Bioinformatics analysis of gene expression profile data to screen key genes involved in pulmonary sarcoidosis

Li, Hongyan; Zhao, Xiaonan; Wang, Jing; Zong, Minru; Yang, Hailing

doi:10.1016/j.gene.2016.09.037

Cited by 45 publications

(26 citation statements)

References 35 publications

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“…The middle nodes indicate the protein which own essential biological function and are highly connected, were identified by estimating the betweenness value and the number of line connections between proteins of each node. The network was constructed using STRING and was visualized by Cytoscape software (http://www.cytoscape.org/) (Li, Zhao, Wang, Zong, & Yang, 2017). …”

Section: Methodsmentioning

confidence: 99%

Maximum‐likelihood approaches reveal signatures of positive selection in BMP15 and GDF9 genes modulating ovarian function in mammalian female fertility

Ahmad

Liu

Jiang

et al. 2017

Ecology and Evolution

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Bone morphogenetic proteins (BMPs) and the growth factors (GDFs) play an important role in ovarian folliculogenesis and essential regulator of processes of numerous granulosa cells. BMP15 gene variations linked to various ovarian phenotypic consequences subject to the species, from infertility to improved prolificacy in sheep, primary ovarian insufficiency in women or associated with minor subfertility in mouse. To study the evolving role of BMP15 and GDF9, a phylogenetic analysis was performed. To find out the candidate gene associated with prolificacy in mammals, the nucleotide sequence of BMP15 and GDF9 genes was recognized under positive selection in various mammalian species. Maximum‐likelihood approaches used on BMP15 and GDF9 genes exhibited a robust divergence and a prompted evolution as compared to other TGFβ family members. Furthermore, among 32 mammalian species, we identified positive selection signals in the hominidae clade resulting to 132D, 147E, 163Y, 191W, and 236P codon sites of BMP15 and 162F, 188K, 206R, 240A, 244L, 246H, 248S, 251D, 253L, 254F and other codon sites of GDF9. The positively selected amino acid sites such as Alanine, Lucien, Arginine, and lysine are important for signaling. In conclusion, this study evidences that GDF9 and BMP15 genes have rapid evolution than other TGFß family members and was subjected to positive selection in the mammalian clade. Selected sites under the positive selection are of remarkable significance for the particular functioning of the protein and consequently for female fertility.

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Section: Methodsmentioning

confidence: 99%

Maximum‐likelihood approaches reveal signatures of positive selection in BMP15 and GDF9 genes modulating ovarian function in mammalian female fertility

Ahmad

Liu

Jiang

et al. 2017

Ecology and Evolution

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“…A protein-protein interaction (PPI) network was created using Cytoscape v3.7.2 to further understand and predict the biological activity of the identified DEGs related to inflammation and immunity based on GO and KEGG enrichment analysis [30]. The DEGs' encoding proteins and their interacting partners were computed from the String v11.0 database for PPI network construction [31]. This PPI network was subsequently visualized in Cytoscape.…”

Section: Ppi Network Construction and Analysismentioning

confidence: 99%

Mammary Transcriptome Profile during Peak and Late Lactation Reveals Differentially Expression Genes Related to Inflammation and Immunity in Chinese Holstein

Han

Fan

Yang

et al. 2020

Animals

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Simple Summary: Milk somatic cell count, referring to the total number of somatic cells per milliliter of bovine milk, changes regularly during the lactation cycle. The somatic cell count of healthy cows is usually higher in late lactation than in peak lactation. When the inflammatory response in dairy cow mammary gland becomes more intense, the milk somatic cell count increases together with the reduction of milk quality and yield. Autoimmunity was thought to play an important role in the prevention of mastitis in late lactation of dairy cattle. However, the underlying mechanisms related to the gene expression levels during the process remain unknown. In this study, transcriptome sequencing was performed to screen the differentially expressed genes related to the inflammation and immunity in healthy Chinese Holstein mammary glands. Our findings are helpful to understand the physiological functions of mammary inflammation of Chinese Holstein during late lactation.Abstract: Somatic cell count (SCC) in milk is widely used in the dairy industry, as an indicator of the health of mammary gland. While the SCC of dairy cattle was higher in late lactation than in peak lactation, its association with gene expressions of mammary gland were largely unknown. In this study, a transcriptomic sequencing approach and bioinformatics analysis were used to investigate the differential expressed genes (DEGs) associated with inflammation and immunity between peak and late periods of lactation in Chinese Holstein. A total of 446 DEGs (padj < 0.05 and fold change >2) were identified, 50 of which belonged to seven pathways and five terms related to inflammation and immunity. Our data suggested that the activation of nuclear transcription factor-κB (NF-κB) pathway and Toll-like receptor signaling pathway caused inflammatory response, and the activation of chemokine signaling pathway and cytokine-cytokine receptor interaction signaling pathway caused a protective immune response to ensure dairy cows health during late lactation. Our findings deepen the understanding of the molecular mechanism and physiological functions of mammary inflammation in Chinese Holstein during late lactation.

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“…e CC is the inverse of the sum of the distance from a node to other nodes. e magnitude of the important parameters is positive proportional to the importance of node in the network [23]. Firstly, we selected "DC > 2 × median" as the primary screening criteria.…”

Section: Potential Targets Of Active Componentsmentioning

confidence: 99%

Uncovering Synergistic Mechanism of Chinese Herbal Medicine in the Treatment of Atrial Fibrillation with Obstructive Sleep Apnea Hypopnea Syndrome by Network Pharmacology

Mao

Zhang

Qiao

et al. 2019

Evidence-Based Complementary and Alternative Medicine

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Paroxysmal atrial fibrillation (AF) combined with obstructive sleep apnea hypopnea syndrome (OSAHS) is very common in clinical practice. Traditional Chinese medicine (TCM) rule of regulating the liver based on psycho-cardiology shows satisfactory effectiveness in the treatment of paroxysmal AF combined with OSAHS. However, its underlying pharmacological mechanism has not yet been elucidated. This study applied network pharmacology to identify 94 active components in the six TCM liver-regulating herbs and 182 corresponding targets from several databases and comprehensive literature studies, as well as retrieved AF combined with OSAHS-related targets. Cytoscape software was adopted to construct the component-component target network and component-putative target-AF combined with OSAHS target network. Then, we obtained 38 putative therapeutic targets against AF combined with OSAHS. After the production of a putative therapeutic target interaction network, topological analysis was adopted to determine the core targets of TCM liver-regulating herbs in the treatment of paroxysmal AF combined with OSAHS. For all putative therapeutic targets, biological process analysis and pathway enrichment analysis were utilized to investigate the possible mechanism of TCM liver-regulating herbs in the treatment of paroxysmal AF combined with OSAHS. Mechanistically, it included positive regulation of nitric oxide biosynthetic process, aging, response to hypoxia, TNF signaling pathway, HIF-1 signaling pathway, PI3K-Akt signaling pathway, neuroactive ligand-receptor interaction, and calcium signaling pathway. Especially, six core targets of TCM liver-regulating herbs, namely, TNF, STAT3, AKT1, IL-6, TP53, and INS, were significant in the regulation of the above biological processes and pathways. This study demonstrates the multicomponent, multitarget, and multipathway feature of TCM liver-regulating herbs, provides an extensional foundation for further research, and facilitates the reasonable application of TCM liver-regulating herbs in treating paroxysmal AF combined with OSAHS.

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Bioinformatics analysis of gene expression profile data to screen key genes involved in pulmonary sarcoidosis

Cited by 45 publications

References 35 publications

Maximum‐likelihood approaches reveal signatures of positive selection in BMP15 and GDF9 genes modulating ovarian function in mammalian female fertility

Maximum‐likelihood approaches reveal signatures of positive selection in BMP15 and GDF9 genes modulating ovarian function in mammalian female fertility

Mammary Transcriptome Profile during Peak and Late Lactation Reveals Differentially Expression Genes Related to Inflammation and Immunity in Chinese Holstein

Uncovering Synergistic Mechanism of Chinese Herbal Medicine in the Treatment of Atrial Fibrillation with Obstructive Sleep Apnea Hypopnea Syndrome by Network Pharmacology

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