Abstract:
:Identifying driver genes that contribute to cancer progression from numerous passenger genes, although a central goal, is a major challenge. The protein-protein interaction network provides convenient and reasonable assistance for driver gene discovery. Random walk-based methods have been widely used to prioritize nodes in social or biological networks. However, most studies select the next arriving node uniformly from the random walker's neighbors. Few consider transiting preference according to the degree of random walker's neighbors. In this study, based on the random walk method, we propose a novel approach named Driver_IRW (Driver genes discovery with Improved Random Walk method), to prioritize cancer genes in cancer-related network. The key idea of Driver_IRW is to assign different transition probabilities for different edges of a constructed cancer-related network in accordance with the degree of the nodes' neighbors. Furthermore, the global centrality (here is betweenness centrality) and Katz feedback centrality are incorporated into the framework to evaluate the probability to walk to the seed nodes. Experimental results on four cancer types indicate that Driver_IRW performs more efficiently than some previously published methods for uncovering known cancer-related genes. In conclusion, our method can aid in prioritizing cancer-related genes and complement traditional frequency and network-based methods.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Wei PJ,Wu FX,Xia J,Su Y,Wang J,Zheng CHdoi
10.3389/fgene.2020.00377subject
Has Abstractpub_date
2020-04-28 00:00:00pages
377issn
1664-8021journal_volume
11pub_type
杂志文章abstract::We report on three new patients with spondyloocular syndrome (SOS) in a consanguineous Pakistani family. All three patients present progressive generalized osteoporosis, short stature, recurrent fractures, hearing loss and visual impairments. WES revealed a novel homozygous frameshift variant in exon 11 of XYLT2 (NG 0...
journal_title:Frontiers in genetics
pub_type: 杂志文章
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journal_title:Frontiers in genetics
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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abstract::Multiple sclerosis (MS) is an autoimmune disease for which it is difficult to find exact disease-related genes. Effectively identifying disease-related genes would contribute to improving the treatment and diagnosis of multiple sclerosis. Current methods for identifying disease-related genes mainly focus on the hypoth...
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00280
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abstract::The sustainable development of aquaculture has been impeded by infectious diseases worldwide. However, the genomic architecture and the genetic basis underlying the disease resistance remain poorly understood, which severely hampers both the understanding of the evolution of fish disease resistance traits and the prev...
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00193
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00280
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abstract::Long non-coding RNAs (lncRNAs) are transcripts which are usually more than 200 nt in length, and which do not have the protein-coding capacity. LncRNAs can be categorized based on their generation from distinct DNA elements, or derived from specific RNA processing pathways. During the past several decades, dramatic pr...
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2018.00744
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doi:10.3389/fgene.2019.01375
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abstract::Primary ciliary dyskinesia (PCD), a rare genetic disorder, is mostly caused by defects in more than 40 known cilia structure-related genes. However, in approximately 20-35% of patients, it is caused by unknown genetic factors, and the inherited pathogenic factors are difficult to confirm. Kartagener syndrome (KTS) is ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00749
更新日期:2019-08-22 00:00:00
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doi:10.3389/fgene.2020.00217
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00010
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pub_type: 杂志文章,评审
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