scholarly journals High TNFRSF12A level associated with MMP-9 overexpression is linked to poor prognosis in breast cancer: Gene set enrichment analysis and validation in large-scale cohorts

PLoS ONE ◽  
2018 ◽  
Vol 13 (8) ◽  
pp. e0202113 ◽  
Author(s):  
Jungho Yang ◽  
Kyueng-Whan Min ◽  
Dong-Hoon Kim ◽  
Byoung Kwan Son ◽  
Kyoung Min Moon ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Poor Prognosis ◽  
Large Scale ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Cancer Gene ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Breast Cancer Gene

scholarly journals m6A-Mediated Tumor Invasion and Methylation Modification in Breast Cancer Microenvironment

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Fei Liu ◽  
Xiaopeng Yu ◽  
Guijin He
Keyword(s):  
Breast Cancer ◽  
Tumor Microenvironment ◽  
Immune Cell ◽  
Principal Component ◽  
Enrichment Analysis ◽  
Genomic Variation ◽  
Gene Set Enrichment Analysis ◽  
Single Sample ◽  
Gene Set Enrichment ◽  
Gene Set

Background. We analyzed the n6-methyladenosine (m6A) modification patterns of immune cells infiltrating the tumor microenvironment of breast cancer (BC) to provide a new perspective for the early diagnosis and treatment of BC. Methods. Based on 23 m6A regulatory factors, we identified m6A-related gene characteristics and m6A modification patterns in BC through unsupervised cluster analysis. To examine the differences in biological processes among various m6A modification modes, we performed genomic variation analysis. We then quantified the relative infiltration levels of different immune cell subpopulations in the tumor microenvironment of BC using the CIBERSORT algorithm and single-sample gene set enrichment analysis. Univariate Cox analysis was used to screen for m6A characteristic genes related to prognosis. Finally, we evaluated the m6A modification pattern of patients with a single BC by constructing the m6Ascore based on principal component analysis. Results. We identified three different m6A modification patterns in 2128 BC samples. A higher abundance of the immune infiltration of the m6Acluster C was indicated by the results of CIBERSORT and the single-sample gene set enrichment analysis. Based on the m6A characteristic genes obtained through screening, the m6Ascore was determined. The BC patients were segregated into m6Ascore groups of low and high categories, which revealed significant survival benefits among patients with low m6Ascores. Additionally, the high-m6Ascore group had a higher mutation frequency and was associated with low PD-L1 expression, and the m6Ascore and tumor mutation burden showed a positive correlation. In addition, treatment effects were better in patients in the high-m6Ascore group. Conclusions. In case of a single patient with BC, the immune cell infiltration characteristics of the tumor microenvironment and the m6A methylation modification pattern could be evaluated using the m6Ascore. Our results provide a foundation for improving personalized immunotherapy of BC.

scholarly journals Overexpression of CENPF correlates with poor prognosis and tumor bone metastasis in breast cancer

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Jingbo Sun ◽  
Jingzhan Huang ◽  
Jin Lan ◽  
Kun Zhou ◽  
Yuan Gao ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Bone Metastasis ◽  
Western Blot ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Free Survival ◽  
Gene Set ◽  
Oncomine Database ◽  
Kaplan Meier

Abstract Background Centromere Protein F (CENPF) associates with the centromere–kinetochore complex and influences cell proliferation and metastasis in several cancers. The role of CENPF in breast cancer (BC) bone metastasis remains unclear. Methods Using the ONCOMINE database, we compared the expression of CENPF in breast cancer and normal tissues. Findings were confirmed in 60 BC patients through immunohistochemical (IHC) staining. Microarray data from GEO and Kaplan–Meier plots were used analyze the overall survival (OS) and relapse free survival (RFS). Using the GEO databases, we compared the expression of CENPF in primary lesions, lung metastasis lesions and bone metastasis lesions, and validated our findings in BALB/C mouse 4T1 BC models. Based on gene set enrichment analysis (GSEA) and western blot, we predicted the mechanisms by which CENPF regulates BC bone metastasis. Results The ONCOMINE database and immunohistochemical (IHC) showed higher CENPF expression in BC tissue compared to normal tissue. Kaplan–Meier plots also revealed that high CENPF mRNA expression correlated to poor survival and shorter progression-free survival (RFS). From BALB/C mice 4T1 BC models and the GEO database, CENPF was overexpressed in primary lesions, other target organs, and in bone metastasis. Based on gene set enrichment analysis (GSEA) and western blot, we predicted that CENPF regulates the secretion of parathyroid hormone-related peptide (PTHrP) through its ability to activate PI3K–AKT–mTORC1. Conclusion CENPF promotes BC bone metastasis by activating PI3K–AKT–mTORC1 signaling and represents a novel therapeutic target for BC treatment.

scholarly journals Concordant integrative gene set enrichment analysis of multiple large-scale two-sample expression data sets

BMC Genomics ◽  
2014 ◽  
Vol 15 (Suppl 1) ◽  
pp. S6 ◽  
Author(s):  
Yinglei Lai ◽  
Fanni Zhang ◽  
Tapan K Nayak ◽  
Reza Modarres ◽  
Norman H Lee ◽  
...  
Keyword(s):  
Large Scale ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Data Sets ◽  
Expression Data ◽  
Gene Set Enrichment ◽  
Gene Set

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
Sign in / Sign up

Export Citation Format

Share Document