scholarly journals Transcriptome in Combination Proteome Unveils the Phenylpropane Pathway Involved in Garlic (Allium sativum) Greening

2021 ◽  
Vol 8 ◽  
Author(s):  
Jinxiang Wu ◽  
Zhonglu Niu ◽  
Xiaoming Lu ◽  
Xiaozhen Tang ◽  
Xuguang Qiao ◽  
...  
Keyword(s):  
Metabolic Pathway ◽  
Allium Sativum ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Go Enrichment ◽  
Phenylpropanoid Biosynthesis ◽  
Full Length Transcript ◽  
Go Enrichment Analysis ◽  
Garlic Greening

Garlic (Allium sativum) is an important vegetable crop that is widely used in cooking and medicine. The greening phenomenon of garlic severely decreases the quality of garlic and hinders garlic processing. To study the mechanism of garlic greening, comprehensive full-length transcript sets were constructed. We detected the differences in greening between Pizhou (PZ) garlic and Laiwu (LW) garlic that were both stored at −2.5°C and protected from light at the same time. The results showed that 60,087 unigenes were respectively annotated to the NR, KEGG, GO, Pfam, eggNOG and Swiss Prot databases, and a total of 30,082 unigenes were annotated. The analysis of differential genes and differential proteins showed that PZ garlic and LW garlic had 923 differentially expressed genes (DEGs), of which 529 genes were up regulated and 394 genes were downregulated. Through KEGG and GO enrichment analysis, it was found that the most significant way of enriching DEGs was the phenylpropane metabolic pathway. Proteomics analysis found that there were 188 differentially expressed proteins (DAPs), 162 up-regulated proteins, and 26 down-regulated proteins between PZ garlic and LW garlic. The content of 10 proteins related to phenylpropanoid biosynthesis in PZ garlic was significantly higher than that of LW garlic. This study explored the mechanisms of garlic greening at a molecular level and further discovered that the formation of garlic green pigment was affected significantly by the phenylpropanoid metabolic pathway. This work provided a theoretical basis for the maintenance of garlic quality during garlic processing and the future development of the garlic processing industries.

scholarly journals Selenium Treatment Enhanced Clearance of Salmonella in Chicken Macrophages (HD11)

Antioxidants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 532 ◽  
Author(s):  
Zhexi Liu ◽  
Jianwei Huang ◽  
Yijuan Nie ◽  
Izhar Qazi ◽  
Yutao Cao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Glutathione Metabolism ◽  
Rna Seq ◽  
Apoptotic Signaling ◽  
Go Enrichment ◽  
Selenium Treatment ◽  
Underlying Mechanisms ◽  
Go Enrichment Analysis

As an important micronutrient, selenium (Se) plays many essential roles in immune response and protection against pathogens in humans and animals, but underlying mechanisms of Se-based control of salmonella growth within macrophages remain poorly elucidated. In this study, using RNA-seq analyses, we demonstrate that Se treatment (at an appropriate concentration) can modulate the global transcriptome of chicken macrophages HD11. The bioinformatic analyses (KEGG pathway analysis) revealed that the differentially expressed genes (DEGs) were mainly enriched in retinol and glutathione metabolism, revealing that Se may be associated with retinol and glutathione metabolism. Meanwhile, Se treatment increased the number of salmonella invading the HD11 cells, but reduced the number of salmonella within HD11 cells, suggesting that enhanced clearance of salmonella within HD11 cells was potentially modulated by Se treatment. Furthermore, RNA-seq analyses also revealed that nine genes including SIVA1, FAS, and HMOX1 were differentially expressed in HD11 cells infected with salmonella following Se treatment, and GO enrichment analysis showed that these DEGs were mainly enriched in an extrinsic apoptotic signaling pathway. In summary, these results indicate that Se treatment may not only affect retinol and glutathione metabolism in macrophages, but could also inhibit salmonella-induced macrophage apoptosis via an extrinsic apoptotic signaling pathway involving SIVA1.

scholarly journals Identification of Novel lncRNA and Differentially Expressed Genes (DEGs) of Testicular Tissues among Cattle, Yak, and Cattle-Yak Associated with Male Infertility

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2420
Author(s):  
Shaokang Zhao ◽  
Tingting Chen ◽  
Xinmao Luo ◽  
Shiyi Chen ◽  
Jie Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Male Gamete ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Hippo Signaling ◽  
Generation Process ◽  
Reproductive Process ◽  
Go Enrichment ◽  
Cellular Apoptosis ◽  
Go Enrichment Analysis

Cattle-yak is an excellent hybrid of cattle and yak; they are characterized by better meat quality and stronger adaptability of harsh environments than their parents. However, male sterility of cattle-yak lay restraints on the transmission of heterosis. In this study, next generation sequence technology was performed to profile the testicular tissues transcriptome (lncRNA and mRNA) of cattle, yak, and cattle-yak. We analyzed the features and functions of significant differentially expressed genes among the three breeds. There are 9 DE lncRNAs and 46 DE mRNAs with comparisons of cattle, yak, and cattle-yak. Among them, the upregulated targeting genes, such as IGF1 and VGLL3 of cattle-yak lncRNA, may be related to the derangement of spermatocyte maturation and cell proliferation. Similarly, we found that the LDOC1 gene, which is related to the process of cellular apoptosis, is overexpressed in cattle-yak. GO enrichment analysis demonstrated that the cattle-yak is lacking the regulation of fertilization (GO: 0009566), spermatogenesis process (GO: 0007283), male gamete generation process (GO: 0048232), sexual reproduction (GO: 0019953), and multi-organism reproductive process (GO: 0044703), such processes may play important and positive roles in spermatogenesis and fertilization. Furthermore, the KEGG enrichment analysis showed that the upregulated DEGs of cattle-yak most enriched in Apoptosis (ko04210) and Hippo signaling pathway (ko04390), may lead to excessively dead of cell and inhibit cell growth, resulting in obstruction of meiosis and spermatogenesis processes. This study will enable us to deeper understand the mechanism of male cattle-yak infertility.

scholarly journals Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10794
Author(s):  
Ceyhun Bereketoglu ◽  
Gozde Nacar ◽  
Tugba Sari ◽  
Bulent Mertoglu ◽  
Ajay Pradhan
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Adaptive Response ◽  
Cell Cycle Progression ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Yeast Cells ◽  
Genome Wide ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level.

scholarly journals The effects of the Xijiao Dihuang decoction combined with Yinqiao powder on miRNA-mRNA profiles in mice infected with influenza a virus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ke Li ◽  
Xiaoming Chen ◽  
Jing Zhong ◽  
Hehe Ye ◽  
Shujing Zhang ◽  
...  
Keyword(s):  
Influenza A ◽  
High Throughput Sequencing ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Kegg Database ◽  
Qrt Pcr ◽  
Go Enrichment ◽  
Differentially Expressed Mirnas ◽  
Therapeutic Mechanisms ◽  
Go Enrichment Analysis

Abstract Background MicroRNAs (miRNAs) play vital roles in acute inflammatory and antiviral responses during influenza A virus (IAV) infection. The Xijiao Dihuang decoction combined with Yinqiao powder (XDY) is applied to remedy viral pneumonia in China and its therapeutic efficacy in pneumonic mice challenged with IAV was demonstrated; however, the underlying mechanisms remain elusive. Thus, this study aimed to explore the miRNA-mRNA profiles in the lungs of IAV-infected mice and investigate the therapeutic mechanisms of XDY involving miRNAs and associated pathways. Methods We detected the cellular miRNA contents in the lungs of mice treated with XDY (23 g/kg/d) for A/FM/1/47 (H1N1) (FM1) infection at 4 days postinoculation (dpi) and 7 dpi. MiRNA and mRNA high-throughput sequencing analyses, and miRNA and mRNA qRT-PCR analyses were used to detect and verify the relevant miRNAs and mRNAs. Conjoint analysis, GO enrichment analysis, and KEGG database analysis were applied to identify the miRNA-mRNA regulatory relationships. Results The quantities of differentially expressed miRNAs and mRNAs were upregulated over time. The data showed that 104 miRNAs and 3485 mRNAs were differentially expressed after challenge with FM1 on day 4, while 191 miRNAs and 6126 mRNAs were differentially expressed on day 7. The GO enrichment analysis and KEGG database data showed that the differentially expressed miRNAs and mRNAs were mainly enriched in JNK activity, MAPK phosphatase activity, and the TLR, Jak-STAT and TNF signalling pathways after treatment of FM1 infection with XDY. Generally, the expression trends of differentially expressed miRNAs and mRNAs based on the qRT-PCR results exhibited good consistency with the results of the high-throughput sequencing analysis. Conclusions MiRNAs and mRNAs were differentially expressed during FM1 infection. The therapeutic mechanisms of XDY in FM1-infected mice, might be related to regulating antiviral immunity and ameliorating excessive inflammatory responses by modulating the expression of dysregulated miRNAs and mRNAs involved in the ERK/JNK-AP-1, and IFN-β/STAT signalling pathways.

scholarly journals Comprehensive biological information analysis of PTEN gene in pan-cancer

2021 ◽  
Author(s):  
Hang Zhang ◽  
Wenhan Zhou ◽  
Xiaoyi Yang ◽  
Shuzhan Wen ◽  
Baicheng Zhao ◽  
...  
Keyword(s):  
3D Structure ◽  
Enrichment Analysis ◽  
Biological Information ◽  
Pten Gene ◽  
Clinical Prognosis ◽  
Regulatory Pathways ◽  
Go Enrichment ◽  
Go Enrichment Analysis ◽  
Pan Cancer ◽  
Low Expression

Abstract Background PTEN is a multifunctional tumor suppressor gene mutating at high frequency in a variety of cancers. However, its expression in pan-cancer, correlated genes, survival prognosis, and regulatory pathways are not completely described. Here, we aimed to conduct a comprehensive analysis from the above perspectives in order to provide reference for clinical application. Methods we studied the expression levels in cancers by using data from TCGA and GTEx database. Obtain expression box plot from UALCAN database. Perform mutation analysis on the cBioportal website. Obtain correlation genes on the GEPIA website. Construct protein network and perform KEGG and GO enrichment analysis on the STRING database. Perform prognostic analysis on the Kaplan-Meier Plotter website. We also performed transcription factor prediction on the PROMO database and performed RNA-RNA association and RNA-protein interaction on the RNAup Web server and RPISEq. The gene 3D structure, protein sequence and conserved domain were obtained in NCBI respectively. Results PTEN was underexpressed in all cancers we studied. It was closely related to the clinical stage of tumors, suggesting PTEN may involved in cancer development and progression. The mutations of PTEN were present in a variety of cancers, most of which were truncation mutations and missense mutations. Among cancers (KIRC, LUAD, THYM, UCEC, Gastric Cancer, Liver Cancer, Lung Cancer, Breast Cancer), patients with low expression of PTEN had a shorter OS time and poorer OS prognosis. The low expression of PTEN can cause the deterioration of RFS in certain cancers (TGCT, UCEC, LIHC, LUAD, THCA), suggesting that the expression of PTEN was related to the clinical prognosis. Our study identified genes correlated with PTEN and performed GO enrichment analysis on 100 PTEN-related genes obtained from the GEPIA website. Conclusions The understanding of PTEN gene and the in-depth exploration of its related regulatory pathways may provide insight for the discovery of tumor-specific biomarkers and clinical potential therapeutic targets.

Transcriptome Signatures Reveal Candidate Key Genes in the Peripheral Blood Mononuclear Cells of Patients With Coronary Artery Disease

2020 ◽  
Author(s):  
Vijayakrishna Kolur ◽  
Basavaraj Vastrad ◽  
Chanabasayya Vastrad ◽  
Iranna Kotturshetti ◽  
Anandkumar Tengli
Keyword(s):  
Coronary Artery Disease ◽  
Gene Ontology ◽  
Coronary Artery ◽  
Regulatory Network ◽  
Target Gene ◽  
Enrichment Analysis ◽  
Hub Genes ◽  
Go Enrichment ◽  
Artery Disease ◽  
Go Enrichment Analysis

Abstract BackgroundCoronary artery disease (CAD) is one of the most common disorders in the cardiovascular system. This study aims to explore potential signaling pathways and important biomarkers that drive CAD development. MethodsThe CAD GEO Dataset GSE113079 was featured to screen differentially expressed genes (DEGs). The pathway and Gene Ontology (GO) enrichment analysis of DEGs were analyzed using the ToppGene. We screened hub and target genes from protein-protein interaction (PPI) networks, target gene - miRNA regulatory network and target gene - TF regulatory network, and Cytoscape software. Validations of hub genes were performed to evaluate their potential prognostic and diagnostic value for CAD. Results1,036 DEGs were captured according to screening criteria (525upregulated genes and 511downregulated genes). Pathway and Gene Ontology (GO) enrichment analysis of DEGs revealed that these up and down regulated genes are mainly enriched in thyronamine and iodothyronamine metabolism, cytokine-cytokine receptor interaction, nervous system process, cell cycle and nuclear membrane. Hub genes were validated to find out potential prognostic biomarkers, diagnostic biomarkers and novel therapeutic target for CAD. ConclusionsIn summary, our findings discovered pivotal gene expression signatures and signaling pathways in the progression of CAD. CAPN13, ACTBL2, ERBB3, GATA4, GNB4, NOTCH2, EXOSC10, RNF2, PSMA1 and PRKAA1 might contribute to the progression of CAD, which could have potential as biomarkers or therapeutic targets for CAD.

scholarly journals Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Weiwen Kong ◽  
Li Ding ◽  
Xue Xia
Keyword(s):  
Disease Resistance ◽  
Magnaporthe Oryzae ◽  
Enrichment Analysis ◽  
Defense Responses ◽  
Resistance Mechanisms ◽  
Xanthomonas Oryzae ◽  
Transcriptional Reprogramming ◽  
Go Enrichment ◽  
Phenylpropanoid Biosynthesis ◽  
Rice Disease

Abstract Background Disease resistance is an important factor that impacts rice production. However, the mechanisms underlying rice disease resistance remain to be elucidated. Results Here, we show that a robust set of genes has been defined in rice response to the infections of Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (Mor). We conducted a comprehensive analysis of the available microarray data from a variety of rice samples with inoculation of Xoo and Mor. A set of 12,932 genes was identified to be regulated by Xoo and another set of 2709 Mor-regulated genes was determined. GO enrichment analysis of the regulated genes by Xoo or Mor suggested mitochondrion may be an arena for the up-regulated genes and chloroplast be another for the down-regulated genes by Xoo or Mor. Cytokinin-related processes were most frequently repressed by Xoo, while processes relevant to jasmonic acid and abscisic acid were most frequently activated by Xoo and Mor. Among genes responsive to Xoo and Mor, defense responses and diverse signaling pathways were the most frequently enriched resistance mechanisms. InterPro annotation showed the zinc finger domain family, WRKY proteins, and Myb domain proteins were the most significant transcription factors regulated by Xoo and Mor. KEGG analysis demonstrated pathways including ‘phenylpropanoid biosynthesis’, ‘biosynthesis of antibiotics’, ‘phenylalanine metabolism’, and ‘biosynthesis of secondary metabolites’ were most frequently triggered by Xoo and Mor, whereas ‘circadian rhythm-plant’ was the most frequent pathway repressed by Xoo and Mor. Conclusions The genes identified here represent a robust set of genes responsive to the infections of Xoo and Mor, which provides an overview of transcriptional reprogramming during rice defense against Xoo and Mor infections. Our study would be helpful in understanding the mechanisms of rice disease resistance.

scholarly journals Mining Featured Biomarkers Linked with Epithelial Ovarian Cancer Based on Bioinformatics

Diagnostics ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 39
Author(s):  
◽  
Chanabasayya Vastrad ◽  
◽  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Target Gene ◽  
Enrichment Analysis ◽  
Microrna Target ◽  
Pathway Enrichment ◽  
Protein Protein Interaction ◽  
Go Enrichment ◽  
Gene Regulatory ◽  
Go Enrichment Analysis

: Epithelial ovarian cancer (EOC) is the18th most common cancer worldwide and the 8th most common in women. The aim of this study was to diagnose the potential importance of, as well as novel genes linked with, EOC and to provide valid biological information for further research. The gene expression profiles of E-MTAB-3706 which contained four high-grade ovarian epithelial cancer samples, four normal fallopian tube samples and four normal ovarian epithelium samples were downloaded from the ArrayExpress database. Pathway enrichment and Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) were performed, and protein-protein interaction (PPI) network, microRNA-target gene regulatory network and TFs (transcription factors ) -target gene regulatory network for up- and down-regulated were analyzed using Cytoscape. In total, 552 DEGs were found, including 276 up-regulated and 276 down-regulated DEGs. Pathway enrichment analysis demonstrated that most DEGs were significantly enriched in chemical carcinogenesis, urea cycle, cell adhesion molecules and creatine biosynthesis. GO enrichment analysis showed that most DEGs were significantly enriched in translation, nucleosome, extracellular matrix organization and extracellular matrix. From protein-protein interaction network (PPI) analysis, modules, microRNA-target gene regulatory network and TFs-target gene regulatory network for up- and down-regulated, and the top hub genes such as E2F4, SRPK2, A2M, CDH1, MAP1LC3A, UCHL1, HLA-C (major histocompatibility complex, class I, C) , VAT1, ECM1 and SNRPN (small nuclear ribonucleoprotein polypeptide N) were associated in pathogenesis of EOC. The high expression levels of the hub genes such as CEBPD (CCAAT enhancer binding protein delta) and MID2 in stages 3 and 4 were validated in the TCGA (The Cancer Genome Atlas) database. CEBPD andMID2 were associated with the worst overall survival rates in EOC. In conclusion, the current study diagnosed DEGs between normal and EOC samples, which could improve our understanding of the molecular mechanisms in the progression of EOC. These new key biomarkers might be used as therapeutic targets for EOC.

scholarly journals A Network Pharmacology Approach to Explore the Pharmacological Mechanism of Xiaoyao Powder on Anovulatory Infertility

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Huiping Liu ◽  
Liuting Zeng ◽  
Kailin Yang ◽  
Guomin Zhang
Keyword(s):  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Active Compounds ◽  
Pharmacological Mechanism ◽  
Go Enrichment ◽  
Human Proteins ◽  
Network Pictures ◽  
Go Enrichment Analysis ◽  
Anovulatory Infertility

Aim.To explore the pharmacological mechanism of Xiaoyao powder (XYP) on anovulatory infertility by a network pharmacology approach.Method.Collect XYP’s active compounds by traditional Chinese medicine (TCM) databases, and input them into PharmMapper to get their targets. Then note these targets by Kyoto Encyclopedia of Genes and Genomes (KEGG) and filter out targets that can be noted by human signal pathway. Get the information of modern pharmacology of active compounds and recipe’s traditional effects through databases. Acquire infertility targets by Therapeutic Target Database (TTD). Collect the interactions of all the targets and other human proteins via String and INACT. Put all the targets into the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to do GO enrichment analysis. Finally, draw the network by Cytoscape by the information above.Result.Six network pictures and two GO enrichment analysis pictures are visualized.Conclusion.According to this network pharmacology approach some signal pathways of XYP acting on infertility are found for the first time. Some biological processes can also be identified as XYP’s effects on anovulatory infertility. We believe that evaluating the efficacy of TCM recipes and uncovering the pharmacological mechanism on a systematic level will be a significant method for future studies.

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