A gene co‐expression network analysis of the candidate genes and molecular pathways associated with feather follicle traits of chicken skin

2020 ◽  
Vol 138 (1) ◽  
pp. 122-134 ◽  
Author(s):  
Gai‐ge Ji ◽  
Ming Zhang ◽  
Yi‐fan Liu ◽  
Yan‐ju Shan ◽  
Yun‐jie Tu ◽  
...  
Keyword(s):  
Network Analysis ◽  
Candidate Genes ◽  
Molecular Pathways ◽  
Chicken Skin ◽  
Feather Follicle

scholarly journals Indirubin attenuates mouse psoriasis-like skin lesion in a CD274-dependent manner: an achievement of RNA sequencing

2018 ◽  
Vol 38 (6) ◽  
Author(s):  
Xiaochun Xue ◽  
Jianhua Wu ◽  
Junhui Li ◽  
Jianguo Xu ◽  
Haiying Dai ◽  
...  
Keyword(s):  
Network Analysis ◽  
Skin Lesion ◽  
Candidate Genes ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Regulatory Mechanisms ◽  
Epidermal Keratinocytes ◽  
Dependent Manner ◽  
Human Epidermal Keratinocytes ◽  
Ifn Γ

It was previously reported that the expression of CD274 was down-regulated in psoriatic epidermis, leading to immune disorders of psoriasis. However, the regulatory mechanisms of CD274 were rarely elucidated. We aimed to explore the regulatory mechanisms of CD274. Skin samples were collected from 18 patients with psoriasis vulgaris and 9 healthy participants for RNA sequencing. Candidate genes were chosen based on degree and k-core difference of genes in the co-expression network. The relations between candidate genes and CD274 were validated by flow cytometry and real-time PCR in primary human epidermal keratinocytes. The therapeutic effect of indirubin was assessed in an imiquimod-treated mouse model. Interferon-γ (IFN-γ), cyclin-dependent kinase (CDK) 1, Toll-like receptor 3 (TLR3), TLR4 and interleukin (IL)-17A were considered as candidate genes. In primary human epidermal keratinocytes, the level of CD274 was obviously increased under the stimulation of IFN-γ and CDK1 inhibitor (indirubin), independent of TLR4, TLR3 or IL-17A. Indirubin alleviated the severity of psoriatic mice in a CD274-dependent manner. Co-expression network analysis served as an effective method for the exploration of molecular mechanisms. We demonstrated for the first time that CD274 was the regulator of indirubin-mediated effect on mouse psoriasis-like skin lesion based on co-expression network analysis, contributing to the alleviation of mouse psoriasis-like skin lesion.

A molecular systems biomedicine approach to Diabetes: characterization, prioritization and network analysis of new candidate genes from the apoptotic machinery

2010 ◽  
Vol 27 ◽  
pp. S44 ◽  
Author(s):  
D. Barbagallo ◽  
S. Piro ◽  
M. Ragusa ◽  
C. Di Pietro ◽  
F. Purrello ◽  
...  
Keyword(s):  
Network Analysis ◽  
Candidate Genes ◽  
Molecular Systems

Abstract 662: Assessing the Biological Consistency in Atherosclerosis Susceptibility Genes Between Mouse and Human Genetic Studies

2016 ◽  
Vol 36 (suppl_1) ◽  
Author(s):  
Moritz von Scheidt ◽  
Yuqi Zhao ◽  
Zeyneb Kurt ◽  
Heribert Schunkert ◽  
Xia Yang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Mouse Models ◽  
Mouse Genetics ◽  
Molecular Pathways ◽  
Genetic Studies ◽  
Vast Number ◽  
Treatment And Prevention ◽  
Using Data ◽  
Cytokine Interactions ◽  
Lipids And Lipoproteins

Atherosclerosis is a complex and heritable disease with a vast number of interacting genes, networks and molecular pathways. Mouse genetics has been utilized as a powerful tool to study human atherosclerosis and has identified hundreds of candidate genes; recent human genetic studies have also identified hundreds of suggestive genetic loci for atherosclerotic coronary artery disease (CAD). However, commonalities and differences of biological mechanisms in atherosclerosis between humans and mice are poorly examined. In this study, we aim to provide a systematic biological overview comparing mice and humans on pathway level. We first comprehensively reviewed and summarized known mouse genes associated with atherosclerosis based on studies of genetically modified mouse models. This effort revealed 743 mouse atherosclerosis genes from over 9,000 Pubmed publications, retrieved using the terms “atherosclerosis” or “atherogenesis” and “gene” or “qtl” and “mouse” or “mice” and “apoe” or “ldlr”, and followed by manual review and confirmation of the effects on atherosclerosis. Second, we conducted pathway analysis of the mouse atherosclerosis genes using data from Biocarta, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome. We found pathways including cytokine interactions or dependency to the immune system are highly over-represented among the mouse atherosclerosis genes. Many of these pathways (e.g., metabolism of lipids and lipoproteins) converged with those reported for human GWAS loci, but also highlighted several pathways (e.g., GPCR signaling) having a hitherto unknown effect on atherosclerosis in mice. Our results suggest that although there are certain differences in individual candidate genes, mouse models remain a promising approach to identify complex molecular pathways of atherosclerosis, and insights gained from mouse genetics of atherosclerosis could be validated and transferred to CAD in humans. Future network analysis of the mouse and human genes and pathways will provide further elucidation of the shared or distinct gene-gene regulation and interactions between species. This study might provide new starting points for drug development, therapeutic treatment and prevention of atherosclerosis and CAD in humans.

A directed network analysis of the cardiome identifies molecular pathways contributing to the development of HFpEF

2020 ◽  
Vol 144 ◽  
pp. 66-75
Author(s):  
Georg Summer ◽  
Annika R. Kuhn ◽  
Chantal Munts ◽  
Daniela Miranda-Silva ◽  
Adelino F. Leite-Moreira ◽  
...  
Keyword(s):  
Network Analysis ◽  
Directed Network ◽  
Molecular Pathways

scholarly journals Shared Pathways Among Autism Candidate Genes Determined by Co-expression Network Analysis of the Developing Human Brain Transcriptome

2015 ◽  
Vol 57 (4) ◽  
pp. 580-594 ◽  
Author(s):  
Ahmed Mahfouz ◽  
Mark N. Ziats ◽  
Owen M. Rennert ◽  
Boudewijn P.F. Lelieveldt ◽  
Marcel J.T. Reinders
Keyword(s):  
Network Analysis ◽  
Human Brain ◽  
Candidate Genes ◽  
Brain Transcriptome

scholarly journals Network analysis of positional candidate genes of schizophrenia highlights myelin-related pathways

2009 ◽  
Vol 14 (4) ◽  
pp. 353-355 ◽  
Author(s):  
T Rietkerk ◽  
M P M Boks ◽  
I E C Sommer ◽  
S de Jong ◽  
R S Kahn ◽  
...  
Keyword(s):  
Network Analysis ◽  
Candidate Genes ◽  
Positional Candidate

scholarly journals Bayesian GWAS and network analysis revealed new candidate genes for number of teats in pigs

2014 ◽  
Vol 56 (1) ◽  
pp. 123-132 ◽  
Author(s):  
L. L. Verardo ◽  
F. F. Silva ◽  
L. Varona ◽  
M. D. V. Resende ◽  
J. W. M. Bastiaansen ◽  
...  
Keyword(s):  
Network Analysis ◽  
Candidate Genes
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