In-Depth Understanding of Camellia oleifera Self-Incompatibility by Comparative Transcriptome, Proteome and Metabolome

Oil-tea tree (Camellia oleifera) is the most important edible oil tree species in China with late-acting self-incompatibility (LSI) properties. The mechanism of LSI is uncertain, which seriously hinders the research on its genetic characteristics, construction of genetic map, selection of cross breeding parents and cultivar arrangement. To gain insights into the LSI mechanism, we performed cytological, transcriptomic, proteomic and metabolomic studies on self- and cross-pollinated pistils. The studies identified 166,591 transcripts, 6851 proteins and 6455 metabolites. Transcriptomic analysis revealed 1197 differentially expressed transcripts between self- and cross-pollinated pistils and 47 programmed cell death (PCD)-control transcripts. Trend analysis by Pearson correlation categorized nine trend graphs linked to 226 differentially expressed proteins and 38 differentially expressed metabolites. Functional enrichment analysis revealed that the LSI was closely associated with PCD-related genes, mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, ATP-binding cassette (ABC) transporters and ubiquitin-mediated proteolysis. These particular trends in transcripts, proteins and metabolites suggested the involvement of PCD in LSI. The results provide a solid genetic foundation for elucidating the regulatory network of PCD-mediated self-incompatibility in C. oleifera.

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Transcriptome analysis reveals defense-related genes and pathways against Xanthomonas campestris pv. vesicatoria in pepper (Capsicum annuum L.)

PLoS ONE ◽

10.1371/journal.pone.0240279 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0240279

Author(s):

Shenghua Gao ◽

Fei Wang ◽

Juntawong Niran ◽

Ning Li ◽

Yanxu Yin ◽

...

Keyword(s):

Transcription Factors ◽

Xanthomonas Campestris ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Defense Responses ◽

Mapk Signaling ◽

Functional Enrichment ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Sequencing Platform

Bacterial spot (BS), incited by Xanthomonas campestris pv. vesicatoria (Xcv), is one of the most serious diseases of pepper. For a comparative analysis of defense responses to Xcv infection, we performed a transcriptomic analysis of a susceptible cultivar, ECW, and a resistant cultivar, VI037601, using the HiSeqTM 2500 sequencing platform. Approximately 120.23 G clean bases were generated from 18 libraries. From the libraries generated, a total of 38,269 expressed genes containing 11,714 novel genes and 11,232 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that the most noticeable pathways were plant-pathogen interaction, MAPK signaling pathway—plant, plant hormone signal transduction and secondary metabolisms. 1,599 potentially defense-related genes linked to pattern recognition receptors (PRRs), mitogen-activated protein kinase (MAPK), calcium signaling, and transcription factors may regulate pepper resistance to Xcv. Moreover, after Xcv inoculation, 364 DEGs differentially expressed only in VI037601 and 852 genes in both ECW and VI037601. Many of those genes were classified as NBS-LRR genes, oxidoreductase gene, WRKY and NAC transcription factors, and they were mainly involved in metabolic process, response to stimulus and biological regulation pathways. Quantitative RT-PCR of sixteen selected DEGs further validated the RNA-seq differential gene expression analysis. Our results will provide a valuable resource for understanding the molecular mechanisms of pepper resistance to Xcv infection and improving pepper resistance cultivars against Xcv.

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Analysis of Serum miRNAs in Alzheimer’s Disease

American Journal of Alzheimer s Disease & Other Dementias® ◽

10.1177/15333175211021712 ◽

2021 ◽

Vol 36 ◽

pp. 153331752110217

Author(s):

Liu Lu ◽

Wen-Zhuo Dai ◽

Xi-Chen Zhu ◽

Tao Ma

Keyword(s):

Gene Expression ◽

Target Genes ◽

Enrichment Analysis ◽

Gene Interaction ◽

Functional Enrichment Analysis ◽

Gene Expression Omnibus ◽

Functional Enrichment ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Regulatory Relationship

This paper was aimed to analyze the microRNA (miRNA) signatures in Alzheimer disease (AD) and find the significant expressions of miRNAs, their target genes, the functional enrichment analysis of the confirmed genes, and potential drug treatment. The miRNA expression information of the gene expression profile data was downloaded from the Gene Expression Omnibus database. The total data sample size is 1309, including 1021 AD samples and 288 normal samples. A total of 21 differentially expressed miRNAs were obtained, of which 16 (hsa-miR-6761-3p, hsa-miR-6747-3p, hsa-miR-6875-3p, hsa-miR-6754-3p, hsa-miR-6736-3p, hsa-miR-6762-3p, hsa-miR-6787-3p, hsa-miR-208a-5p, hsa-miR-6740-3p, hsa-miR-6778-3p, hsa-miR-595, hsa-miR-6753-3p, hsa-miR-4747-3p, hsa-miR-3646, hsa-miR-6716-3p and hsa-miR-4435) were up-regulated and 5 (hsa-miR-125a-3p, hsa-miR-22-3p, hsa-miR-24-3p, hsa-miR-6131 and hsa-miR-125b-1-3p) were down-regulated in AD. A total of 6 miRNAs (hsa-miR-595, hsa-miR-3646, hsa-miR-4435 hsa-miR-125a-3p, hsa-miR-22-3p and hsa-miR-24-3p) and 78 miRNA-disease-related gene sub-networks were predicted, and 116 ceRNA regulatory relationship pairs, and the ceRNA regulatory network were obtained. The results of enrichment analysis suggested that the main target pathways of several miRNAs differentially expressed in AD were mitogen-activated protein kinase signal pathway. According to the prediction results of Drug-Gene Interaction database 2.0, we obtained 53 pairs of drug-gene interaction, including 7 genes (PTGS2, EGFR, CALM1, PDE4D, FGFR2, HMGCR, cdk6) and 53 drugs. We hope our results are helpful to find a viable way to prevent, delay the onset, diagnose, and treat AD.

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Identification of Ten-lncRNA Signatures Predict Disease-free and Overall Survival for Hepatocellular Carcinoma

10.21203/rs.3.rs-613111/v2 ◽

2021 ◽

Author(s):

Si-shu Yang ◽

Jiong Lu ◽

Xian-ze Xiong

Keyword(s):

Hepatocellular Carcinoma ◽

Overall Survival ◽

Disease Free Survival ◽

Enrichment Analysis ◽

Mapk Signaling ◽

The Cancer Genome Atlas ◽

Functional Enrichment ◽

Mitogen Activated Protein Kinase ◽

Pathway Enrichment Analysis ◽

Disease Free

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A Transcriptomic Analysis Reveals Diverse Regulatory Networks That Respond to Cold Stress in Strawberry (Fragaria×ananassa)

International Journal of Genomics ◽

10.1155/2019/7106092 ◽

2019 ◽

Vol 2019 ◽

pp. 1-13

Author(s):

Yong Zhang ◽

Yunting Zhang ◽

Yuanxiu Lin ◽

Ya Luo ◽

Xiaorong Wang ◽

...

Keyword(s):

Cold Stress ◽

Regulatory Networks ◽

Response Regulator ◽

Enrichment Analysis ◽

Mapk Signaling ◽

Transcriptomic Analysis ◽

Functional Enrichment ◽

Mitogen Activated Protein Kinase ◽

Fragaria Ananassa ◽

Alpha Linolenic Acid

Strawberry is often subjected to cold stress in temperate regions when insulation measures are not strictly applied in protected cultivation. Cold stress adversely influences plant growth and development by triggering a massive change to the transcriptome. To provide the potential strategies in improving strawberry cold tolerance and give a glimpse into the understanding of the complex cold signaling pathways in plants, this study identified attractive candidate genes and revealed diverse regulatory networks that responded to cold stress in strawberry (Fragaria×ananassa) by a transcriptomic analysis. Totally, there were 2397 differentially expressed genes (DEGs) under cold stress treatment (T1) vs. normal treatment (CK). Of these, 1180 DEGs were upregulated, while 1217 DEGs were downregulated. Functional enrichment analysis showed that DEGs were significantly (adjusted P value < 0.05) overrepresented in six pathways including plant hormone signal transduction, flavonoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling, starch and sucrose metabolism, circadian rhythm, and alpha-linolenic acid metabolism. The cold signaling initiated expression of downstream cold-responsive (COR) genes with cis-acting element ABRE or CRT/DRE in the ABA-independent or ABA-dependent pathway to impel plant defense against the stress. Strikingly, GIGANTEA (gene id 101308922), two-component response regulator-like PRR95 (gene id 101295449), and ethylene-responsive transcription factor ERF105-like (gene id 101295082) were dramatically induced under low-temperature treatment, indicating that they played an important role in response to cold stress in strawberry.

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Identification of Ten-LncRNA Signatures Predict Disease-Free and Overall Survival for Hepatocellular Carcinoma

10.21203/rs.3.rs-613111/v1 ◽

2021 ◽

Author(s):

Jiong Lu ◽

Sishu Yang ◽

xianze xiong

Keyword(s):

Hepatocellular Carcinoma ◽

Overall Survival ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Mapk Signaling ◽

Functional Enrichment ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Operating Characteristics ◽

Disease Free

Abstract Background: The prognosis of hepatocellular carcinoma (HCC) is bleak though it has been improved over recent years. Early diagnosis could improve the survival. Plenty of researches indicate that long non-coding RNAs (lncRNAs) could play an important role in prognostic prediction of cancer as a kind of biomarker. Methods: We downloaded clinicopathological characteristics and lncRNA expression data of HCC patients from The Cancer Genome Atlas (TCGA) database. The ratio of training sets to validation sets was 2:1. Significant differentially expressed lncRNAs were identified by log-rank test and cox regression. All the significant lncRNAs were selected into the least absolute shrinkage and selection operator regression (LASSO) analysis and constructed risk-score formula by linear combination. Performance of the signatures were validated by receiver operating characteristics (ROC) curves and Kaplan-Meier survival curves. The correlated messenger RNAs (mRNA) were evaluated by functional enrichment analysis. Results: We identified and validated ten-lncRNAs based signatures to predict disease-free survival (DFS) and overall survival (OS) of HCC respectively. Stratified survival analysis showed that the performance of lncRNAs related signatures was better than tumor, node, metastasis(TNM) staging system. Functional enrichment analysis showed that organelle fission and regulation of mRNA metabolic process were significantly enriched in differentially expressed lncRNAs (DElncRNAs). Transcriptional misregulation in cancer and mitogen-activated protein kinase (MAPK) signaling pathway were significantly enriched pathways in the pathway enrichment analysis. Conclusion: we constructed two lncRNAs based signatures which could predict prognosis of HCC more accurate than the traditional ways.

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Identification of Candidate Genetic Markers and a Novel 4-genes Diagnostic Model in Osteoarthritis through Integrating Multiple Microarray Data

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323666200428120310 ◽

2020 ◽

Vol 23 (8) ◽

pp. 805-813

Author(s):

Ai Jiang ◽

Peng Xu ◽

Zhenda Zhao ◽

Qizhao Tan ◽

Shang Sun ◽

...

Keyword(s):

Signaling Pathway ◽

Microarray Data ◽

Differential Expression Analysis ◽

Enrichment Analysis ◽

Mapk Signaling ◽

Functional Enrichment ◽

Joint Disease ◽

Support Vector ◽

Diagnostic Model ◽

Data Sets

Background: Osteoarthritis (OA) is a joint disease that leads to a high disability rate and a low quality of life. With the development of modern molecular biology techniques, some key genes and diagnostic markers have been reported. However, the etiology and pathogenesis of OA are still unknown. Objective: To develop a gene signature in OA. Method: In this study, five microarray data sets were integrated to conduct a comprehensive network and pathway analysis of the biological functions of OA related genes, which can provide valuable information and further explore the etiology and pathogenesis of OA. Results and Discussion: Differential expression analysis identified 180 genes with significantly expressed expression in OA. Functional enrichment analysis showed that the up-regulated genes were associated with rheumatoid arthritis (p < 0.01). Down-regulated genes regulate the biological processes of negative regulation of kinase activity and some signaling pathways such as MAPK signaling pathway (p < 0.001) and IL-17 signaling pathway (p < 0.001). In addition, the OA specific protein-protein interaction (PPI) network was constructed based on the differentially expressed genes. The analysis of network topological attributes showed that differentially upregulated VEGFA, MYC, ATF3 and JUN genes were hub genes of the network, which may influence the occurrence and development of OA through regulating cell cycle or apoptosis, and were potential biomarkers of OA. Finally, the support vector machine (SVM) method was used to establish the diagnosis model of OA, which not only had excellent predictive power in internal and external data sets (AUC > 0.9), but also had high predictive performance in different chip platforms (AUC > 0.9) and also had effective ability in blood samples (AUC > 0.8). Conclusion: The 4-genes diagnostic model may be of great help to the early diagnosis and prediction of OA.

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Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

Current Bioinformatics ◽

10.2174/1574893614666190204152500 ◽

2019 ◽

Vol 14 (7) ◽

pp. 591-601 ◽

Cited By ~ 1

Author(s):

Aravind K. Konda ◽

Parasappa R. Sabale ◽

Khela R. Soren ◽

Shanmugavadivel P. Subramaniam ◽

Pallavi Singh ◽

...

Keyword(s):

Expression Pattern ◽

Gene Networks ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Wrky Transcription Factor ◽

Functional Enrichment ◽

Differentially Expressed ◽

Callose Deposition ◽

Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

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MicroRNA sequence analysis identifies microRNAs associated with peri-implantitis in dogs

Bioscience Reports ◽

10.1042/bsr20170768 ◽

2017 ◽

Vol 37 (5) ◽

Cited By ~ 10

Author(s):

Xiaolin Wu ◽

Xipeng Chen ◽

Wenxiang Mi ◽

Tingting Wu ◽

Qinhua Gu ◽

...

Keyword(s):

Sequence Analysis ◽

Target Genes ◽

Alveolar Bone ◽

Biological Effects ◽

Bone Destruction ◽

Mapk Signaling ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Mirna Sequence ◽

Differentially Expressed Mirnas

Peri-implantitis, which is characterized by dense inflammatory infiltrates and increased osteoclast activity, can lead to alveolar bone destruction and implantation failure. miRNAs participate in the regulation of various inflammatory diseases, such as periodontitis and osteoporosis. Therefore, the present study aimed to investigate the differential expression of miRNAs in canine peri-implantitis and to explore the functions of their target genes. An miRNA sequence analysis was used to identify differentially expressed miRNAs in peri-implantitis. Under the criteria of a fold-change >1.5 and P<0.01, 8 up-regulated and 30 down-regulated miRNAs were selected for predictions of target genes and their biological functions. Based on the results of Gene Ontology (GO) and KEGG pathway analyses, these miRNAs may fine-tune the inflammatory process in peri-implantitis through an intricate mechanism. The results of quantitative real-time PCR (qRT-PCR) revealed that let-7g, miR-27a, and miR-145 may play important roles in peri-implantitis and are worth further investigation. The results of the present study provide insights into the potential biological effects of the differentially expressed miRNAs, and specific enrichment of target genes involved in the mitogen-activated protein kinase (MAPK) signaling pathway was observed. These findings highlight the intricate and specific roles of miRNAs in inflammation and osteoclastogenesis, both of which are key aspects of peri-implantitis, and thus may contribute to future investigations of the etiology, underlying mechanism, and treatment of peri-implantitis.

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Identification of a prognostic long non-coding RNA signature in breast cancer

10.21203/rs.3.rs-27286/v1 ◽

2020 ◽

Author(s):

Gaochen Lan ◽

Xiaoling Yu ◽

Yanna Zhao ◽

Jinjian Lan ◽

Wan Li ◽

...

Keyword(s):

Breast Cancer ◽

Cox Regression ◽

Prognostic Biomarker ◽

Expression Profiles ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Functional Enrichment ◽

Differentially Expressed ◽

Cox Regression Analysis

Abstract Background: Breast cancer is the most common malignant disease among women. At present, more and more attention has been paid to long non-coding RNAs (lncRNAs) in the field of breast cancer research. We aimed to investigate the expression profiles of lncRNAs and construct a prognostic lncRNA for predicting the overall survival (OS) of breast cancer.Methods: The expression profiles of lncRNAs and clinical data with breast cancer were obtained from The Cancer Genome Atlas (TCGA). Differentially expressed lncRNAs were screened out by R package (limma). The survival probability was estimated by the Kaplan‑Meier Test. The Cox Regression Model was performed for univariate and multivariate analysis. The risk score (RS) was established on the basis of the lncRNAs’ expression level (exp) multiplied regression coefficient (β) from the multivariate cox regression analysis with the following formula: RS=exp a1 * β a1 + exp a2 * β a2 +……+ exp an * β an. Functional enrichment analysis was performed by Metascape.Results: A total of 3404 differentially expressed lncRNAs were identified. Among them, CYTOR, MIR4458HG and MAPT-AS1 were significantly associated with the survival of breast cancer. Finally, The RS could predict OS of breast cancer (RS=exp CYTOR * β CYTOR + exp MIR4458HG * β MIR4458HG + exp MAPT-AS1 * β MAPT-AS1). Moreover, it was confirmed that the three-lncRNA signature could be an independent prognostic biomarker for breast cancer (HR=3.040, P=0.000).Conclusions: This study established a three-lncRNA signature, which might be a novel prognostic biomarker for breast cancer.

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Diagnostic model of combined ceRNA and DNA methylation related genes in esophageal carcinoma

PeerJ ◽

10.7717/peerj.8831 ◽

2020 ◽

Vol 8 ◽

pp. e8831 ◽

Cited By ~ 1

Author(s):

Xiaojiao Guan ◽

Yao Yao ◽

Guangyao Bao ◽

Yue Wang ◽

Aimeng Zhang ◽

...

Keyword(s):

Gene Expression ◽

Esophageal Cancer ◽

Esophageal Carcinoma ◽

Differentially Expressed Genes ◽

Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Diagnostic Model ◽

Link Type ◽

Key Genes

Esophageal cancer is a common malignant tumor in the world, and the aim of this study was to screen key genes related to the development of esophageal cancer using a variety of bioinformatics analysis tools and analyze their biological functions. The data of esophageal squamous cell carcinoma from the Gene Expression Omnibus (GEO) were selected as the research object, processed and analyzed to screen differentially expressed microRNAs (miRNAs) and differential methylation genes. The competing endogenous RNAs (ceRNAs) interaction network of differentially expressed genes was constructed by bioinformatics tools DAVID, String, and Cytoscape. Biofunctional enrichment analysis was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression of the screened genes and the survival of the patients were verified. By analyzing GSE59973 and GSE114110, we found three down-regulated and nine up-regulated miRNAs. The gene expression matrix of GSE120356 was calculated by Pearson correlation coefficient, and the 11696 pairs of ceRNA relation were determined. In the ceRNA network, 643 lncRNAs and 147 mRNAs showed methylation difference. Functional enrichment analysis showed that these differentially expressed genes were mainly concentrated in the FoxO signaling pathway and were involved in the corresponding cascade of calcineurin. By analyzing the clinical data in The Cancer Genome Atlas (TCGA) database, it was found that four lncRNAs had an important impact on the survival and prognosis of esophageal carcinoma patients. QRT-PCR was also conducted to identify the expression of the key lncRNAs (RNF217-AS1, HCP5, ZFPM2-AS1 and HCG22) in ESCC samples. The selected key genes can provide theoretical guidance for further research on the molecular mechanism of esophageal carcinoma and the screening of molecular markers.

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