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gene set enrichment

Peng Xu, Guofeng Zhang, Shuangxing Hou, Long-Gui Sha
OBJECTIVE: In this study, we aimed to evaluate the expression and functions of MAPK8 in temozolomide (TMZ) -resistant glioblastoma cells as well as to explore the mechanism of TMZ resistance in glioblastoma cells. METHODS: Gene Expression Omnibus (GEO) database was used for identifying the differentially expressed genes (DEGs) in TMZ resistant samples. The functional partner genes of TMZ were screened out by Gene-drug interaction network (STITCH) and the glioblastoma-related genes were selected by gene search engine with evidence sentences (Digsee)...
July 23, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Xing Liu, Yiming Li, Zhiyan Sun, Shaowu Li, Kai Wang, Xing Fan, Yuqing Liu, Lei Wang, Yinyan Wang, Tao Jiang
The presence of contrast enhancement (CE) on magnetic resonance (MR) imaging is conventionally regarded as an indicator for tumor malignancy. However, the biological behaviors and molecular mechanism of enhanced tumor are not well illustrated. The aim of this study was to investigate the molecular profiles associated with anaplastic gliomas (AGs) presenting CE on postcontrast T1-weighted MR imaging. In this retrospective database study, RNA sequencing and MR imaging data of 91 AGs from the Cancer Genome Atlas (TCGA) and 64 from the Chinese Glioma Genome Atlas (CGGA) were collected...
August 16, 2018: Cancer Medicine
Huiling Xue, Zhe Wang, Yongjie Hua, Shanshan Ke, Yao Wang, Junpeng Zhang, Yi-Hsuan Pan, Wenjie Huang, David M Irwin, Shuyi Zhang
Beige adipocytes can be induced from white adipocytes and precursors upon stimulation by cold temperatures and act like brown adipocytes to increase energy expenditure. Most in vivo studies examining the mechanisms for the induction of beige adipocytes have focused on subcutaneous white adipose tissue (sWAT; benign fat) in the mouse. How intra-abdominal WAT (aWAT; malignant fat) develops into beige adipocytes remains obscure, largely because there is a lack of a good animal model for the induction of beige adipocytes from aWAT...
July 2018: Science Advances
Yonghua Bao, Yongchen Guo, Yiqiong Yang, Xiaonan Wei, Shanshan Zhang, Yongmeng Zhang, Kai Li, Ming Yuan, Dongli Guo, Virgilia Macias, Xiangdong Zhu, Wei Zhang, Wancai Yang
The serine protease PRSS8 has shown important physiological and pathological functions, but its roles in cancer initiation and progression are unclear. We developed and dynamically characterized a conditional knockout Prss8fl/fl , p-Villin-Cre+ mouse model. We found that genetic deficiency of the Prss8 gene caused spontaneous colitis and an inflamed rectum at an early age and caused intestinal tumors at a late age, which were linked to increased intestinal cell proliferation and migration but decreased cell differentiation...
August 16, 2018: Oncogene
Jubao Duan, Harald H H Göring, Alan R Sanders, Winton Moy, Jessica Freda, Eugene I Drigalenko, Mark Kos, Deli He, Pablo V Gejman
The dopaminergic hypothesis of schizophrenia (SZ) postulates that dopaminergic over activity causes psychosis, a central feature of SZ, based on the observation that blocking dopamine (DA) improves psychotic symptoms. DA is known to have both receptor- and non-receptor-mediated effects, including oxidative mechanisms that lead to apoptosis. The role of DA-mediated oxidative processes in SZ has been little studied. Here, we have used a cell perturbation approach and measured transcriptomic profiles by RNAseq to study the effect of DA exposure on transcription in B-cell transformed lymphoblastoid cell lines (LCLs) from 514 SZ cases and 690 controls...
August 16, 2018: Translational Psychiatry
Yu Feng Zhu, Ming Dong
BACKGROUND: Colorectal cancer (CRC) is one of the most common cancers worldwide. Tumor suppressor candidate 3 (TUSC3) has been reported be associated with embryogenesis and metabolism. The aim of this study is to investigate the expression of TUSC3 in CRC tissues, and to evaluate the clinical pathological characters and prognostic significance. METHOD: First, we performed a bioinformatics analysis by using Oncomine and COEXPEDIA databases. Gene Set Enrichment Analysis (GSEA) was performed using TCGA data set...
July 17, 2018: Pathology, Research and Practice
Victor F Oliveira, Lauro A G Moares, Ester A Mota, Liana K Jannotti-Passos, Paulo M Z Coelho, Ana C A Mattos, Flávia F B Couto, Brian E Caffrey, Annalisa Marsico, Renata Guerra-Sá
Long noncoding RNAs (lncRNAs) are transcripts generally longer than 200 nucleotides with no or poor protein coding potential, and most of their functions are also poorly characterized. Recently, an increasing number of studies have shown that lncRNAs can be involved in various critical biological processes such as organism development or cancer progression. Little, however, is known about their effects in helminths parasites, such as Schistosoma mansoni . Here, we present a computational pipeline to identify and characterize lncRNAs from RNA-seq data with high confidence from S...
2018: BioMed Research International
Matthew J Cecchini, Karishma Hosein, Christopher J Howlett, Mariamma Joseph, Marco Mura
BACKGROUND: The clinical-radiographic distinction between idiopathic pulmonary fibrosis (IPF) and non-specific interstitial pneumonia (NSIP) is challenging. We sought to investigate the gene expression profiles of IPF and NSIP vs. normal controls. METHODS: Gene expression from explanted lungs of patients with IPF (n = 22), NSIP (n = 10) and from normal controls (n = 11) was assessed. Microarray analysis included Significance Analysis of Microarray (SAM), Ingenuity Pathway, Gene-Set Enrichment and unsupervised hierarchical clustering analyses...
August 15, 2018: Respiratory Research
F M Rezende, G O Dietsch, F Peñagaricano
The service sire has been recognized as an important factor affecting herd fertility in dairy cattle. Recent studies suggest that genetic factors explain part of the difference in fertility among Holstein sires. The main objective of this study was to dissect the genetic architecture of sire fertility in US Jersey cattle. The dataset included 1.5 K Jersey bulls with sire conception rate (SCR) records and 96 K single nucleotide polymorphism (SNP) markers spanning the whole genome. The analysis included whole-genome scans for both additive and non-additive effects and subsequent functional enrichment analyses using KEGG Pathway, Gene Ontology (GO) and Medical Subject Headings (MeSH) databases...
August 14, 2018: Animal Genetics
Yifei Dai, Liang Sun, Weijie Qiang
Currently, cancer has become one of the major refractory diseases threatening human health. Complementary and alternative medicine (CAM) has gradually become an alternative choice for patients, which can be attributed to the high cost of leading cancer treatments (including surgery, radiotherapy, and chemotherapy) and the severe related adverse effects. As a critical component of CAM, traditional Chinese medicine (TCM) has increasing application in preventing and treating cancer over the past few decades. Huanglian Jiedu Decoction (HJD), a classical Chinese compound formula, has been recognized to exert a beneficial effect on cancer treatment, with few adverse effects reported...
2018: Evidence-based Complementary and Alternative Medicine: ECAM
Chenggong Hu, Yongfang Zhou, Chang Liu, Yan Kang
A risk assessment model was constructed using differentially expressed long non‑coding (lnc)RNAs for the prognosis of glioma. Transcriptome sequencing of the lncRNAs and mRNAs from glioma samples were obtained from the TCGA database. The samples were divided into bad and good prognosis groups based on survival time, then differently expressed lncRNAs between these two groups were screened using DEseq and edgeR packages. Multivariate Cox regression analysis was performed to establish a risk assessment system according to the weighted regression coefficient of lncRNA expression...
August 10, 2018: Oncology Reports
Jie Liu, Qi Wang, Rongrong Zhang, Chu Zhang, Jihui Lin, Xiaojie Huang
Endometriosis affects 6‑10% of women of reproductive age. Though a significant amount of research has explored the pathogenesis of endometriosis, little is clear. Elucidating the mechanisms is urgently required for improving the therapeutic efficiency of endometriosis treatment. Long non‑coding RNAs (lncRNAs) have recently acquired extensive attention as regulatory components in a variety of biological processes and diseases. However, the functions of many lncRNAs in endometriosis are poorly understood...
August 14, 2018: Molecular Medicine Reports
Yan-Yan Li, Chun Yang, Pingting Zhou, Shijie Zhang, Yuan Yao, Dong Li
Lung cancer is one of the most malignant cancers worldwide, and lung adenocarcinoma (LAC) remains the most common histologic subtype. However, the functional significance of RNA expression-based prognosis prediction in LAC is still unclear and needs to be further studied. By utilizing the Cox multivariate regression, we established a risk score staging system to predict the outcome of patients with LAC and subsequently identified 10 genes, including PTPRH, OGFRP1, LDHA, AL365203.1, LINC02178, AL512488.1, LINC01312, AL353746...
August 13, 2018: Journal of Cellular Biochemistry
Abdel G Elkahloun, Yara Rodriguez, Seham Alaiyed, Erin Wenzel, Juan M Saavedra
The Angiotensin II Receptor Blocker (ARB) Telmisartan reduces inflammation through Angiotensin II AT1 receptor blockade and peroxisome proliferator-activated receptor gamma (PPARγ) activation. However, in a mouse microglia-like BV2 cell line, imitating primary microglia responses with high fidelity and devoid of AT1 receptor gene expression or PPARγ activation, Telmisartan reduced gene expression of pro-injury factors, enhanced that of anti-inflammatory genes, and prevented LPS-induced increase in inflammatory markers...
August 13, 2018: Molecular Neurobiology
Hongyan Ren, Chiara Fabbri, Rudolf Uher, Marcella Rietschel, Ole Mors, Neven Henigsberg, Joanna Hauser, Astrid Zobel, Wolfgang Maier, Mojca Z Dernovsek, Daniel Souery, Annamaria Cattaneo, Gerome Breen, Ian W Craig, Anne E Farmer, Peter McGuffin, Cathryn M Lewis, Katherine J Aitchison
A key feature of major depressive disorder (MDD) is anhedonia, which is a predictor of response to antidepressant treatment. In order to shed light on its genetic underpinnings, we conducted a genome-wide association study (GWAS) followed by investigation of biological pathway enrichment using an anhedonia dimension for 759 patients with MDD in the GENDEP study. The GWAS identified 18 SNPs associated at genome-wide significance with the top one being an intronic SNP (rs9392549) in PRPF4B (pre-mRNA processing factor 4B) located on chromosome 6 (P = 2...
August 13, 2018: Translational Psychiatry
Olivia Molenda, Shuiquan Tang, Line Lomheim, Vasu K Gautam, Sofia Lemak, Alexander F Yakunin, Karen L Maxwell, Elizabeth A Edwards
Dehalococcoides mccartyi are obligate organohalide-respiring bacteria that play an important detoxifying role in the environment. They have small genomes (~1.4 Mb) with a core region interrupted by two high plasticity regions (HPRs) containing dozens of genes encoding reductive dehalogenases involved in organohalide respiration. The genomes of eight new strains of D. mccartyi were closed from metagenomic data from a related set of enrichment cultures, bringing the total number of genomes to 24. Two of the newly sequenced strains and three previously sequenced strains contain CRISPR-Cas systems...
August 13, 2018: ISME Journal
Rebecca A G De Souza, Natalia Kosior, Sarah B Thomson, Anthony Mathelier, Allen W Zhang, Kristina Bečanović, Wyeth W Wasserman, Blair R Leavitt
BACKGROUND: Huntington's disease is a late onset neurological disorder caused by a trinucleotide CAG repeat expansion mutation in the HTT gene encoding for the protein huntingtin. Despite considerable ongoing research, the wild-type function of huntingtin is not yet fully understood. OBJECTIVE: To improve knowledge of HTT gene regulation at the transcriptional level and inform future studies aimed at uncovering the HTT gene's normal function. METHODS: The HTT gene region was functionally characterized through an in silico analysis using publicly available data sets...
2018: Journal of Huntington's Disease
Z S Wallace, S B Rosenthal, K M Fisch, T Ideker, R Sasik
Motivation: Modern biological experiments often produce candidate lists of genes presumably related to the studied phenotype. One can ask if the gene list as a whole makes sense in the context of existing knowledge: Are the genes in the list reasonably related to each other or do they look like a random assembly? There are also situations when one wants to know if two or more gene sets are closely related. Gene enrichment tests based on counting the number of genes two sets have in common are adequate if we presume that two genes are related only when they are in fact identical...
August 9, 2018: Bioinformatics
Christina K Cajigas-Du Ross, Shannalee R Martinez, Leanne Woods-Burnham, Alfonso M Durán, Sourav Roy, Anamika Basu, Joshua A Ramirez, Greisha L Ortiz-Hernández, Leslimar Ríos-Colón, Evgeny Chirshev, Evelyn S Sanchez-Hernandez, Ubaldo Soto, Celine Greco, Claude Boucheix, Xin Chen, Juli Unternaehrer, Charles Wang, Carlos A Casiano
Patients with metastatic castration-resistant prostate cancer (mCRPC) develop resistance to conventional therapies including docetaxel (DTX). Identifying molecular pathways underlying DTX resistance is critical for developing novel combinatorial therapies to prevent or reverse this resistance. To identify transcriptomic signatures associated with acquisition of chemoresistance we profiled gene expression in DTX-sensitive and -resistant mCRPC cells using RNA sequencing (RNA-seq). PC3 and DU145 cells were selected for DTX resistance and this phenotype was validated by immunoblotting using DTX resistance markers (e...
July 13, 2018: Oncotarget
Zhiyu Dong, Junwen Wang, Tingting Zhan, Shuchang Xu
Purpose: Esophageal adenocarcinoma (EAC) is the most common type of esophageal cancer in Western countries. It is usually detected at an advanced stage and has a poor prognosis. The aim of this study was to identify key genes and miRNAs in EAC. Methods: The mRNA microarray data sets GSE1420, GSE26886, and GSE92396 and miRNA data set GSE16456 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were obtained using R software...
2018: OncoTargets and Therapy
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