scholarly journals A miRNAs Based Exploration of promising Biomarkers in Cervical Cancer using Bioinformatic Methods

2021 ◽  
Author(s):  
Elakkiya Elumalai ◽  
Malarvizhi A ◽  
Sri Shyla T ◽  
Aruna Devi OM ◽  
Krishna Kant Gupta
Keyword(s):  
Cervical Cancer ◽  
Target Genes ◽  
Early Stage ◽  
Expression Profiles ◽  
Gynecologic Cancer ◽  
Interaction Network ◽  
Principal Component ◽  
P Value ◽  
Protein Protein Interaction ◽  
Cancer Early Detection

Cervical Cancer (CC) is a gynecologic cancer. In this cancer early detection is incredibly tough because most of the patients are not have any specific symptoms that results in suspending the proper identification. In this work, we selected TCGA CESC datasets and miRNA Seq analysis was done. The expression profiles of miRNAs in cervical cancer datasets were investigated using bioinformatics tools. The expression profiles of miRNA in Normal tissue, primary tumor and metastatic samples were analyzed. Based on p-value, principal component analysis and comparative literature survey, we reported 6 over-expressed (5X) miRNA at metastatic stage namely, hsa-mir-363, hsa-mir-429, hsa-mir-141, hsa-mir-93, hsa-mir-203b and hsa-mir-18a. Expression profiles were compared in heatmap. The target genes for the selected miRNAs were investigated for interaction and pathway details. The identification of two hub proteins (PTEN and MYC) in Protein-Protein Interaction Network was followed by pathway analysis. Our results indicate that hsa-mir-363, hsa-mir-429, hsa-mir-141, hsa-mir-93, hsa-mir-203b and hsa-mir-18a could be a potential diagnostic biomarkers for early-stage CESC and serve as prognostic predictors for patients with CESC.

scholarly journals Exploring Heat-Response Mechanisms of MicroRNAs Based on Microarray Data of Rice Post-meiosis Panicle

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Yan Peng ◽  
Xianwen Zhang ◽  
Yuewu Liu ◽  
Xinbo Chen
Keyword(s):  
Heat Stress ◽  
Target Genes ◽  
Expression Profiles ◽  
Time Lag ◽  
Interaction Network ◽  
Biological Processes ◽  
Functional Identification ◽  
Protein Protein Interaction ◽  
Heat Response ◽  
Protein Protein Interaction Network

To explore heat response mechanisms of mircoRNAs (miRNAs) in rice post-meiosis panicle, microarray analysis was performed on RNA isolated from rice post-meiosis panicles which were treated at 40°C for 0 min, 10 min, 20 min, 60 min, and 2 h. By integrating paired differentially expressed (DE) miRNAs and mRNA expression profiles, we found that the expression levels of 29 DE-miRNA families were negatively correlated to their 178 DE-target genes. Further analysis showed that the majority of miRNAs in 29 DE-miRNA families resisted the heat stress by downregulating their target genes and a time lag existed between expression of miRNAs and their target genes. Then, GO-Slim classification and functional identification of these 178 target genes showed that (1) miRNAs were mainly involved in a series of basic biological processes even under heat conditions; (2) some miRNAs might play important roles in the heat resistance (such as osa-miR164, osa-miR166, osa-miR169, osa-miR319, osa-miR390, osa-miR395, and osa-miR399); (3) osa-miR172 might play important roles in protecting the rice panicle under the heat stress, but osa-miR437, osa-miR418, osa-miR164, miR156, and miR529 might negatively affect rice fertility and panicle flower; and (4) osa-miR414 might inhibit the flowering gene expression by downregulation of LOC_Os 05g51830 to delay the heading of rice. Finally, a heat-induced miRNA-PPI (protein-protein interaction) network was constructed, and three miRNA coregulatory modules were discovered.

Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

2021 ◽  
Vol 15 (8) ◽  
pp. 927-936 ◽  
Author(s):  
Yan Peng ◽  
Yuewu Liu ◽  
Xinbo Chen
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Hot Spot ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Promising Tool ◽  
Differentially Expressed Mirnas ◽  
Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identified. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

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 Characterization of long non-coding RNA expression profiles in lymph node metastasis of early-stage cervical cancer

2016 ◽  
Vol 35 (6) ◽  
pp. 3185-3197 ◽  
Author(s):  
CHUNLIANG SHANG ◽  
WENHUI ZHU ◽  
TIANYU LIU ◽  
WEI WANG ◽  
GUANGXIN HUANG ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Lymph Node ◽  
Early Stage ◽  
Expression Profiles ◽  
Rna Expression ◽  
Node Metastasis ◽  
Non Coding Rna ◽  
Early Stage Cervical Cancer ◽  
Long Non Coding Rna

scholarly journals Identification of MicroRNA as Sepsis Biomarker Based on miRNAs Regulatory Network Analysis

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Jie Huang ◽  
Zhandong Sun ◽  
Wenying Yan ◽  
Yujie Zhu ◽  
Yuxin Lin ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Delayed Diagnosis ◽  
Interaction Network ◽  
High Sensitivity ◽  
Regulate Gene Expression ◽  
Protein Protein Interaction ◽  
Small Noncoding Rnas ◽  
Mirna Expression Profiles ◽  
Pathways Analysis

Sepsis is regarded as arising from an unusual systemic response to infection but the physiopathology of sepsis remains elusive. At present, sepsis is still a fatal condition with delayed diagnosis and a poor outcome. Many biomarkers have been reported in clinical application for patients with sepsis, and claimed to improve the diagnosis and treatment. Because of the difficulty in the interpreting of clinical features of sepsis, some biomarkers do not show high sensitivity and specificity. MicroRNAs (miRNAs) are small noncoding RNAs which pair the sites in mRNAs to regulate gene expression in eukaryotes. They play a key role in inflammatory response, and have been validated to be potential sepsis biomarker recently. In the present work, we apply a miRNA regulatory network based method to identify novel microRNA biomarkers associated with the early diagnosis of sepsis. By analyzing the miRNA expression profiles and the miRNA regulatory network, we obtained novel miRNAs associated with sepsis. Pathways analysis, disease ontology analysis, and protein-protein interaction network (PIN) analysis, as well as ROC curve, were exploited to testify the reliability of the predicted miRNAs. We finally identified 8 novel miRNAs which have the potential to be sepsis biomarkers.

scholarly journals Pengaruh Pendidikan Kesehatan Tentang Inspeksi Asam Asetat (IVA) Terhadap Motivasi Wus dalam Deteksi Kanker Serviks di Puskesmas Putri Ayu Jambi

2019 ◽  
Vol 19 (1) ◽  
pp. 42
Author(s):  
Hesty Hesty ◽  
Rahmah Rahmah ◽  
Nurfitriani Nurfitriani
Keyword(s):  
Cervical Cancer ◽  
Health Education ◽  
Early Stage ◽  
Sampling Technique ◽  
World Health ◽  
Control Group ◽  
P Value ◽  
Childbearing Age ◽  
Control Group Design ◽  
Experimental Group

World Health Organization (WHO), cervical cancer is the number two cause of death in the world for women from all existing cancer. Every two minutes a woman dies of this disease. This cancer attack at an early stage does not cause any symptoms. That is why, why does this type of cancer fall into the category of the silent killer. One of the promotive and preventive efforts in women of childbearing age as primary prevention can be through the provision of health education about cervical cancer using the Acetic Acid Inspection (IVA) method. The purpose of this study is to find out whether there is an influence of health education about IVA on WUS motivation in cervical cancer detection in health centers. Putri Ayu Jambi. This type of quantitative research with non randomized pretest-posttest with control group design, with purposive sampling technique totaling 22 WUS, 11 people as controls and 11 experimental people. The instrument in the form of questionnaires was analyzed by univariate and bivariate Paired Test t-test, which was conducted from April to July 2018.  The results of the study revealed that of the 22 WUSs studied, the average motivation of the pretest in the experimental group was 41.1818 and the control group was 39.9091, while the results of the posttest of the experimental group after being given counseling and leaflets increased by 42.9091 with p-value 0.034. There is an influence of health education about IVA tests on WUS motivation in detecting cervical cancer. It is suggested that the Puskesmas can improve activities in planning disease control programs, especially carrying out counseling and counseling both in the puskesmas building and in the working area of the puskesmas by involving cadres in their environment so that WUS is moved to take the IVA examination.

scholarly journals What Are The Determinants of Parametrial Invasion In Patients With Early Stage Cervical Cancer: A Cross Sectional Study

2021 ◽  
Author(s):  
Niloufar Hoorshad ◽  
Narges Zamani ◽  
Shahrzad Sheikh Hasani ◽  
Amirhossein Poopak ◽  
Amirsina Sharifi
Keyword(s):  
Cervical Cancer ◽  
Tumor Size ◽  
Early Stage ◽  
Univariate Analysis ◽  
Surgical Margin ◽  
P Value ◽  
Positive Surgical Margin ◽  
Stromal Invasion ◽  
Number Of Patients ◽  
Early Stage Cervical Cancer

Abstract Background: There was an increase in number of patients presented with early-stage cervical cancer (CC). Tumors with favorable pathological features might be candidates for less radical surgery.Methods: We retrospectively reviewed 700 patients with histologically confirmed CC between January 2011 and March 2020. Chi-square, Fisher's exact tests and multivariate logistic regression analysis were used to assess relations between parametrial involvement (PI) and clinic-pathological variables.Results: Total number of 132 patients with stage IA to IIA were eligible to participate. Squamous cell carcinoma was reported in 100 (75.8%) patients, adenocarcinoma and other tumor pathologies were found in 24(18.2%) and 8(6.1%), respectively. Considering the FIGO stage, 11 (8.4%) patients had IA, 111 (83%%) IB and 10 (7.6%) IIA. Nine patients (6.8%) had PI on permanent pathologic report. Univariate analysis demonstrated that following variables were statistically different between patients with and without PI: age ≥ 50, tumor size ≥ 3cm, lower segment involvement, poorly differentiated pathology, deep stromal invasion, pelvic lymph node, lympho-vascular involvement and positive surgical margin (all p values < 0.05). Among these variables only tumor size ≥ 3 cm (OR: 2.1, 95% CI: 1.11-4.16, p value: 0.02), deep stromal invasion (OR: 2.2, 95% CI: 1.9-7.43, p value: 0.02) and positive surgical margin (OR: 5.1, 95% CI: 3.97-11.15, p value: 0.008) were independent risk factor of PI in multivariate analysis.Conclusions: Early stage CC can be surgically approached in a more conservative manner if patients have tumor size < 3 cm and do not have deep stromal invasion in conization.

scholarly journals PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kota Fujisawa ◽  
Mamoru Shimo ◽  
Y.-H. Taguchi ◽  
Shinya Ikematsu ◽  
Ryota Miyata
Keyword(s):  
Gene Expression ◽  
Feature Extraction ◽  
Target Genes ◽  
Gene Selection ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Principal Component ◽  
Data Set ◽  
Immune Related Genes ◽  
Unsupervised Feature Extraction

AbstractCoronavirus disease 2019 (COVID-19) is raging worldwide. This potentially fatal infectious disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the complete mechanism of COVID-19 is not well understood. Therefore, we analyzed gene expression profiles of COVID-19 patients to identify disease-related genes through an innovative machine learning method that enables a data-driven strategy for gene selection from a data set with a small number of samples and many candidates. Principal-component-analysis-based unsupervised feature extraction (PCAUFE) was applied to the RNA expression profiles of 16 COVID-19 patients and 18 healthy control subjects. The results identified 123 genes as critical for COVID-19 progression from 60,683 candidate probes, including immune-related genes. The 123 genes were enriched in binding sites for transcription factors NFKB1 and RELA, which are involved in various biological phenomena such as immune response and cell survival: the primary mediator of canonical nuclear factor-kappa B (NF-κB) activity is the heterodimer RelA-p50. The genes were also enriched in histone modification H3K36me3, and they largely overlapped the target genes of NFKB1 and RELA. We found that the overlapping genes were downregulated in COVID-19 patients. These results suggest that canonical NF-κB activity was suppressed by H3K36me3 in COVID-19 patient blood.

scholarly journals Genes Involved in the Transcriptional Regulation of Pluripotency Are Expressed in Malignant Tumors of the Uterine Cervix and Can Induce Tumorigenic Capacity in a Nontumorigenic Cell Line

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Graciela Ruiz ◽  
Heriberto A. Valencia-González ◽  
Delia Pérez-Montiel ◽  
Felipe Muñoz ◽  
Rodolfo Ocadiz-Delgado ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Stem Cell ◽  
Transcription Factors ◽  
Cancer Stem Cell ◽  
Cell Line ◽  
Target Genes ◽  
Malignant Tumors ◽  
Expression Profiles ◽  
Ectopic Expression ◽  
Normal Tissues

Transcription factors OCT4, SOX2, KLF4, C-MYC, and NANOG (OSKM-N) regulate pluripotency and stemness, and their ectopic expression reprograms human and murine fibroblasts that constitute the key of regenerative medicine. To determine their contribution to cell transformation, we analyzed the gene expression profiles of these transcription factors in cervical cancer samples and found that they are preferentially expressed in the tumor component. Also, cancer stem cell-enriched cultures grown as sphere cultures showed overexpression of OSKM-N genes. Importantly, we observed that lentiviral-mediated transduction of these factors confers, to a nontumorigenic immortalized human cell line, properties of cancer stem cells as the ability to form tumors in a mouse model. When we performed a meta-analysis using microarray data from cervical cancer biopsies and normal tissues, we found that the expression of OSKM-N and some target genes allowed separating tumor and normal tissues between samples, which enhanced the importance of OSKM-N in the tumorigenesis. Finally, we analyzed and compared both transcript and protein expression profiles of these factors within a cohort of patients with cervical cancer. To our knowledge, this is the first time that the expression of OSKM-N is described to induce one of the main characteristics of the cancer stem cell, the tumorigenicity. And, more importantly, its exogenous expression in a nontumorigenic cell line is sufficient to induce a tumorigenic phenotype; furthermore, the differential expression of this transcription factor distinguishes tumor tissue and normal tissue in cervical samples.

Analysis of the miRNA transcriptome during testicular development and spermatogenesis of the Mongolian horse

2020 ◽  
Vol 32 (6) ◽  
pp. 582
Author(s):  
Bei Li ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Dandan Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Mammalian Species ◽  
Mature Mirnas ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
P Value ◽  
Testicular Development ◽  
Interaction Sites ◽  
Mongolian Horse

Numerous studies have shown that microRNAs (miRNAs) are essential for testicular development and spermatogenesis. In order to further characterise these physiological processes, three immature and three mature testes of the Mongolian horse were collected and six libraries were established. Using small RNA sequencing technology, 531 mature miRNAs were identified, including 46 novel miRNAs without previously ascribed functions. Among the 531 miRNAs, 421 were expressed in both immature and mature libraries, 65 miRNAs were found solely in immature testis libraries and 45 miRNAs were found solely in mature testis libraries. Furthermore, among the miRNAs that were identified in both immature and mature libraries, 107 were significantly differentially expressed (corrected P value (padj)&lt;0.05). Among the miRNAs that were only expressed in immature testes, two miRNAs were differentially expressed, whereas among the miRNAs that were only expressed in mature testes, nine miRNAs were differentially expressed. Comprehensive analysis of miRNA and mRNA expression profiles predicted 107 miRNA–mRNA interaction sites. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the predicted target genes suggested roles of the differentially expressed miRNAs in testicular development and spermatogenesis. These findings identify miRNAs as key factors in the development of the testes and spermatogenesis in the Mongolian horse, which may also help us to understand the mechanisms of fertility in related mammalian species.

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