Abstract:
:Disease relationship studies for understanding the pathogenesis of complex diseases, diagnosis, prognosis, and drug development are important. Traditional approaches consider one type of disease data or aggregating multiple types of disease data into a single network, which results in important temporal- or context-related information loss and may distort the actual organization. Therefore, it is necessary to apply multilayer network model to consider multiple types of relationships between diseases and the important interplays between different relationships. Further, modules extracted from multilayer networks are smaller and have more overlap that better capture the actual organization. Here, we constructed a weighted four-layer disease-disease similarity network to characterize the associations at different levels between diseases. Then, a tensor-based computational framework was used to extract Conserved Disease Modules (CDMs) from the four-layer disease network. After filtering, nine significant CDMs were reserved. The statistical significance test proved the significance of the nine CDMs. Comparing with modules got from four single layer networks, CMDs are smaller, better represent the actual relationships, and contain potential disease-disease relationships. KEGG pathways enrichment analysis and literature mining further contributed to confirm that these CDMs are highly reliable. Furthermore, the CDMs can be applied to predict potential drugs for diseases. The molecular docking techniques were used to provide the direct evidence for drugs to treat related disease. Taking Rheumatoid Arthritis (RA) as a case, we found its three potential drugs Carvedilol, Metoprolol, and Ramipril. And many studies have pointed out that Carvedilol and Ramipril have an effect on RA. Overall, the CMDs extracted from multilayer networks provide us with an impressive understanding disease mechanisms from the perspective of multi-layer network and also provide an effective way to predict potential drugs for diseases based on its neighbors in a same CDM.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Yu L,Yao S,Gao L,Zha Ydoi
10.3389/fgene.2018.00745subject
Has Abstractpub_date
2019-01-18 00:00:00pages
745issn
1664-8021journal_volume
9pub_type
杂志文章abstract::The genetic diversity of the sheep breeds in the Arab countries might be considered to be a mirror of the ecology of the region. In this study, the genetic structure and diversity of sheep breeds from Saudi Arabia (Harri, Najdi, Naemi, Arb, and Rufidi) and Awassi sheep from Jordan as an out-group were investigated usi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00408
更新日期:2018-09-25 00:00:00
abstract::The goal of this work was to determine the effect of nonablative syngeneic transplantation of young bone marrow (BM) to laboratory animals (mice) of advanced age upon maximum duration of their lifespan. To do this, transplantation of 100 million nucleated cells from BM of young syngeneic donors to an old nonablated an...
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abstract::Huang-lian (Coptis plants in China) are essential medicinal plants in China, C. chinensis var. chinensis and C. deltoidea have been domesticated and cultivated for 700 years. In this study, the genetic diversity patterns and biogeographical information of cultivated Huang-lian and their wild relatives Coptis species w...
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pub_type: 杂志文章
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abstract::Over millions of years, vertebrate species populated vast environments spanning the globe. Among the most challenging habitats encountered were those with limited availability of oxygen, yet many animal and human populations inhabit and perform life cycle functions and/or daily activities in varying degrees of hypoxia...
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pub_type: 杂志文章,评审
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abstract::Alport syndrome is a hereditary progressive chronic kidney disease caused by mutations in type IV collagen genes COL4A3/4/5. X-linked Alport syndrome (XLAS) is caused by mutations in the COL4A5 gene and is the most common form of Alport syndrome. A strong correlation between the type of COL4A5 mutation and the age dev...
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pub_type: 杂志文章
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abstract::The global prevalence of metabolic disorders, such as obesity, diabetes and fatty liver disease, is dramatically increasing. Both genetic and environmental factors are well-known contributors to the development of these diseases and therefore, the study of epigenetics can provide additional mechanistic insight. Dietar...
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pub_type: 杂志文章,评审
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abstract:Background:Genetic association studies have identified single nucleotide polymorphisms (SNPs) related to chronic obstructive pulmonary disease (COPD) susceptibility. The aim of this study was to identify HHIP genetic variants associated with COPD, pulmonary function, and serum and sputum HHIP protein levels in Mexican ...
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abstract::Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-prot...
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pub_type: 杂志文章
doi:10.3389/fgene.2018.00104
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2018.00478
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abstract::A case-control study was used to explore the association between the methylation status in the promoter regions of the cGAS, MAVS, and TRAF3 genes and the diseases of cervical precancerous lesions (CPL) and cervical cancer (CC) in a Southern Chinese population, and to further explore their interaction effects with hig...
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pub_type: 杂志文章
doi:10.3389/fgene.2019.01123
更新日期:2019-11-14 00:00:00
abstract::People want to live long, healthy lives. Previous surveys suggest very limited interest in much longer lifespans, but we show that stipulating good health changes responses to favor longer lives by an order of magnitude. Advances in aging research hold out hope for greatly slowed aging with associated good health. Und...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00353
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abstract::The emerald ash borer (EAB), Agrilus planipennis, is a highly destructive quarantine pest. The olfactory and visual systems of A. planipennis play different but critical roles at newly emerged and sexually mature stages; however, the molecular basis underlying these differences remain unclear. Consequently, based on d...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.604757
更新日期:2021-01-15 00:00:00
abstract::Small-Tailed Han (STH) sheep are known for their high fecundity, but the survival of lambs is compromised and influences the commercial return from farming these sheep, with this being attributed in part to starvation from insufficient milk production by the ewes. In this study, the transcriptome profiles of the mamma...
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pub_type: 杂志文章
doi:10.3389/fgene.2020.00472
更新日期:2020-05-21 00:00:00
abstract::Tools for genomic island prediction use strategies for genomic comparison analysis and sequence composition analysis. The goal of comparative analysis is to identify unique regions in the genomes of related organisms, whereas sequence composition analysis evaluates and relates the composition of specific regions with ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00619
更新日期:2018-12-12 00:00:00
abstract::Familial hemophagocytic lymphohistiocytosis Type 2 (FHL2) associated central nervous system (CNS) involvement is less understood in children, especially when considering neurologic manifestations as part of the initial presentation. We conducted a retrospective review of the clinical manifestations and genetic abnorma...
journal_title:Frontiers in genetics
pub_type:
doi:10.3389/fgene.2020.00126
更新日期:2020-03-04 00:00:00
abstract::Obesity has become a major public health issue which is caused by a combination of genetic and environmental factors. Genome-wide DNA methylation studies have identified that DNA methylation at Cytosine-phosphate-Guanine (CpG) sites are associated with obesity. However, subsequent functional validation of the results ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00663
更新日期:2018-12-19 00:00:00
abstract::Across species and tissues and especially in the mammalian brain, production of gene isoforms is widespread. While gene expression coordination has been previously described as a scale-free coexpression network, the properties of transcriptome-wide isoform production coordination have been less studied. Here we evalua...
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::As one of the hotspot regions for sympatric speciation studies, Evolution Canyon (EC) became an ideal place for its high level of microclimatic divergence interslopes. In this study, to highlight the genetic mechanisms of sympatric speciation, phenotypic variation on flowering time and transcriptomic divergence were i...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00506
更新日期:2018-11-14 00:00:00
abstract::The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as 'at-risk'. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recen...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00927
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abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression. They are aberrantly expressed in many human cancers and are potential therapeutic targets and molecular biomarkers. METHODS:In this study, we for the first time validated the reported data on the entire set of published differential...
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pub_type: 杂志文章
doi:10.3389/fgene.2013.00247
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2015.00010
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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
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00762
更新日期:2020-07-15 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00013
更新日期:2015-02-03 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00466
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doi:10.3389/fgene.2019.00489
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2013.00264
更新日期:2013-12-20 00:00:00
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pub_type: 杂志文章
doi:10.3389/fgene.2019.00527
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pub_type: 杂志文章
doi:10.3389/fgene.2015.00031
更新日期:2015-02-17 00:00:00