scholarly journals Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein-protein interaction network

2021 ◽  
Author(s):  
Backiyarani Suthanthiram ◽  
Sasikala Rajendran ◽  
Sharmiladevi Simeon ◽  
Uma Subbaraya
Keyword(s):  
Candidate Genes ◽  
Signaling Pathway ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Auxin Signaling ◽  
Pathway Enrichment Analysis ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

Abstract Banana, one of the most important staple, delicious fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein-protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By exploring the PPI of candidate genes from the putative network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLV-WUSHEL signaling pathway in addition to gibberellin mediated auxin signaling pathway in parthenocarpy. Further validation of candidate genes in seeded and seedless accession of Musa spp using qRT-PCR put forward AGL8, MADS16, IAA (GH3.8), RGA1, EXPA1, GID1C, HK2 and BAM1 as possible target genes in natural parthenocarpy. In contrary, expression profile of ACLB-2 and ZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through protein-protein interaction network.

scholarly journals Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein–protein interaction network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Suthanthiram Backiyarani ◽  
Rajendran Sasikala ◽  
Simeon Sharmiladevi ◽  
Subbaraya Uma
Keyword(s):  
Candidate Genes ◽  
Protein Interaction ◽  
Target Genes ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Auxin Signaling ◽  
Pathway Enrichment Analysis ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
The Difference

AbstractBanana, one of the most important staple fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein–protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By further validating these candidate genes in seeded and seedless accession of Musa spp. we put forward MaAGL8, MaMADS16, MaGH3.8, MaMADS29, MaRGA1, MaEXPA1, MaGID1C, MaHK2 and MaBAM1 as possible target genes in the study of natural parthenocarpy. In contrary, expression profile of MaACLB-2 and MaZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. By exploring the PPI of validated genes from the network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLAVATA(CLV)–WUSHEL(WUS) signaling pathway in addition to gibberellin mediated auxin signaling in parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through PPI network.

scholarly journals Network Pharmacology study of Curcuma longa L.: Potential Target Proteins and their Functional Enrichment Analysis.

2020 ◽  
Author(s):  
SANGEETA KUMARI
Keyword(s):  
Signaling Pathway ◽  
Mechanism Of Action ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Curcuma Longa ◽  
Interaction Network ◽  
Functional Enrichment ◽  
Target Proteins ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

Abstract Objective This study’s primary goal is unraveling the mechanism of action of bioactives of Curcuma longa L. at the molecular level using protein-protein interaction network.Results We used target proteins to create protein-protein interaction network (PPIN) and identified significant node and edge attributes of PPIN. We identified the cluster of proteins in the PPIN, which were used to identify enriched pathways. . We identified closeness centrality and jaccard score as most important node and edge attribute of the PPIN respectively. The enriched pathways of various clusters were overlapped suggesting synergistic mechanism of action. The three pathways found to be common among three clusters were Gonadotropin-releasing hormone receptor pathway, Endothelin signaling pathway, and Inflammation mediated by chemokine and cytokine signaling pathway.

scholarly journals The molecular mechanisms associated with PIN7, a protein-protein interaction network of seven pleiotropic proteins

2019 ◽  
Author(s):  
Jarmila Nahálková
Keyword(s):  
Signaling Pathway ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Molecular Mechanisms ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
P53 Signaling ◽  
Age Related ◽  
P53 Signaling Pathway ◽  
Protein Protein Interaction Network

The protein-protein interaction network of seven pleiotropic proteins (PIN7) contains proteins with multiple functions in the aging and age-related diseases (TPPII, CDK2, MYBBP1A, p53, SIRT6, SIRT7, and BSG). At the present work, the pathway enrichment, the gene function prediction and the protein node prioritization analysis were applied for the examination of main molecular mechanisms driving PIN7 and the extended network. Seven proteins of PIN7 were used as an input for the analysis by GeneMania, a Cytoscape application, which constructs the protein interaction network. The software also extends it using the interactions retrieved from databases of experimental and predicted protein-protein and genetic interactions. The analysis identified the p53 signaling pathway as the most dominant mediator of PIN7. The extended PIN7 was also analyzed by Cytohubba application, which showed that the top-ranked protein nodes belong to the group of histone acetyltransferases and histone deacetylases. These enzymes are involved in the reverse epigenetic regulation mechanisms linked to the regulation of PTK2, NFκB, and p53 signaling interaction subnetworks of the extended PIN7. The analysis emphasized the role of PTK2 signaling, which functions upstream of the p53 signaling pathway and its interaction network includes all members of the sirtuin family. Further, the analysis suggested the involvement of molecular mechanisms related to metastatic cancer (prostate cancer, small cell lung cancer), hemostasis, the regulation of the thyroid hormones and the cell cycle G1/S checkpoint. The additional data-mining analysis showed that the small protein interaction network MYBBP1A-p53-TPPII-SIRT6-CD147 controls Warburg effect and MYBBP1A-p53-TPPII-SIRT7-BSG influences mTOR signaling and autophagy. Further investigations of the detail mechanisms of these interaction networks would be beneficial for the development of novel treatments for aging and age-related diseases.

scholarly journals The Influence of Let-7b-5p Target Gene in Cholangiocarcinoma and its Bioinformatic Analysis

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Xibing Zhang ◽  
Jianghua Ran ◽  
Fang Liu ◽  
Yingpeng Zhao ◽  
Zongqiang Hu
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Network ◽  
Target Gene ◽  
Interaction Network ◽  
Receptor Interaction ◽  
Pathway Enrichment Analysis ◽  
Signal Pathways ◽  
Biological Functions ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

Objective: To analyze the biological functions and its clinical significance of let-7b-5p target gene in cholangiocarcinoma utilizing bioinformatics. Methods: The paper focuses on the let-7b-5p target gene, and predicts its biological functions as well as related signal pathways through GO biological function and KEGG signal pathway enrichment analysis. The STRING database and Cytoscape are used to construct a protein-protein interaction network to screen core genes. Results: The results of GO analysis showed that let-7b-5p target gene was mainly enriched in biological processes such as Small GTPase binding, Rho GTPase binding, and Rac GTPase binding. The results of KEGG analysis showed that let-7b-5p target gene was significantly enriched in key signaling pathways including Focal adhesion and ECM-receptor interaction. Through protein-protein interaction network and module analysis, CXCL8 and SDC2 were screened as the core site. Conclusion: let-7b-5p can participate in the regulation of biological functions of tumor cells in cholangiocarcinoma, suggesting that it may play an important role as a tumor suppressor gene and biomarker in the occurrence and development of cholangiocarcinoma, which provides new ideas for its diagnosis and treatment.

scholarly journals Network pharmacology study of Curcuma longa L.: potential target proteins and their functional enrichment analysis

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Sangeeta Kumari ◽  
Hosahalli S. Subramanya
Keyword(s):  
Signaling Pathway ◽  
Mechanism Of Action ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Curcuma Longa ◽  
Interaction Network ◽  
Functional Enrichment ◽  
Target Proteins ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

Abstract Objective This study’s primary goal is unraveling the mechanism of action of bioactives of Curcuma longa L. at the molecular level using protein–protein interaction network. Results We used target proteins to create protein–protein interaction network (PPIN) and identified significant node and edge attributes of PPIN. We identified the cluster of proteins in the PPIN, which were used to identify enriched pathways. We identified closeness centrality and jaccard score as most important node and edge attribute of the PPIN respectively. The enriched pathways of various clusters were overlapped suggesting synergistic mechanism of action. The three pathways found to be common among three clusters were Gonadotropin-releasing hormone receptor pathway, Endothelin signaling pathway, and Inflammation mediated by chemokine and cytokine signaling pathway.

scholarly journals Network Pharmacology Study of Curcuma Longa: Potential Target Proteins and their Functional Enrichment Analysis.

2020 ◽  
Author(s):  
SANGEETA KUMARI
Keyword(s):  
Signaling Pathway ◽  
Mechanism Of Action ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Curcuma Longa ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Protein Protein Interaction ◽  
Function Module ◽  
Protein Protein Interaction Network

Abstract Objective: This study’s primary goal is unraveling the mechanism of action of bioactives of Curcuma longa L. at the molecular level using protein-protein interaction network.Results: We used target proteins to create protein-protein interaction network (PPI) and identified significant node and edge attributes of PPI. To find the function module, we identified the cluster of proteins which were further queried to GO enrichment analysis. Closeness centrality and jaccard score identified as most important node and edge attribute of the protein-protein interaction network respectively. The mapped pathways of various function module of the network were overlapped and showed synergistic mechanism of action. Three most important identified pathways were Gonadotropin-releasing hormone receptor pathway, Endothelin signaling pathway, and Inflammation mediated by chemokine and cytokine signaling pathway.

scholarly journals A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 316 ◽  
Author(s):  
Krishnamoorthy Srikanth ◽  
Seung-Hwan Lee ◽  
Ki-Yong Chung ◽  
Jong-Eun Park ◽  
Gul-Won Jang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Carcass Traits ◽  
Interaction Network ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Protein Protein Interaction ◽  
Regulatory Snps ◽  
Protein Protein Interaction Network

Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10−7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein–protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.

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