scholarly journals Transcriptome Sequencing Reveals Sex Differences in Human Meniscal Cell Response to Estrogen Based on Dosing Kinetics

2020 ◽  
Author(s):  
Kelsey E Knewtson ◽  
Jesus G Gonzalez Flores ◽  
Donna M Pacicca ◽  
Jennifer L Robinson
Keyword(s):  
Differentially Expressed Genes ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Initial Study ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Estrogen Signaling ◽  
Joint Health ◽  
Estrogen Dose ◽  
Meniscal Cells

Osteoarthritis is a disease marked by progressive and irreversible hyaline cartilage and fibrocartilage breakdown that affects the lives of millions of patients worldwide. Female sex and menopause are both risk factors for knee osteoarthritis, indicating that estrogen could play a role in this disease. In this study, RNA sequencing was used to determine the effects of estrogen treatment on human meniscal cells. Differences in the number and type of differentially expressed genes were seen based on donor sex, estrogen dose, and dosing kinetics. Significantly more differentially expressed genes were seen from male meniscal cells in response to all dosing conditions compared to female cells. Importantly, more genes were differentially expressed in cells treated with continuous dosing of estrogen, which has been shown to stimulate genomic estrogen signaling, as compared to pulsed dosing. Additionally, functional enrichment analysis revealed that many genes of the extracellular matrix, which is important for joint health and injury repair, were differentially expressed. Overall, this initial study lays the groundwork for future avenues to pursue the effect of estrogen delivery on regenerative pathways. This critical analysis will then inform the design and implementation of estrogen replacement therapies to promote meniscal health and reduce the onset of osteoarthritis.

scholarly journals Identification of nine key genes by bioinformatics analysis for predicting poor prognosis in smoking-induced lung adenocarcinoma

2020 ◽  
Vol 9 (2) ◽  
pp. LMT30
Author(s):  
Chuanli Ren ◽  
Weixiu Sun ◽  
Xu Lian ◽  
Chongxu Han
Keyword(s):  
Lung Adenocarcinoma ◽  
Differentially Expressed Genes ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Kaplan Meier ◽  
Key Genes ◽  
Core Genes

Aim: To screen and identify key genes related to the development of smoking-induced lung adenocarcinoma (LUAD). Materials & methods: We obtained data from the GEO chip dataset GSE31210. The differentially expressed genes were screened by GEO2R. The protein interaction network of differentially expressed genes was constructed by STRING and Cytoscape. Finally, core genes were screened. The overall survival time of patients with the core genes was analyzed by Kaplan–Meier method. Gene ontology and Kyoto encyclopedia of genes and genomes bioaccumulation was calculated by DAVID. Results: Functional enrichment analysis indicated that nine key genes were actively involved in the biological process of smoking-related LUAD. Conclusion: 23 core genes and nine key genes among them were correlated with adverse prognosis of LUAD induced by smoking.

scholarly journals Comparative transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine–cytokine receptor interaction pathway related to health status

Genome ◽  
2017 ◽  
Vol 60 (12) ◽  
pp. 1021-1028 ◽  
Author(s):  
M.H. Ye ◽  
H. Bao ◽  
Y. Meng ◽  
L.L. Guan ◽  
P. Stothard ◽  
...  
Keyword(s):  
Health Status ◽  
Differentially Expressed Genes ◽  
Peripheral Blood ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Cytokine Receptor ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Marker Genes

While some research has looked into the host genetic response in pigs challenged with specific viruses or bacteria, few studies have explored the expression changes of transcripts in the peripheral blood of sick pigs that may be infected with multiple pathogens on farms. In this study, the architecture of the peripheral blood transcriptome of 64 Duroc sired commercial pigs, including 18 healthy animals at entry to a growing facility (set as a control) and 23 pairs of samples from healthy and sick pen mates, was generated using RNA-Seq technology. In total, 246 differentially expressed genes were identified to be specific to the sick animals. Functional enrichment analysis for those genes revealed that the over-represented gene ontology terms for the biological processes category were exclusively immune activity related. The cytokine–cytokine receptor interaction pathway was significantly enriched. Nine functional genes from this pathway encoding members (as well as their receptors) of the interleukins, chemokines, tumor necrosis factors, colony stimulating factors, activins, and interferons exhibited significant transcriptional alteration in sick animals. Our results suggest a subset of novel marker genes that may be useful candidate genes in the evaluation and prediction of health status in pigs under commercial production conditions.

scholarly journals Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Siying He ◽  
Hui Sun ◽  
Yifang Huang ◽  
Shiqi Dong ◽  
Chen Qiao ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Interaction Analysis ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas

Purpose. MiRNAs have been widely analyzed in the occurrence and development of many diseases, including pterygium. This study aimed to identify the key genes and miRNAs in pterygium and to explore the underlying molecular mechanisms. Methods. MiRNA expression was initially extracted and pooled by published literature. Microarray data about differentially expressed genes was downloaded from Gene Expression Omnibus (GEO) database and analyzed with the R programming language. Functional and pathway enrichment analyses were performed using the database for Annotation, Visualization and Integrated Discovery (DAVID). The protein-protein interaction network was constructed with the STRING database. The associations between chemicals, differentially expressed miRNAs, and differentially expressed genes were predicted using the online resource. All the networks were constructed using Cytoscape. Results. We found that 35 miRNAs and 301 genes were significantly differentially expressed. Functional enrichment analysis showed that upregulated genes were significantly enriched in extracellular matrix (ECM) organization, while downregulated genes were mainly involved in cell death and apoptotic process. Finally, we concluded the chemical-gene affected network, miRNA-mRNA interacted networks, and significant pathway network. Conclusion. We identified lists of differentially expressed miRNAs and genes and their possible interaction in pterygium. The networks indicated that ECM breakdown and EMT might be two major pathophysiological mechanisms and showed the potential significance of PI3K-Akt signalling pathway. MiR-29b-3p and collagen family (COL4A1 and COL3A1) might be new treatment target in pterygium.

scholarly journals Expression analyses of cave mollies ( Poecilia mexicana ) reveal key genes involved in the early evolution of eye regression

2019 ◽  
Vol 15 (10) ◽  
pp. 20190554 ◽  
Author(s):  
Kerry L. McGowan ◽  
Courtney N. Passow ◽  
Lenin Arias-Rodriguez ◽  
Michael Tobler ◽  
Joanna L. Kelley
Keyword(s):  
Differentially Expressed Genes ◽  
Habitat Type ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Light Sensitivity ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Poecilia Mexicana ◽  
Poeciliid Fish ◽  
In The Beginning

Eye regression occurs across cave-dwelling populations of many species and is often coupled with a decrease or loss in eye function. Teleost fishes are among the few vertebrates to undergo widespread colonization of caves and often exhibit eye regression with blindness. Cave populations of the poeciliid fish Poecilia mexicana (cave molly) exhibit reduced—albeit functional—eyes, offering the opportunity to investigate partial eye regression. We sequenced eye transcriptomes of cave and surface populations of P. mexicana to identify differentially expressed genes that potentially underlie eye regression in cave mollies. We identified 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signaling. Twenty-six of these genes were downregulated in cave compared to surface populations. Functional enrichment analysis revealed eye-related gene ontologies that were under-represented in cave mollies. In addition, a set of co-expressed genes related to vision and circadian rhythm was correlated with habitat type (cave versus surface). Our study suggests that differential gene expression plays a key role in the beginning evolutionary stages of eye regression in P. mexicana , shedding further light on regressive evolution in cavefish.

scholarly journals Transcriptome Sequencing Analysis Provides Insights Into the Response to Fusarium oxysporum in Lilium pumilum

2019 ◽  
Vol 15 ◽  
pp. 117693431983881
Author(s):  
Xiangfeng He ◽  
Wanyue Li ◽  
Wenzhu Zhang ◽  
Xiaotong Jin ◽  
Awraris Getachew Shenkute ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Differentially Expressed Genes ◽  
De Novo ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Basal Rot ◽  
Phenylpropanoid Biosynthesis

Lily basal rot, caused by Fusarium oxysporum f. sp. lilii, is one of the most serious diseases of lily. Although the lily germplasm which is resistant to F. oxysporum has been used in disease-resistant breeding, few studies on its molecular mechanism of disease resistance have been reported. To comprehensively study the mechanism of resistance to F. oxysporum, transcriptome sequencings of root tissues from Lilium pumilum inoculated with F. oxysporum or sterile water for 6, 12, or 24 h were performed. A total of 50 GB of data were obtained from the transcriptome sequencings of the 6 L. pumilum samples, and 217 098 Unigenes were obtained after the de novo assembly, of which 38.36% Unigenes were annotated. The sequencing results showed that the numbers of differentially expressed genes at 6, 12, and 24 h after inoculation compared with the control were 111, 254, and 2500, respectively. The functional enrichment analysis of the differentially expressed genes showed that several pathways were involved in responses of L. pumilum, mainly including starch and sucrose metabolism, glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, vitamin B6 (VB6) biosynthesis, acid biosynthesis, proteasome, and ribosome. Transcription factor analysis revealed that the WRKY and ERF families played important roles in responses of L. pumilum to F. oxysporum. The results of this study elucidate the molecular responses to F. oxysporum in lily and lay a theoretical foundation for improving lily breeding and strategies for lily basal rot resistance.

scholarly journals Based on bioinformatics analysis, NF1, BTRC and MAPK14 are the potential biomarkers in the progression of osteoarthritis synovitis

2021 ◽  
Author(s):  
Mingyi Yang ◽  
Yani Su ◽  
Yao Ma ◽  
Yirixiati Aihaiti ◽  
Peng Xu
Keyword(s):  
Differentially Expressed Genes ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Hub Genes ◽  
Hub Gene ◽  
Potential Biomarkers

Abstract Objective: To study the potential biomarkers and related pathways in osteoarthritis (OA) synovial lesions, and to provide theoretical basis and research directions for the pathogenesis and treatment of OA. Methods: Download the microarray data sets GSE12021 and GSE82107 from Gene Expression Omnibus. GEO2R recognizes differentially expressed genes. Perform functional enrichment analysis of differentially expressed genes and construct protein-protein interaction network. Cytoscape performs module analysis and enrichment analysis of top-level modules. Further identify the Hub gene and perform functional enrichment analysis. TargetScan, miRDB and miRWalk three databases predict the target miRNAs of Hub gene and identify key miRNAs. Results: Finally, 10 Hub genes and 17 key miRNAs related to the progression of OA synovitis were identified. NF1, BTRC and MAPK14 may play a vital role in OA synovial disease. Conclusion: The Hub genes and key miRNAs discovered in this study may be potential biomarkers in the development of OA synovitis, and provide research methods and target basis for the pathogenesis and treatment of OA.

scholarly journals Fine mapping of goat polledness variant in six Chinese native breeds

2021 ◽  
Author(s):  
Yong Li ◽  
tao chen ◽  
Manman Yang ◽  
hu han ◽  
Dan Jiang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Genome Wide Association Study ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Specific Element ◽  
A Genome

Background: The genetic mechanism of goat polledness has been studied for decades, but identifying causative variants and functional genes remains challenging. Results: Using a genome-wide association study (GWAS), we identified a significant striking locus for polledness in two different goat breeds. To reduce the linkage disequilibrium among variants for localizing causative variants in the finer region, we sequenced 79 goats from six Chinese native breeds (Jining Gray, Matou, Guizhou black, Yunnan black bone, Chaidamu, and Ujumqin) and identified 483.5 kb CNV (150,334,567-150,818,099) translocated into the previously identified 11.7 kb polled intersex syndrome region, which was consistent with previous research using intersex goat populations. Within the 483.5 kb CNV, a ~322 bp horn-specific element, similar to the superfamily of tRNA-derived families of SINEs, located at the first intron of the ERG gene was identified. The results of the GO enrichment analysis showed that the Horn-SINE element-associated genes were involved in both nervous system and head development. Finally, we used RNA sequencing to investigate gene expression profiles in the horn bud and skin tissues of horned and polled goats. We identified 1077 and 1222 differentially expressed genes between the horn bud and skin tissue in polled and horned goats, respectively. We also identified 367 differentially expressed genes in horn buds between polled and horned animals and found that the two CNV-related genes, ERG and FOXL2 were upregulated in the horn bud of polled goats. Gene functional enrichment analysis demonstrated that the downregulated genes in the horn bud of polled goats were enriched in skeletal system development, whereas the upregulated genes were significantly overexpressed in muscle tissue development.

scholarly journals Identification of key gene in colorectal cancer using bioinformatics analysis.

2020 ◽  
Author(s):  
Rongrong Xiao ◽  
Ping Wang ◽  
Tian Xia ◽  
Chun-Yi Li ◽  
Ting Jiang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Colon Cancer ◽  
Tumor Microenvironment ◽  
Differentially Expressed Genes ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Ppi Network ◽  
Hub Genes

Abstract Background Tumor microenvironment plays important roles in the development of cancer. The aim of our study was to examine the expression of genes in colorectal cancer and also to evaluate the association value between expression level of these genes and clinical features. Methods We combined The Cancer Genome Atlas (TCGA) datasets to identify differentially expressed genes in colon cancer. Using these differentially expressed genes, we constructed protein-protein interaction network and conducted functional enrichment analysis. Genes with degree beyond 10 in the PPI network were regarded as hub genes. Then, we verified of the expression of molecules in Oncomine datasets and conducted Kaplan-Meier curve and log-rank test and functional enrichment analysis on these hub genes. Finally, we analyzed the relationship clinicopathological features analysis with the key gene. Results There were 719 differentially expressed genes identified to be associated with colon cancer microenvironment. We screened out 10 hub genes by construction of PPI network. The functions of these hub genes were enriched in cytokine-cytokine receptor interaction, alcoholism and systemic lupus erythematosus, which provided further insight into the roles of these genes in the tumor microenvironment. GNG4, with the highest degrees in the PPI network, were highly exprepressed in metastasis(P = 9.5-05) ,N1(P = 0.0025) and N2(,0.037).It was a relationship with stage. It was significantly different between with stage I and IV, II and III, II and IV,III and IV (P = 0.0015,0.029,3.9-05,0.00074,0.01,respectively) Conclusions We identified GNG4 can be regarded as a prognostic biomarker in colon cancer.

scholarly journals bcbioRNASeq: R package for bcbio RNA-seq analysis

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1976 ◽  
Author(s):  
Michael J. Steinbaugh ◽  
Lorena Pantano ◽  
Rory D. Kirchner ◽  
Victor Barrera ◽  
Brad A. Chapman ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
R Package ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Control Analysis ◽  
Rna Seq ◽  
Sequencing Data ◽  
Post Process

RNA-seq analysis involves multiple steps from processing raw sequencing data to identifying, organizing, annotating, and reporting differentially expressed genes. bcbio is an open source, community-maintained framework providing automated and scalable RNA-seq methods for identifying gene abundance counts. We have developed bcbioRNASeq, a Bioconductor package that provides ready-to-render templates and wrapper functions to post-process bcbio output data. bcbioRNASeq automates the generation of high-level RNA-seq reports, including identification of differentially expressed genes, functional enrichment analysis and quality control analysis.

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