HGNChelper: identification and correction of invalid gene symbols for human and mouse

Oh, Sehyun; Abdelnabi, Jasmine; Al-Dulaimi, Ragheed; Aggarwal, Ayush; Ramos, Marcel; Davis, Sean; Riester, Markus

doi:10.12688/f1000research.28033.1

Cited by 25 publications

(27 citation statements)

References 11 publications

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“…In studies where raw count matrices were unavailable (Couturier2020, Bhaduri2020), BAM files were converted to FASTQ files and re-aligned to GRCh38 using CellRanger v3.1/4.0. All gene names were updated to the latest HUGO nomenclature using HGNChelper (Oh et al, 2020). All clinical/diagnostic metadata was harmonized and preserved.…”

Section: Methodsmentioning

confidence: 99%

Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma

Ruiz-Moreno

Salas

Samuelsson

et al. 2022

Preprint

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Glioblastoma, isocitrate dehydrogenase (IDH)-wildtype (hereafter, GB), is an aggressive brain malignancy associated with a dismal prognosis and poor quality of life. Single-cell RNA sequencing has helped to grasp the complexity of the cell states and dynamic changes in GB. Large-scale data integration can help to uncover unexplored tumor pathobiology. Here, we resolved the composition of the tumor milieu and created a cellular map of GB ("GBmap"), a curated resource that harmonizes 26 datasets gathering 240 patients and spanning over 1.1 million cells. We showcase the applications of our resource for reference mapping, transfer learning, and biological discoveries. Our results uncover the sources of pro-angiogenic signaling and the multifaceted role of mesenchymal-like cancer cells. Reconstructing the tumor architecture using spatially resolved transcriptomics unveiled a high level of well-structured neoplastic niches. The GBmap represents a framework that allows the streamlined integration and interpretation of new data and provides a platform for exploratory analysis, hypothesis generation and testing.

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Section: Methodsmentioning

confidence: 99%

Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma

Ruiz-Moreno

Salas

Samuelsson

et al. 2022

Preprint

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“…Aligned sequences we processed using the Seurat package (version 4.0.2) in R [33]. Gene names between experiments were correlated using the HGNChelper package [34], using the suggested gene symbol for each gene except when it would create a duplicate reference. Genes were filtered from individual runs if they did not appear in three or more cells.…”

Section: Data Processing and Integrationmentioning

confidence: 99%

Comparative single-cell transcriptomes of dose and time dependent epithelial-mesenchymal spectrums

Panchy

Watanabe

Takahashi

et al. 2022

Preprint

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Epithelial-mesenchymal transition (EMT) is a key cellular process involved in development and disease progression. Single-cell transcriptomes can characterize intermediate EMT states observed in tumors and fibrotic tissues, but previous in vitro models focused on time-dependent responses after stimulation with single dose of EMT signals. It was therefore unclear whether single-cell transcriptomes support stable intermediate EMT phenotypes crucial for disease progression. We performed single-cell RNA-sequencing with human mammary epithelial cells treated with various concentrations of TGF-β. We found that the dose-dependent EMT harbors multiple intermediate states at the single-cell level after two weeks of treatment, suggesting a stable continuum. After correcting batch effects from experiments, we performed comparative analyses of the dose- and time-dependent EMT. We found that the dose-dependent EMT shows a stronger anti-correlation between epithelial and mesenchymal transcriptional programs and a better resolution of transition stages compared to the time-dependent process. These properties enable higher sensitivity to detect genes whose expressions are associated with core EMT regulatory networks. Nonetheless, we found cell clusters unique to the time-dependent EMT, which correspond to en route cell populations that do not appear at steady states. Furthermore, combining dose- and time-dependent cell clusters gave rise to more accurate prognosis for cancer patients compared to individual EMT spectrum. Our new data and analyses reveal a stable EMT continuum at the single-cell resolution and the transcriptomic level. The dose-dependent experimental model can complement the widely used time-course experiments to reflect physiologically or pathologically relevant EMT phenotypes in a comprehensive manner.

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“…The set of evolutionarily conserved human miRNA binding sites was developed by Agarwal et al using context++ model prediction and downloaded from the TargetScan database 7.1 (June 2016 release) [ 10 ]. HGNChelper R package (version 0.8.1) and updated reference map via function getCurrentHumanMap were used to update obsolete gene symbols and historical aliases to current gene symbols maintained by The HUGO Gene Nomenclature Committee (HGNC) database [ 27 ]. The dataset contains 116,371 predicted miRNA binding sites in the 3′-UTRs of 12,436 human genes.…”

Section: Methodsmentioning

confidence: 99%

Comparative Analysis of microRNA Binding Site Distribution and microRNA-Mediated Gene Expression Repression of Oncogenes and Tumor Suppressor Genes

Tian

Wang

Zhang

et al. 2022

Genes

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MicroRNAs (miRNAs) are a family of short, noncoding RNAs that can regulate gene expression levels of over half of the human genome. Previous studies on the role of miRNAs in cancer showed overall widespread downregulation of miRNAs as a hallmark of human cancer, though individual miRNAs can be both tumor suppressive and oncogenic, and cancer genes are speculated to be more targeted by miRNA. However, the extents to which oncogenes and tumor suppressor genes (TSG) are controlled by miRNA have not been compared. To achieve this goal, we constructed lists of oncogenes and TSGs and compared them with each other, and with the whole protein-coding gene population, in terms of miRNA binding sites distribution and expression level changes upon genetic disruption of miRNA production. As expected, the results show that cancer gene mRNAs anchor more miRNA binding sites, and are under a higher degree of miRNA-mediated repression at both mRNA abundance and translation efficiency levels than the whole protein-coding gene population. Importantly, on average, TSG mRNAs are more highly targeted and regulated by miRNA than oncogene mRNAs. To the best of our knowledge, this is the first comparison of miRNA regulation of oncogenes and TSGs.

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HGNChelper: identification and correction of invalid gene symbols for human and mouse

Cited by 25 publications

References 11 publications

Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma

Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma

Comparative single-cell transcriptomes of dose and time dependent epithelial-mesenchymal spectrums

Comparative Analysis of microRNA Binding Site Distribution and microRNA-Mediated Gene Expression Repression of Oncogenes and Tumor Suppressor Genes

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