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gene set enrichment

Karin Vanessa Carias, Rachel Wevrick
Gilles de la Tourette Syndrome (TS) is a neurodevelopmental disorder that causes children to make repeated, brief involuntary movements or sounds. TS can be co-morbid with other neurodevelopmental disorders, including autism spectrum disorder (ASD). Clusters of biologically related genes have been associated with neurodevelopmental disorders, suggesting shared pathologies. However, the genetic contribution to TS remains poorly defined. We asked whether children with both TS and ASD differed clinically from children with ASD alone, and identified potentially deleterious genetic events in children with TS and ASD...
February 7, 2019: Journal of Psychiatric Research
Yang Du, Yun Yu, Yang Hu, Xiao-Wan Li, Ze-Xu Wei, Rui-Yuan Pan, Xue-Song Li, Guang-En Zheng, Xiao-Yan Qin, Qing-Shan Liu, Yong Cheng
Genetic variants conferring risk for schizophrenia (SCZ) have been extensively studied, but the role of posttranscriptional mechanisms in SCZ is not well studied. Here we performed the first genome-wide microRNA (miRNA) expression profiling in serum-derived exosome from 49 first-episode, drug-free SCZ patients and 46 controls and identified miRNAs and co-regulated modules that were perturbed in SCZ. Putative targets of these SCZ-affected miRNAs were enriched strongly for genes that have been implicated in protein glycosylation and were also related to neurotransmitter receptor and dendrite (spine) development...
February 16, 2019: Schizophrenia Bulletin
Tong-Peng Xu, Pei Ma, Wen-Yu Wang, You Shuai, Yan-Fen Wang, Tao Yu, Rui Xia, Yong-Qian Shu
It was found in this study that long intergenic non-protein coding RNA 346 (LINC00346) was an lncRNA aberrantly expressed in gastric cancer (GC) based on multiple Gene Expression Omnibus (GEO) databases of GC cohorts. The LINC00346 gene was recurrently amplified and upregulated in GC, and its expression was positively correlated with poor pathologic stage, large tumor size, and poor prognosis. In addition, the oncogenic transcription factors KLF5 and MYC could bind to the LINC00346 promoter and enhance its expression...
February 15, 2019: Cell Death and Differentiation
Hongjuan He, Xiaojuan Zhao, Ziqing Zhu, Le Du, Erfei Chen, Shuzhen Liu, Qiqi Li, Jing Dong, Jin Yang, Lei Lei
Mutations in transforming growth factor beta receptor II (TGFBR2) are detected in up to 30% of overall colorectal cancer (CRC). Dysregulation of some microRNAs participated in the CRC pathogenesis. In this study, we used the gene ontology analyses, the Kyoto Encyclopedia of Genes and Genomes pathway analyses and gene set enrichment analysis to indicate that miR-3191 was involved in the regulation of transforming growth factor beta (TGF-BETA) signal pathway in CRC. These bioinformatics results were supported by data obtained from CRC samples and experiments in vitro...
February 15, 2019: Journal of Biochemical and Molecular Toxicology
Zhihua Gong, Qingzhu Jia, Junying Chen, Xinwei Diao, Jianbao Gao, Xinxin Wang, Bo Zhu
INTRODUCTION: Whether the efficacy of PD-1/PD-L1 inhibitors declines with senescence remains controversial for lung adenocarcinoma (LUAD). Responsiveness to anti-PD-1/PD-L1 therapy is thought to rely on neoantigen exposure and immune elements in the tumor microenvironment. In this study, we explored the features of the tumor immune microenvironment in elderly patients with treatment-naïve LUAD. METHODS: Transcriptome profiles and clinical characteristics of patients with LUAD were retrieved from TCGA as a discovery cohort...
February 12, 2019: Journal of Thoracic Oncology
Thais de Castro Barbosa, Petter S Alm, Anna Krook, Romain Barrès, Juleen R Zierath
Paternal preconceptional high-fat diet (HFD) alters whole-body glucose and energy homeostasis over several generations, which may be mediated by altered transcriptomic profiles of metabolic organs. We investigated the effect of paternal HFD on the hepatic transcriptomic and metabolic signatures of female grand-offspring. Paternal HFD strongly impacted the liver transcriptome of the second-generation offspring. Gene set enrichment analysis (GSEA) revealed grandpaternal-HFD altered the TNF-α signaling via NFκB pathway, independent of the grand-offspring's diet...
February 15, 2019: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Giovanni Scala, Angela Serra, Veer Singh Marwah, Laura Aliisa Saarimäki, Dario Greco
BACKGROUND: Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations, such as ontologies and molecular pathways. Annotating results from omics experiments into functional categories is essential not only to understand the underlying regulatory dynamics but also to compare multiple experimental conditions at a higher level of abstraction...
February 15, 2019: BMC Bioinformatics
Feng Fang, Xiaoqing Wang, Tianqiang Song
Objective: Hepatocellular carcinoma (HCC) is a common malignancy associated with high morbidity and mortality rates worldwide. Early diagnosis plays an important role in the improvement of HCC prognosis. Methods: In this study, we conducted a comprehensive analysis of HCC DNA methylation and gene expression datasets in The Cancer Genome Atlas (TCGA), to identify a prognostic signature for HCC diagnosis and survival prediction. First, we identified differential methylation CpG (dmCpG) sites in HCC samples and compared them with those in adjacent normal liver tissues; this was followed by univariate analysis and Sure Independence Screening (SIS) in the training set...
November 2018: Cancer Biology & Medicine
Xiang-Bo Ji, Jun Luo, Xiu-Li Feng, Qiu-Liang Xu, Teng Man, Dong Zhao, Xin-Feng Li, Gai-Ping Zhang, Pu-Yan Chen
Background: In the recent past, many studies have been focused on extracts of BF and multiple biologically active factors and their effects on humoral immune system in chickens and birds. However, the mechanism of those immunomodulatory peptides on the B lineage cells proliferation and antibody production in chicken is fairly unknown. DT40 cell line, an avian leucosis virus-induced chicken pre-B cell line, expresses immunoglobulin M (IgM) isotype B cell reporter in the plasma membrane...
December 2018: African Health Sciences
Michihiro Ito, Kotaro Watanabe, Toru Maruyama, Tetsushi Mori, Kentaro Niwa, Seinen Chow, Haruko Takeyama
Gut bacteria of phytophagous and omnivorous marine invertebrates often possess alginate lyases (ALGs), which are key enzymes for utilizing macroalgae as carbon neutral biomass. We hypothesized that the exclusive feeding of a target alga to marine invertebrates would shift the gut bacterial diversity suitable for degrading the algal components. To test this hypothesis, we reared sea hare (Dolabella auricularia) and sea snail (Batillus cornutus) for two to four weeks with exclusive feeding of a brown alga (Ecklonia cava)...
February 14, 2019: Scientific Reports
Maud Plantinga, Colin G de Haar, Ester Dünnebach, Denise A M H van den Beemt, Kitty W M Bloemenkamp, Michal Mokry, Jaap Jan Boelens, Stefan Nierkens
Dendritic cells (DCs) are professional antigen-presenting cells which instruct both the innate and adaptive immune systems. Once mature, they have the capacity to activate and prime naïve T cells for recognition and eradication of pathogens and tumor cells. These characteristics make them excellent candidates for vaccination strategies. Most DC vaccines have been generated from ex vivo culture of monocytes (mo). The use of mo-DCs as vaccines to induce adaptive immunity against cancer has resulted in clinical responses but, overall, treatment success is limited...
February 5, 2019: Cancers
Yuanhui Qi, Qiying Yi, Yamin Liu, Yanxia Hu, Dongshen Ni, Jianing Liu, Qin Zhou, Yajun Xie
Glucocorticoid hormones have been widely used in clinical practice as potent anti-inflammatory and immunosuppressive agents. However, the underlying mechanisms of how they work remain unaddressed. Here, we used RNA-set to profile spleen gene expression in adult mice after consistent intraperitoneal injection of dexamethasone. We identified 13565 genes in control (injected with 0.9% NaCl) and 13702 genes in dexamethasone-injected group, 12920 genes were expressed in both, but 645 genes were identified only in control and 782 genes were identified only in the dexamethasone group...
February 11, 2019: Gene
Ingeborg E de Kruijff, Anieta M Sieuwerts, Wendy Onstenk, Agnes Jager, Paul Hamberg, Felix E de Jongh, Marcel Smid, J Kraan, Mieke A Timmermans, John W M Martens, Stefan Sleijfer
The androgen receptor (AR) has potential clinical relevance in metastatic breast cancer (mBC) since it might be a treatment target and has been associated with endocrine resistance. A minimal-invasive way to determine AR expression on metastatic tumor cells is by characterization of circulating tumor cells (CTCs). Here, we assessed AR mRNA expression in CTCs (CTC-AR) and in matched primary tumor samples from mBC patients representing different breast cancer subtypes. In addition, we explored CTC-AR-status in relation to outcome on endocrine therapy...
February 13, 2019: International Journal of Cancer. Journal International du Cancer
Mengru Zeng, Jialu Liu, Wenxia Yang, Shumin Zhang, Fuyou Liu, Zheng Dong, Youming Peng, Lin Sun, Li Xiao
Diabetic nephropathy (DN) is a primary cause of renal failure. However, studies providing renal gene expression profiles of diabetic tubulointerstitial injury are scarce and its molecular mechanisms still await clarification. To identify vital genes involved in the diabetic tubulointerstitial injury, three microarray data sets from gene expression omnibus (GEO) were downloaded. A total of 127 differentially expressed genes (DEGs) were identified by limma package. Gene set enrichment analysis (GSEA) plots showed that sister chromatid cohesion was the most significant enriched gene set positively correlated with the DN group while retinoid X receptor binding was the most significant enriched gene set positively correlated with the control group...
February 13, 2019: Journal of Cellular Physiology
Dasheng Liu, David Horvath, Peng Li, Wenmin Liu
Alternanthera philoxeroides recently expanded its range northwards in China. It is unknown if the range expansion has a genetic and/or epigenetic basis, or merely an environmental basis due to a warming climate. To test these possibilities, we used an RNAseq approach with a common greenhouse design to examine gene expression in individuals from the northern edge and central portion of alligator weed range from China to determine if there were differences in their responses to cold temperatures. We hypothesized that if the recent range expansion was primarily environmental, we would observe few differences or only differences unrelated to low-temperature adaptations...
2019: Frontiers in Plant Science
Jacques Bietrix, Camille Kolenda, Anaïs Sapin, Marisa Haenni, Jean-Yves Madec, Michèle Bes, Céline Dupieux, Jason Tasse, Fréderic Laurent
Background: Methicillin resistance in Staphylococcus aureus (MRSA) is classically conferred by the acquisition of the mec A gene encoding an additional penicillin binding protein with low affinity for beta-lactams. A mec A variant, named mec C, was described in 2011. MRSA isolates harboring mec C of both animal and human origin have since been collected in different European countries. In France, animal cases were reported in 4 dairy farms between 2008 and 2013 in the Meurthe-et-Moselle county, all located in a 30 km perimeter, suggesting a possible dissemination of mec C-positive MRSA strains...
2019: Frontiers in Microbiology
Marta Farré, Jaebum Kim, Anastasia A Proskuryakova, Yang Zhang, Anastasia I Kulemzina, Qiye Li, Yang Zhou, Yingqi Xiong, Jennifer L Johnson, Polina Perelman, Warren E Johnson, Wesley C Warren, Anna V Kukekova, Guojie Zhang, Stephen J O'Brien, Oliver A Ryder, Alexander S Graphodatsky, Jian Ma, Harris A Lewin, Denis M Larkin
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls, was characterized by mostly intrachromosomal changes while the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes...
February 13, 2019: Genome Research
Sandi A Kwee, Maarit Tiirikainen, Miles M Sato, Jared D Acoba, Runmin Wei, Wei Jia, Loic Le Marchand, Linda L Wong
Studies involving transcriptomics have revealed multiple molecular subtypes of hepatocellular carcinoma (HCC). PET/CT has also identified distinct molecular imaging subtypes, including those with increased and decreased choline metabolism as measured by tissue uptake of the radiopharmaceutical 18F-flurocholine. Gene signatures reflecting the molecular heterogeneity of HCC may identify the biological and clinical significance of these imaging subtypes. In this study, 41 patients underwent 18F-fluorocholine PET/CT followed by tumor resection and gene expression profiling...
February 13, 2019: Cancer Research
Sunjoo Bang, Sangjoon Son, Sooyoung Kim, Hyunjung Shin
BACKGROUND: Biomarker discovery studies have been moving the focus from a single target gene to a set of target genes. However, the number of target genes in a drug should be minimum to avoid drug side-effect or toxicity. But still, the set of target genes should effectively block all possible paths of disease progression. METHODS: In this article, we propose a network based computational analysis for target gene identification for multi-target drugs. The min-cut algorithm is employed to cut all the paths from onset genes to apoptotic genes on a disease pathway...
February 13, 2019: BMC Bioinformatics
Martin Porsch, Esra Özdemir, Martin Wisniewski, Sebastian Graf, Fabian Bull, Katrin Hoffmann, Atanas Ignatov, Johannes Haybaeck, Ivo Große, Thomas Kalinski, Norbert Nass
Acquired tamoxifen resistance is a persistent problem for the treatment of estrogen receptor positive, premenopausal breast cancer patients and predictive biomarkers are still elusive. We here analyzed gene expression changes in a cellular model to identify early and late changes upon tamoxifen exposure and thereby novel prognostic biomarkers. Estrogen receptor positive MCF-7 cells were incubated with 4OH-tamoxifen (10 nM) and gene expression analyzed by array hybridization during 12 weeks. Array results were confirmed by nCounter- and qRT-PCR technique...
February 13, 2019: RNA Biology
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