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All of gene expression (AOE): An integrated index for public gene expression databases.

ABSTRACT: Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA). We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE. AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.

SUBMITTER: Bono H

PROVIDER: S-EPMC6980531 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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All of gene expression (AOE): An integrated index for public gene expression databases.

Bono Hidemasa H

PloS one 20200124 1

Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA). We construc ...[more]

PMID: 31978081

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Project description:BackgroundGlioma is the most common type of intracranial tumor with high malignancy and poor prognosis despite the use of various aggressive treatments. Targeted therapy and immunotherapy are not effective and new biomarkers need to be explored. Some Procollagen-lysine 2-oxyglutarate 5-dioxygenase (PLOD) family members have been found to be involved in the metastasis and progression of tumors. Both PLOD2 and PLOD3 had been reported to be highly expressed in gliomas, while the prognostic value of PLOD1 remains to be further illustrated, so we want to investigate the PLOD1 expression in glioma and its clinical implication.MethodsWe collected gene expression and corresponding clinical data of glioma from the Chinese Glioma Genome Atlas (CGGA) database, The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. First, we analyzed the expression and mutation of PLOD1 in gliomas and its relationship with clinicopathologic characteristics. Then, we conducted survival analysis, prognostic analysis and nomogram construction of the PLOD1 gene. Finally, we conducted gene ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) to explore possible mechanisms and gene co-expression analysis was also be performed.ResultsThe results showed that the expression level of PLOD1 was higher in gliomas than normal tissues, and high expression of PLOD1 was related to poor survival which can serve as an oncogenic factor and an independent prognostic indicator for glioma patients. Both the GO and GSEA analysis showed high expression of PLOD1 were enriched in Extracellular matrix (ECM) related pathways, the co-expression analysis revealed that PLOD1 was positively related to HSPG2, COL6A2, COL4A2, FN1, COL1A1, COL4A1, CD44, COL3A1, COL1A2 and SPP1, and high expression of these genes were also correlated to poor prognosis of glioma.ConclusionsThe results showed that high expression of PLOD1 leads to poor prognosis, and PLOD1 is an independent prognostic factor and a novel biomarker for the treatment of glioma. Furthermore, targeting PLOD1 is most likely a potential therapeutic strategy for glioma patients.

Dataset Information

All of gene expression (AOE): An integrated index for public gene expression databases.

Publications

All of gene expression (AOE): An integrated index for public gene expression databases.

Similar Datasets

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