Abstract:
:The identification of functional modules in gene interaction networks is a key step in understanding biological processes. Network interpretation is essential for unveiling biological mechanisms, candidate biomarkers, or potential targets for drug discovery/repositioning. Plenty of biological module identification algorithms are available, although none is explicitly designed to perform the task on single-cell RNA sequencing (scRNA-seq) data. Here, we introduce MTGO-SC, an adaptation for scRNA-seq of our biological network module detection algorithm MTGO. MTGO-SC isolates gene functional modules by leveraging on both the network topological structure and the annotations characterizing the nodes (genes). These annotations are provided by an external source, such as databases and literature repositories (e.g., the Gene Ontology, Reactome). Thanks to the depth of single-cell data, it is possible to define one network for each cell cluster (typically, cell type or state) composing each sample, as opposed to traditional bulk RNA-seq, where the emerging gene network is averaged over the whole sample. MTGO-SC provides two complexity levels for interpretation: the gene-gene interaction and the intermodule interaction networks. MTGO-SC is versatile in letting the users define the rules to extract the gene network and integrated with the Seurat scRNA-seq analysis pipeline. MTGO-SC is available at https://github.com/ne1s0n/MTGOsc.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Nazzicari N,Vella D,Coronnello C,Di Silvestre D,Bellazzi R,Marini Sdoi
10.3389/fgene.2019.00953subject
Has Abstractpub_date
2019-10-09 00:00:00pages
953issn
1664-8021journal_volume
10pub_type
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00748
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pub_type: 杂志文章
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pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00727
更新日期:2019-09-20 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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journal_title:Frontiers in genetics
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doi:10.3389/fgene.2019.00206
更新日期:2019-03-19 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00558
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.583932
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00174
更新日期:2015-05-13 00:00:00
abstract::Filet quality traits determine consumer satisfaction and affect profitability of the aquaculture industry. Soft flesh is a criterion for fish filet downgrades, resulting in loss of value. Filet firmness is influenced by many factors, including rate of protein turnover. A 50K transcribed gene SNP chip was used to genot...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00386
更新日期:2019-05-03 00:00:00
abstract::At the time of translation, nascent proteins are thought to be sorted into their final subcellular localization sites, based on the part of their amino acid sequences (i.e., sorting or targeting signals). Thus, it is interesting to computationally recognize these signals from the amino acid sequences of any given prot...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.607812
更新日期:2020-11-25 00:00:00
abstract:Background/Aims:Leiomyosarcoma (LMS) is a tumor derived from malignant mesenchymal tissue associated with poor prognosis. Determining potential prognostic markers for LMS can provide clues for early diagnosis, recurrence, and treatment. Methods:RNA sequence data and clinical features of 103 LMS were obtained from the ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01408
更新日期:2020-02-04 00:00:00
abstract::Autosomal recessive non-syndromic hearing loss (ARNSHL) is a highly heterogeneous disease involving more than 70 pathogenic genes. However, most ARNSHL families have small-sized pedigrees with limited genetic information, rendering challenges for the molecular diagnosis of these patients. Therefore, we attempted to es...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00639
更新日期:2019-07-17 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00254
更新日期:2018-07-17 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00263
更新日期:2012-12-14 00:00:00
abstract::Atherosclerosis and its comorbidities are the major contributors to the global burden of death worldwide. Lower extremities arterial disease (LEAD) is a common manifestation of atherosclerotic disease of arteries of lower extremities. MicroRNAs belong to epigenetic factors that regulate gene expression and have not ye...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01200
更新日期:2019-11-22 00:00:00
abstract::Background: There is a continued debate and inconsistent findings in previous literature about the relationship of catechol-O-methyltransferase (COMT) and Parkinson's disease (PD) susceptibility as well as cognitive dysfunction. To substantiate this existing gap, we comprehensively examine COMT genotype effects on the...
journal_title:Frontiers in genetics
pub_type:
doi:10.3389/fgene.2019.00644
更新日期:2019-07-12 00:00:00
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pub_type: 杂志文章
doi:10.3389/fgene.2018.00404
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00419
更新日期:2014-12-04 00:00:00
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doi:10.3389/fgene.2015.00171
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pub_type: 杂志文章
doi:10.3389/fgene.2019.00004
更新日期:2019-01-22 00:00:00
abstract::In this study, we examined whether smoking and drinking affect sperm quality and the DNA methylation of the repetitive element LINE-1, MEST, P16, H19, and GNAS in sperm. Semen samples were obtained from 143 male residents in a minority-inhabited district of Guizhou province in southwest China. Quantitative DNA methyla...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01001
更新日期:2019-10-18 00:00:00
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2017.00216
更新日期:2017-12-14 00:00:00
abstract:Background:Recent evidence has indicated that long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) to modulate mRNAs expression by sponging microRNAs (miRNAs). However, the specific mechanism and function of lncRNA-miRNA-mRNA regulatory network in non-small cell lung cancer (NSCLC) remains ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.511676
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00494
更新日期:2018-10-23 00:00:00
abstract::Selection for improved host response to infectious disease offers a desirable alternative to chemical treatment but has proven difficult in practice, due to low heritability estimates of disease traits. Disease data from field studies is often binary, indicating whether an individual has become infected or not followi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00215
更新日期:2012-10-22 00:00:00
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pub_type: 杂志文章
doi:10.3389/fgene.2020.594091
更新日期:2020-11-16 00:00:00