RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

Hiromasa, Ono; Ogasawara, Osamu; Okubo, Kosaku; Bono, Hidemasa

doi:10.1038/sdata.2017.105

Cited by 61 publications

(56 citation statements)

References 45 publications

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“…AOE can also be used by professionals to construct reference expression datasets for specific organisms. We have also developed a Reference Expression dataset (RefEx) for humans and mice [10]. We are planning to implement RefEx for other organisms, by making use of these reference expression datasets retrieved by AOE.…”

Section: Discussionmentioning

confidence: 99%

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

Bono

2020

PLoS ONE

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Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE).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/.

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Section: Discussionmentioning

confidence: 99%

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

Bono

2020

PLoS ONE

Self Cite

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“…AOE can also be used by professionals to construct reference expression datasets for specific organisms. We have also developed Reference Expression dataset (RefEx) for humans and mice [10]. We are planning to implement RefEx for other organisms, making use of these reference expression datasets retrieved by AOE.…”

Section: Discussionmentioning

confidence: 99%

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

Bono

2019

Preprint

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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/.

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“…Hypoxia response element consensus sequences (ACGTG or GCGTG) 12,13 at 3,000 bp upstream from exon 1 of the TMEM180 gene were analysed using NCBI Gene databases (https://www.ncbi.nlm.nih.gov/gene/). TMEM180 gene expression in normal tissues and cancer tissues was analysed using the microarray gene expression dataset from RefEx (http://refex.dbcls.jp/) 44 and Oncomine (http://www.oncomine.org/) 45 , respectively. The comparison of TMEM180 gene expression between 286 colorectal adenocarcinoma patient samples and 41 normal tissue samples using TCGA cancer genomics data was performed using UALCAN (http://ulcan.path.uab.edu/index.html) 46 .…”

Section: Database Analysismentioning

confidence: 99%

Significant antitumour effect of an antibody against TMEM180, a new cancer-specific molecule

Yasunaga

Saijou

Hanaoka

et al. 2018

Preprint

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The present state of therapy for colorectal cancer (CRC) is far from satisfactory, highlighting the need for new targets for this disease. We identified a new colorectal cancer (CRC)-specific molecule, TMEM180, a predicted eleven-pass transmembrane protein that apparently functions as a cation symporter. Our anti-TMEM180 monoclonal antibody (mAb) eradicated SW480 CRC xenografts in mice. The TMEM180 promoter region contains ten hypoxia-responsive element consensus sequences; accordingly SW480 cells upregulated TMEM180 under low-oxygen conditions. TMEM180 expression in SW480 cells was positively correlated with anchorage-independent colony formation and tumourigenesis.TMEM180-positive SW480 cells resided at the tumour-stroma interface manifested by ɑSMA-positive fibroblasts, also known as the tumour niche. Some clusters of TMEM180-positive cells adjacent to the niche were integrin ɑ6-positive. These data indicate that TMEM180 represents a possible cancer stem cell marker and that a mAb against this protein could be used as antibody-based therapeutic against CRC.

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RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

Cited by 61 publications

References 45 publications

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

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

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

Significant antitumour effect of an antibody against TMEM180, a new cancer-specific molecule

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