scholarly journals Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3136
Author(s):  
Sunirmal Sheet ◽  
Jong-Seok Kim ◽  
Min-Jeong Ko ◽  
Na-Yeon Kim ◽  
Young-Jo Lim ◽  
...  
Keyword(s):  
Body Weight ◽  
Candidate Genes ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Potential Candidate ◽  
Height Ratio ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
A Genome ◽  
Insight Into

As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that help us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with enrichment analysis on 757 dogs using 118,879 SNPs. The genomic heritability (h2) was 0.33 for height and 0.28 for weight trait in Jindo. At p-value < 5 × 10−5, ten, six, thirteen and eleven SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our results, HHIP, LCORL and NCAPG for height, IGFI and FGFR3 for length, DLK1 and EFEMP1 for LHR and PTPN2, IGFI and RASAL2 for weight can be the potential candidate genes because of the significant SNPs located in their intronic or upstream regions. The gene-set enrichment analysis highlighted here nine and seven overlapping significant (p < 0.05) gene ontology (GO) terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signalling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding of the Jindo dog’s population.

scholarly journals Insight Into the Causative Genes and Pathways Associated With Height, Length, Length to Height Ratio and Body Weight Traits of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment and Pathway-based GWAS Analysis

2021 ◽  
Author(s):  
Sunirmal Sheet ◽  
Jong Seok Kim ◽  
Min Jeong Ko ◽  
Na Yeon Kim ◽  
Young Jo Lim ◽  
...  
Keyword(s):  
Body Weight ◽  
Genome Wide Association Study ◽  
Gene Set Enrichment Analysis ◽  
Potential Candidate ◽  
Economic Traits ◽  
Height Ratio ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
A Genome ◽  
Insight Into

Abstract As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Artificial breeding has produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that led us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with pathway-based analysis on 757 dogs using 118,879 SNPs. A higher heritability (h2) was detected for height (0.33) and weight (0.28) trait in Jindo. At a threshold of p-value < 5E-05, 10, 6, 13, and 11 SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our result, HHIP, LCORL, and NCAPG for height, IGFI and FGFR3 for length, DLK1 and EFEMP1 for LHR, and PTPN2, IGFI, and RASAL2 for weight can be the potential candidate genes because the significant SNPs located in their intronic or upstream regions. An additive and dominant mode of inheritance was noticed from the phenotype-genotype correlation plot for top variants. The gene-set enrichment analysis highlighted here 9 and 7 overlapping significant (p < 0.05) GO terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signaling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding /management of the Jindo dog’s population.

scholarly journals Identification of Candidate Genes and Pathways Associated with Obesity-Related Traits in Canines via Gene-Set Enrichment and Pathway-Based GWAS Analysis

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2071
Author(s):  
Sunirmal Sheet ◽  
Srikanth Krishnamoorthy ◽  
Jihye Cha ◽  
Soyoung Choi ◽  
Bong-Hwan Choi
Keyword(s):  
Body Weight ◽  
Blood Sugar ◽  
Nervous System Development ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Kegg Pathways ◽  
Gwas Analysis ◽  
A Genome ◽  
Go Terms

The present study aimed to identify causative loci and genes enriched in pathways associated with canine obesity using a genome-wide association study (GWAS). The GWAS was first performed to identify candidate single-nucleotide polymorphisms (SNPs) associated with obesity and obesity-related traits including body weight and blood sugar in 18 different breeds of 153 dogs. A total of 10 and 2 SNPs were found to be significantly (p < 3.74 × 10−7) associated with body weight and blood sugar, respectively. None of the SNPs were identified to be significantly associated with obesity trait. We subsequently followed up the GWAS analysis with gene-set enrichment and pathway analyses. A gene-set with 1057, 1409, and 1243 SNPs annotated to 449, 933 and 820 genes for obesity, body weight, and blood sugar, respectively was created by sub-setting the GWAS result at a threshold of p < 0.01 for the gene-set enrichment analysis. In total, 84 GO and 21 KEGG pathways for obesity, 114 GO and 44 KEGG pathways for blood sugar, 120 GO and 24 KEGG pathways for body weight were found to be enriched. Among the pathways and GO terms, we highlighted five enriched pathways (Wnt signaling pathway, adherens junction, pathways in cancer, axon guidance, and insulin secretion) and seven GO terms (fat cell differentiation, calcium ion binding, cytoplasm, nucleus, phospholipid transport, central nervous system development, and cell surface) that were found to be shared among all the traits. Our data provide insights into the genes and pathways associated with obesity and obesity-related traits.

scholarly journals Higher Acid-Base Imbalance Associated with Respiratory Failure Could Decrease the Survival of Patients with Scrub Typhus during Intensive Care Unit Stay: A Gene Set Enrichment Analysis

2019 ◽  
Vol 8 (10) ◽  
pp. 1580 ◽  
Author(s):  
Kyoung Min Moon ◽  
Kyueng-Whan Min ◽  
Mi-Hye Kim ◽  
Dong-Hoon Kim ◽  
Byoung Kwan Son ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Respiratory Failure ◽  
Scrub Typhus ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Acid Base ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Gene Sets

Ninety percent of patients with scrub typhus (SC) with vasculitis-like syndrome recover after mild symptoms; however, 10% can suffer serious complications, such as acute respiratory failure (ARF) and admission to the intensive care unit (ICU). Predictors for the progression of SC have not yet been established, and conventional scoring systems for ICU patients are insufficient to predict severity. We aimed to identify simple and robust indicators to predict aggressive behaviors of SC. We evaluated 91 patients with SC and 81 non-SC patients who were admitted to the ICU, and 32 cases from the public functional genomics data repository for gene expression analysis. We analyzed the relationships between several predictors and clinicopathological characteristics in patients with SC. We performed gene set enrichment analysis (GSEA) to identify SC-specific gene sets. The acid-base imbalance (ABI), measured 24 h before serious complications, was higher in patients with SC than in non-SC patients. A high ABI was associated with an increased incidence of ARF, leading to mechanical ventilation and worse survival. GSEA revealed that SC correlated to gene sets reflecting inflammation/apoptotic response and airway inflammation. ABI can be used to indicate ARF in patients with SC and assist with early detection.

scholarly journals Drug perturbation gene set enrichment analysis (dpGSEA): a new transcriptomic drug screening approach

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mike Fang ◽  
Brian Richardson ◽  
Cheryl M. Cameron ◽  
Jean-Eudes Dazard ◽  
Mark J. Cameron
Keyword(s):  
Drug Targets ◽  
T Regulatory Cells ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Regulatory Cells ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Gene Sets ◽  
Gastroenteropancreatic Neuroendocrine Tumor ◽  
Public Datasets

Abstract Background In this study, we demonstrate that our modified Gene Set Enrichment Analysis (GSEA) method, drug perturbation GSEA (dpGSEA), can detect phenotypically relevant drug targets through a unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Results We detail our dpGSEA method and show its effectiveness in detecting specific perturbation of drugs in independent public datasets by confirming fluvastatin, paclitaxel, and rosiglitazone perturbation in gastroenteropancreatic neuroendocrine tumor cells. In drug discovery experiments, we found that dpGSEA was able to detect phenotypically relevant drug targets in previously published differentially expressed genes of CD4+T regulatory cells from immune responders and non-responders to antiviral therapy in HIV-infected individuals, such as those involved with virion replication, cell cycle dysfunction, and mitochondrial dysfunction. dpGSEA is publicly available at https://github.com/sxf296/drug_targeting. Conclusions dpGSEA is an approach that uniquely enriches on drug-defined gene sets while considering directionality of gene modulation. We recommend dpGSEA as an exploratory tool to screen for possible drug targeting molecules.

scholarly journals Key pathways involved in prostate cancer based on gene set enrichment analysis and meta analysis

2011 ◽  
Vol 10 (4) ◽  
pp. 3856-3887 ◽  
Author(s):  
Q.Y. Ning ◽  
J.Z. Wu ◽  
N. Zang ◽  
J. Liang ◽  
Y.L. Hu ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Meta Analysis ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Key Pathways

scholarly journals A Novel Prognostic Model Based On Cytosolic DNA Sensing-Related Gene Signature for Pancreatic Cancer

2021 ◽  
Author(s):  
Chuan-Qi Xu ◽  
Kui-Sheng Yang ◽  
Shu-Xian Zhao ◽  
Jian Lv
Keyword(s):  
Pancreatic Cancer ◽  
Prognostic Factor ◽  
Prognostic Model ◽  
Risk Group ◽  
Enrichment Analysis ◽  
Independent Prognostic Factor ◽  
Gene Set Enrichment Analysis ◽  
Dna Sensing ◽  
Gene Set Enrichment ◽  
Gene Set

Abstract Objective: Pancreatic cancer (PC) is one of the most malignant tumors. Cytosolic DNA sensing have been found to play an essential role in tumor. In this study, a cytosolic DNA sensing-related genes (CDSRGs) signature was constructed and the potential mechanisms also been discussed.Methods: The RNA expression and clinical data of PC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Subsequently, univariate (UCR) and multivariate Cox regression (MCR) analyses were conducted to establish a prognostic model in the TCGA patients, which was verified by GEO patients. Cancer immune infiltrates were investigated via single sample gene set enrichment analysis (ssGSEA) and Tumor Immune Estimation Resource (TIMER). Finally, Gene Set Enrichment Analysis (GSEA) was used to investigate the related signaling pathways.Results: A prognostic model comprising four genes (POLR2E,IL18, MAVS, and FADD) was established. The survival rate of patients in the low-risk group was significantly higher than that of patients in the high-risk group. In addition, CDSRGs-risk score was proved as an independent prognostic factor in PC. Immune infiltrates and drug sensitivity are associated with POLR2E,IL18, MAVS, and FADD expression.Conclusions: In summary, we present and validated a CDSRGs risk model that is an independent prognostic factor and indicates the immune characteristics of PC. This prognostic model may facilitate the personalized treatment and monitoring.

scholarly journals Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma

2021 ◽  
Vol 4 (5) ◽  
pp. e201900332
Author(s):  
Elena A Afanasyeva ◽  
Moritz Gartlgruber ◽  
Tatsiana Ryl ◽  
Bieke Decaesteker ◽  
Geertrui Denecker ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Time Lapse ◽  
Dna Methyltransferases ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Risk Characteristics ◽  
Weak Points ◽  
Treatment Research ◽  
Time Lapse Imaging

The migrational propensity of neuroblastoma is affected by cell identity, but the mechanisms behind the divergence remain unknown. Using RNAi and time-lapse imaging, we show that ADRN-type NB cells exhibit RAC1- and kalirin-dependent nucleokinetic (NUC) migration that relies on several integral components of neuronal migration. Inhibition of NUC migration by RAC1 and kalirin-GEF1 inhibitors occurs without hampering cell proliferation and ADRN identity. Using three clinically relevant expression dichotomies, we reveal that most of up-regulated mRNAs in RAC1- and kalirin–GEF1–suppressed ADRN-type NB cells are associated with low-risk characteristics. The computational analysis shows that, in a context of overall gene set poverty, the upregulomes in RAC1- and kalirin–GEF1–suppressed ADRN-type cells are a batch of AU-rich element–containing mRNAs, which suggests a link between NUC migration and mRNA stability. Gene set enrichment analysis–based search for vulnerabilities reveals prospective weak points in RAC1- and kalirin–GEF1–suppressed ADRN-type NB cells, including activities of H3K27- and DNA methyltransferases. Altogether, these data support the introduction of NUC inhibitors into cancer treatment research.

scholarly journals DPYSL2 as potential diagnostic and prognostic biomarker linked to immune infiltration in lung adenocarcinoma

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Yang-Jie Wu ◽  
Ai-Tao Nai ◽  
Gui-Cheng He ◽  
Fei Xiao ◽  
Zhi-Min Li ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Roc Curve ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
List Type ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Normal Tissues ◽  
Kaplan Meier ◽  
Kaplan Meier Plotter

Abstract Background Dihydropyrimidinase like 2 (DPYSL2) has been linked to tumor metastasis. However, the function of DPSY2L in lung adenocarcinoma (LUAD) is yet to be explored. Methods Herein, we assessed DPYSL2 expression in various tumor types via online databases such as Oncomine and Tumor Immune Estimation Resource (TIMER). Further, we verified the low protein and mRNA expressions of DPYSL2 in LUAD via the ULCAN, The TCGA and GEPIA databases. We applied the ROC curve to examine the role of DPYSL2 in diagnosis. The prognostic significance of DPYSL2 was established through the Kaplan–Meier plotter and the Cox analyses (univariate and multivariate). TIMER was used to explore DPYSL2 expression and its connection to immune infiltrated cells. Through Gene Set Enrichment Analysis, the possible mechanism of DPYSL2 in LUAD was investigated. Results In this study, database analysis revealed lower DPYSL2 expression in LUAD than in normal tissues. The ROC curve suggested that expression of DPYSL2 had high diagnostic efficiency in LUAD. The DPYSL2 expression had an association with the survival time of LUAD patients in the Kaplan–Meier plotter and the Cox analyses. The results from TIMER depicted a markedly positive correlation of DPYSL2 expression with immune cells infiltrated in LUAD, such as macrophages, dendritic cells, CD4+ T cells, and neutrophils. Additionally, many gene markers for the immune system had similar positive correlations in the TIMER analysis. In Gene Set Enrichment Analysis, six immune-related signaling pathways were associated with DPYSL2. Conclusions In summary, DPYSL2 is a novel biomarker with diagnostic and prognostic potential for LUAD as well as an immunotherapy target. Highlights Expression of DPYSL2 was considerably lower in LUAD than in normal tissues. Investigation of multiple databases showed a high diagnostic value of DPYSL2 in LUAD. DPYSL2 can independently predict the LUAD outcomes. Immune-related mechanisms may be potential ways for DPYSL2 to play a role in LUAD.

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