scholarly journals miRNA profiles of canine cutaneous mast cell tumours with early nodal metastasis and evaluation as potential biomarkers

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Valentina Zamarian ◽  
Roberta Ferrari ◽  
Damiano Stefanello ◽  
Fabrizio Ceciliani ◽  
Valeria Grieco ◽  
...  
Keyword(s):  
Factor Analysis ◽  
Mast Cell ◽  
Mirna Expression ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Nodal Metastasis ◽  
Pathway Enrichment Analysis ◽  
Multiple Factor Analysis ◽  
Cutaneous Mast Cell ◽  
Multiple Factor

Abstract Cutaneous mast cell tumours (MCTs) are common skin neoplasms in dogs. MicroRNAs (miRNAs) are post-transcriptional regulators involved in several cellular processes, and they can function as tumour promoters or suppressors. However, the role of miRNAs in canine MCTs has not yet been elucidated. Thus, the current study aimed to characterize miRNA profiles and to assess their value as biomarkers for MCTs. miRNA expression profiles were assessed in formalin-fixed, paraffin-embedded samples by next-generation sequencing. Ten samples were MCT tissues, and 7 were healthy adjacent tissues. Nine dysregulated miRNAs (DE-miRNAs) were then validated using RT-qPCR in a larger group of MCT samples, allowing the calculation of ROC curves and performance of multiple factor analysis (MFA). Pathway enrichment analysis was performed to investigate miRNA biological functions. The results showed that the expression of 63 miRNAs (18 up- and 45 downregulated) was significantly affected in MCTs. Five DE-miRNAs, namely, miR-21-5p, miR-92a-3p, miR-338, miR-379 and miR-885, were validated by RT-qPCR. The diagnostic accuracy of a panel of 3 DE-miRNAs—miR-21, miR-379 and miR-885—exhibited increased efficiency in discriminating animals with MCTs (AUC = 0.9854) and animals with lymph node metastasis (AUC = 0.8923). Multiple factor analysis revealed clusters based on nodal metastasis. Gene Ontology and KEGG analyses confirmed that the DE-miRNAs were involved in cell proliferation, survival and metastasis pathways. In conclusion, the present study demonstrated that the miRNA expression profile is changed in the MCT microenvironment, suggesting the involvement of the altered miRNAs in the epigenetic regulation of MCTs and identifying miR-21, miR-379 and miR-885 as promising biomarkers.

scholarly journals Sex differences in microRNA expression in first and third trimester human placenta

2021 ◽  
Author(s):  
Amy E. Flowers ◽  
Tania L Gonzalez ◽  
Nikhil V. Joshi ◽  
Laura E Eisman ◽  
Ekaterina L Clark ◽  
...  
Keyword(s):  
Sex Differences ◽  
Mirna Expression ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
First Trimester ◽  
Pathway Enrichment Analysis ◽  
Sexually Dimorphic ◽  
Third Trimester ◽  
Placental Function ◽  
The Third

Maternal and fetal pregnancy outcomes related to placental function vary based on fetal sex, which may be the result of sexually dimorphic epigenetic regulation of RNA expression. We identified sexually dimorphic miRNA expression throughout gestation in human placentae. Next-generation sequencing was used to identify miRNA expression profiles in first and third trimester uncomplicated pregnancies using tissue obtained at chorionic villous sampling (n=113) and parturition (n=47). Sequencing and differential expression (DE) analysis identified 432 mature miRNAs expressed in the first trimester female, 425 in the first trimester male, 400 in the third trimester female, and 508 in the third trimester male placenta (baseMean >10). Of these, 11 sexually dimorphic (FDR<0.05, baseMean >10) miRNAs were identified in the first and 4 miRNAs were identified in the third trimester, including miR-361-5p, significant in both trimesters, all upregulated in females. Across gestation, 207 miRNAs were DE across gestation, common to both females and males, miR-4483, the most DE across gestation. There were twice as many female-specific differences across gestation as male-specific (44 miRNAs vs 21 miRNAs), indicating that miRNA abundance across human gestation is sexually dimorphic. Pathway enrichment analysis identified significant pathways that were differentially regulated in first and third trimester as well as across gestation. This work provides the normative sex dimorphic miRNA atlas in first and third trimester, as well as the sex independent and sex specific placenta miRNA atlas across gestation which may be used to identify biomarkers of placental function and direct functional studies investigating placental sex differences.

scholarly journals Multiple factor analysis of eating patterns to detect groups at risk of malnutrition among home-dwelling older subjects in 2015

BMJ Open ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. e023548
Author(s):  
Marc-Antoine Sanchez ◽  
Didier Armaingaud ◽  
Yasmine Messaoudi ◽  
Aude Letty ◽  
Rachid Mahmoudi ◽  
...  
Keyword(s):  
Older Adults ◽  
Factor Analysis ◽  
Food Intake ◽  
Dietary Habits ◽  
Eating Patterns ◽  
Multiple Factor Analysis ◽  
Older Subjects ◽  
Multiple Factor ◽  
Group 1 ◽  
Meal Delivery

ObjectiveWe aimed to describe eating patterns among home-dwelling older subjects to establish typologies of eaters at higher or lower risk of malnutrition.DesignCross-sectional study between June and September 2015 using a standardised questionnaire. The questionnaire was given to home-help employees (responsible for delivering meals to home-dwelling older persons and helping them to eat). The employees were asked to complete the questionnaire three times during the same week, for the same older adults, in order to identify the totality of their food intake.SettingRegistered customers of the home meal delivery company ‘Azaé’ (France).Participants605 older home-dwelling persons were randomly selected among customers served by the home meal delivery company.OutcomesMultiple factor analysis was used to understand the different modes of food consumption and to establish eating profiles. Hierarchical classification was performed to construct eating profiles corresponding to the dietary habits of the respondents.ResultsAverage age of the older adults was 85.3 years; 73.5% were women. Overall, 59% of participants reported that they ate out of habit, while 33.7% said they ate for pleasure. We identified four different groups of eaters, at varying levels of risk for malnutrition. Individuals in group 4 had the highest food intake in terms of quantity; and were less dependent than individuals in group 1 (p=0.05); group 1 was at highest risk of malnutrition.ConclusionImproved understanding of eating habits can help detect risky behaviours and help caregivers to promote better nutrition among home-dwelling older subjects.

scholarly journals Bioinformatics-Based Study to Investigate Potential Differentially Expressed Genes and miRNAs in Hashimoto’s Thyroiditis

2021 ◽  
Author(s):  
Li Guoquan ◽  
Du Junwei ◽  
He Qi ◽  
Fu Xinghao ◽  
Ji Feihong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Inflammatory Responses ◽  
Expression Profiles ◽  
Treatment Options ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Chronic Lymphocytic Thyroiditis ◽  
Hub Genes

Abstract BackgroundHashimoto's thyroiditis (HT), also known as chronic lymphocytic thyroiditis, is a common autoimmune disease, which mainly occurs in women. The early manifestation was hyperthyroidism, however, hypothyroidism may occur if HT was not controlled for a long time. Numerous studies have shown that multiple factors, including genetic, environmental, and autoimmune factors, were involved in the pathogenesis of the disease, but the exact mechanisms were not yet clear. The aim of this study was to identify differentially expressed genes (DEGs) by comprehensive analysis and to provide specific insights into HT. MethodsTwo gene expression profiles (GSE6339, GSE138198) about HT were downloaded from the Gene Expression Omnibus (GEO) database. The DEGs were assessed between the HT and normal groups using the GEO2R. The DEGs were then sent to the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The hub genes were discovered using Cytoscape and CytoHubba. Finally, NetworkAnalyst was utilized to create the hub genes' targeted microRNAs (miRNAs). ResultsA total of 62 DEGs were discovered, including 60 up-regulated and 2 down-regulated DEGs. The signaling pathways were mainly engaged in cytokine interaction and cytotoxicity, and the DEGs were mostly enriched in immunological and inflammatory responses. IL2RA, CXCL9, IL10RA, CCL3, CCL4, CCL2, STAT1, CD4, CSF1R, and ITGAX were chosen as hub genes based on the results of the protein-protein interaction (PPI) network and CytoHubba. Five miRNAs, including mir-24-3p, mir-223-3p, mir-155-5p, mir-34a-5p, mir-26b-5p, and mir-6499-3p, were suggested as likely important miRNAs in HT. ConclusionsThese hub genes, pathways and miRNAs contribute to a better understanding of the pathophysiology of HT and offer potential treatment options for HT.

scholarly journals Identification of Differentially Expressed Genes and associated pathways common to Eyelid and Non-Ocular Basal Cell Carcinoma to understand the Molecular Biology of BCC

2021 ◽  
Author(s):  
Perumal Jayaraj ◽  
Seema Sen ◽  
Pranjal Vats ◽  
Shefali Dahiya ◽  
Vanshika Mohindroo
Keyword(s):  
Basal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Basal Cell ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Bioinformatic Analysis ◽  
Malignant Neoplasms ◽  
Pathway Enrichment Analysis ◽  
Hub Genes ◽  
Pathway Enrichment

Background: Eyelid BCC accounts for more than 90% of Eyelid malignant neoplasms. Various aberrant signalling pathways and genes in Non-Ocular BCC have been found whereas Eyelid bcc remains elusive. Objective: This study aims to find the common DEGs of Eyelid and Non-Ocular BCC using bioinformatic analysis and text mining to gain more insights into the molecular aspects common to both BCC non-ocular and Eyelid BCC and to identify common potential prognostic markers. Material and method: The Gene Expression profiles of Eyelid BCC (GSE103439) and Non-Ocular BCC (GSE53462) were obtained from the NCBI GEO database followed by identification of common DEGs. Protein-Protein interaction and Pathway Enrichment analysis of these screened genes was done using bioinformatic tools like STRING, Cytoscape and BiNGO, DAVID, KEGG respectively. Results: A total of 181 genes were found common in both datasets. A PPI network was formed for the screened genes and 20 HUB genes were sorted which included CTNNB1, MAPK14, BTRC, EGFR, ADAM17. Pathway enrichment of HUB genes showed that they were dysregulated in carcinogenic and apoptotic pathways that seem to play a role in the progression of both the BCC. Conclusion: The result and findings of bioinformatic analysis highlighted the molecular pathways and genes enriched in both Eyelid BCC as well as Non- Ocular BCC. The identified pathways should be studied further to recognise common molecular events that would lead to the progression of BCC. This may provide a window to explore the prognostic and therapeutic strategies common to both BCC. Keywords: Basal cell carcinoma (BCC), Cancer, Microarray, Ophthalmology, Tumour marker

scholarly journals The appropriateness of sum scores as estimates of factor scores in the multiple factor analysis of ordered-categorical responses.

2020 ◽  
Author(s):  
Pere Ferrando ◽  
Urbano Lorenzo-Seva
Keyword(s):  
Factor Analysis ◽  
Unit Weight ◽  
Factor Scores ◽  
Multiple Factor Analysis ◽  
Non Linear ◽  
Categorical Responses ◽  
Sum Scores ◽  
Biased Estimates ◽  
Ordered Categorical ◽  
Multiple Factor

<p>Unit-weight sum scores (UWSSs) are routinely used as estimates of factor scores on the basis of solutions obtained with the non-linear exploratory factor analysis (EFA) model for ordered-categorical responses. Theoretically, this practice results in a loss of information and accuracy, and is expected to lead to biased estimates. However, the practical relevance of these limitations is far from clear. In this article we adopt an empirical view, and propose indices and procedures (some of them new) for assessing the appropriateness of UWSSs in non-linear EFA applications. A new automated approach for obtaining UWSSs that maximize fidelity and correlational accuracy is proposed. The appropriateness of UWSSs under different conditions and the behavior of the present proposal in comparison with other more common approaches are assessed with a simulation study. A tutorial for interested practitioners is presented using an illustrative example based on a well-known personality questionnaire. All the procedures proposed in the article have been implemented in a well-known noncommercial EFA program. </p>

scholarly journals Recodificación de escalas en investigaciones sociológicas: una nueva metodología de validación. Aplicación a una encuesta política

2019 ◽  
Vol 77 (2) ◽  
pp. 130
Author(s):  
Elena Abascal ◽  
Vidal Díaz de Rada ◽  
Ignacio García Lautre ◽  
M. Isabel Landaluce
Keyword(s):  
Factor Analysis ◽  
Multiple Factor Analysis ◽  
Multiple Factor

La recodificación de variables es una etapa habitual en el análisis de datos de encuesta. No está exenta de riesgos, como pueden ser la introducción de sesgos o las posibles deformaciones de los datos originales. En este trabajo se propone una metodología de validación de cualquier recodificación, tanto de variables de escala métrica, como de escala categórica para reducir el número de categorías. El objetivo de la metodología propuesta es comprobar la adecuación de la recodificación, indicando en qué medida los datos recodificados mantienen la misma estructura de los datos originales. La metodología se basa en el uso de un método factorial, Multiple Factor Analysis (MFA), aplicado sobre una tabla global obtenida como yuxtaposición de los datos medidos con la escala original y los mismos datos medidos con la escala recodificada. El procedimiento ha sido testado a partir de un conjunto de datos reales extraídos de una encuesta de opinión pública sobre los principales políticos del Parlamento Español.

scholarly journals University performace through Multiple Factor Analysis

2019 ◽  
Author(s):  
Delimiro Alberto Visbal Cadavid ◽  
Mónica Martínez-Gómez ◽  
Rolando Escorcia-Caballero
Keyword(s):  
Higher Education ◽  
Factor Analysis ◽  
Higher Education Institutions ◽  
Public Higher Education ◽  
Multiple Factor Analysis ◽  
High Level ◽  
The University ◽  
High Degree ◽  
Multiple Factor ◽  
Year 2013

This work applies the Multiple Factor Analysis (MFA) as an exploratory methodology to analize the indicators of the education´s management that belong to 32 Colombian public Higher Education Institutions (HEIs) along the year 2013. The product of this work indicates that the majority of HEIs have similar structures, being different and better scored the following: La Universidad Nacional (UNAL), Antioquia (UDEA), Nacional Abierta y a Distancia (UNAD), Pamplona y del Valle. Also the UDEA has a high development in extension, formation, capacity and research which is considered one of the best HEIS in the country. The university of Valle has a high degree of welfare, formation and extension, besides moderate capacities on research in comparission with the UDEA wich is superior to the rest of the HEIs. Pamplona has too a high level of formation, extension and moderate weflare, research and capacity in relation to the UNAD. It worth to mention that UNAL is the best located on extension. However, it is surpassed by other University (UDEA) because has a better development in some variables associated to research and extension. To finish, there are other HEIs with too many weaknesses on the indicators of the education´s management wich are UFPS Ocaña, Sucre and Pacifico. These universities show certain problems of research, extension and capacity, but fundamentally strong shortcomings in formation and welfare.

Sign in / Sign up

Export Citation Format

Share Document