify the effect of LINC01320 in vivo, we carried out tumor xenotransplantation. Results. We conclude that LINC01320 is highly expressed in PC tissues and cell strains. LINC01320 high expression was bound up with a poor prognosis. LINC01320 gene knockout inhibited the growth, migration, and invasiveness of PC cells. In addition, LINC01320 is expressed by miR-324-3p, which is also supported by in vivo experiments. Conclusion. LINC01320 is highly expressed in PC, and it can suppress the growth and migration of PC cells through targeted regulation of miR-324-3p, which is expected to become a latent target for clinical treatment.

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Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database

Cited by 60 publications

References 15 publications

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms

The mouse Gene Expression Database (GXD): 2021 update

Effects of lncRNA LINC01320 on Proliferation and Migration of Pancreatic Cancer Cells through Targeted Regulation of miR-324-3p

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