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gene expression meta analysis

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https://www.readbyqxmd.com/read/29470489/integration-of-machine-learning-and-meta-analysis-identifies-the-transcriptomic-bio-signature-of-mastitis-disease-in-cattle
#1
Somayeh Sharifi, Abbas Pakdel, Mansour Ebrahimi, James M Reecy, Samaneh Fazeli Farsani, Esmaeil Ebrahimie
Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in dairy cattle. Rapid detection of this disease is so important in order to prevent transmission to other cows and helps to reduce inappropriate use of antibiotics. With the rapid progress in high-throughput technologies, and accumulation of various kinds of '-omics' data in public repositories, there is an opportunity to retrieve, integrate, and reanalyze these resources to improve the diagnosis and treatment of different diseases and to provide mechanistic insights into host resistance in an efficient way...
2018: PloS One
https://www.readbyqxmd.com/read/29467826/a-novel-joint-analysis-framework-improves-identification-of-differentially-expressed-genes-in-cross-disease-transcriptomic-analysis
#2
Wenyi Qin, Hui Lu
Motivation: Detecting differentially expressed (DE) genes between disease and normal control group is one of the most common analyses in genome-wide transcriptomic data. Since most studies don't have a lot of samples, researchers have used meta-analysis to group different datasets for the same disease. Even then, in many cases the statistical power is still not enough. Taking into account the fact that many diseases share the same disease genes, it is desirable to design a statistical framework that can identify diseases' common and specific DE genes simultaneously to improve the identification power...
2018: BioData Mining
https://www.readbyqxmd.com/read/29464044/the-transcriptional-and-mutational-landscapes-of-lipid-metabolism-related-genes-in-colon-cancer
#3
Lara P Fernández, Ricardo Ramos-Ruiz, Jesús Herranz, Roberto Martín-Hernández, Teodoro Vargas, Marta Mendiola, Laura Guerra, Guillermo Reglero, Jaime Feliu, Ana Ramírez de Molina
Metabolic alterations encountered in tumors are well recognized and considered as a hallmark of cancer. In addition to Warburg Effect, epidemiological and experimental studies support the crucial role of lipid metabolism in colorectal cancer (CRC). The overexpression of four lipid metabolism-related genes ( ABCA1, ACSL1, AGPAT1 and SCD genes) has been proposed as prognostic marker of stage II CRC (ColoLipidGene signature). In order to explore in depth the transcriptomic and genomic scenarios of ABCA1 , ACSL1 , AGPAT1 and SCD genes, we performed a transcriptomic meta-analysis in more than one thousand CRC individuals...
January 19, 2018: Oncotarget
https://www.readbyqxmd.com/read/29459679/meta-analysis-of-genome-wide-association-studies-for-cattle-stature-identifies-common-genes-that-regulate-body-size-in-mammals
#4
Aniek C Bouwman, Hans D Daetwyler, Amanda J Chamberlain, Carla Hurtado Ponce, Mehdi Sargolzaei, Flavio S Schenkel, Goutam Sahana, Armelle Govignon-Gion, Simon Boitard, Marlies Dolezal, Hubert Pausch, Rasmus F Brøndum, Phil J Bowman, Bo Thomsen, Bernt Guldbrandtsen, Mogens S Lund, Bertrand Servin, Dorian J Garrick, James Reecy, Johanna Vilkki, Alessandro Bagnato, Min Wang, Jesse L Hoff, Robert D Schnabel, Jeremy F Taylor, Anna A E Vinkhuyzen, Frank Panitz, Christian Bendixen, Lars-Erik Holm, Birgit Gredler, Chris Hozé, Mekki Boussaha, Marie-Pierre Sanchez, Dominique Rocha, Aurelien Capitan, Thierry Tribout, Anne Barbat, Pascal Croiseau, Cord Drögemüller, Vidhya Jagannathan, Christy Vander Jagt, John J Crowley, Anna Bieber, Deirdre C Purfield, Donagh P Berry, Reiner Emmerling, Kay-Uwe Götz, Mirjam Frischknecht, Ingolf Russ, Johann Sölkner, Curtis P Van Tassell, Ruedi Fries, Paul Stothard, Roel F Veerkamp, Didier Boichard, Mike E Goddard, Ben J Hayes
Stature is affected by many polymorphisms of small effect in humans1 . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3 . Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10-8 ) explained at most 13...
February 19, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29451302/comparing-cytotoxic-backbones-for-first-line-trastuzumab-containing-regimens-in-her2-positive-advanced-esophagogastric-cancer-a-meta-analysis
#5
Emil Ter Veer, Aafke Creemers, Laura de Waal, Martijn G H van Oijen, Hanneke W M van Laarhoven
According to the ToGA study, trastuzumab plus cisplatin and capecitabine/5-fluorouracil (5-FU) is standard first-line treatment for HER2-positive advanced esophagogastric cancer. We examined the relative efficacy and safety of alternative trastuzumab-based cytotoxic backbone regimens compared to the standard ToGA regimen using meta-analysis. We searched Medline, EMBASE, CENTRAL and ASCO and ESMO up to March 2017 for studies investigating alternative first-line trastuzumab-based regimens for HER2-positive esophagogastric cancer, defined as high protein expression IHC3+ or IHC2+ and gene amplification by in-situ-hybridisation...
February 16, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29444152/the-interaction-between-cannabis-use-and-the-val158met-polymorphism-of-the-comt-gene-in-psychosis-a-transdiagnostic-meta-analysis
#6
Thomas Stephanus Johannes Vaessen, Lea de Jong, Annika Theresia Schäfer, Thomas Damen, Aniek Uittenboogaard, Pauline Krolinski, Chinyere Vicky Nwosu, Florentina Maria Egidius Pinckaers, Iris Leah Marije Rotee, Antonius Petrus Wilhelmus Smeets, Ayşegül Ermiş, James L Kennedy, Dorien H Nieman, Arun Tiwari, Jim van Os, Marjan Drukker
BACKGROUND: Neither environmental nor genetic factors are sufficient to predict the transdiagnostic expression of psychosis. Therefore, analysis of gene-environment interactions may be productive. OBJECTIVE: A meta-analysis was performed using papers investigating the interaction between cannabis use and catechol-O-methyl transferase (COMT) polymorphism Val158Met (COMTVal158Met). DATA SOURCES: PubMed, Embase, PsychInfo. STUDY ELIGIBILITY CRITERIA: All observational studies assessing the interaction between COMTVal158Met and cannabis with any psychosis or psychotic symptoms measure as an outcome...
2018: PloS One
https://www.readbyqxmd.com/read/29440914/associations-between-abcg2-gene-polymorphisms-and-gefitinib-toxicity-in-non-small-cell-lung-cancer-a-meta-analysis
#7
Lina Tang, Chunling Zhang, Hairong He, Zhenyu Pan, Di Fan, Yinli He, Haisheng You, Yuanjie Li
Background: Gefitinib is frequently used to treat patients with non-small cell lung cancer (NSCLC) and is excreted out from cells via the ATP-binding cassette transporter ABCG2. ABCG2 gene polymorphisms have been suggested to be associated with ABCG2 protein expression and function and may influence the risk of gefitinib toxicity in NSCLC patients. Previous studies on the associations between ABCG2 gene polymorphisms and the toxicity of gefitinib in NSCLC patients have produced conflicting results...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29436659/cholangiocarcinoma%C3%A2-associated-genes-identified-by-integrative-analysis-of-gene-expression-data
#8
Wei Zhong, Lianzhi Dai, Jing Liu, Song Zhou
Cholangiocarcinoma (CCA) is characterized by delayed diagnosis and poor survival rate. Research efforts have focused on novel diagnostic technologies for this type of cancer. Transcriptomic microarray technology is a useful research strategy for investigating the molecular properties of CCA. The objective of the present study was to identify candidate biomarkers with high potential for clinical application in CCA using a meta‑analysis‑based approach. Gene expression profiles of CCA were downloaded from the Gene Expression Omnibus database for integrated analysis...
February 12, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29435194/mirna-dysregulation-and-the-risk-of-metastasis-and-invasion-in-papillary-thyroid-cancer-a-systematic-review-and-meta-analysis
#9
REVIEW
Tiantian Wang, Hao Xu, Ming Qi, Sheng Yan, Xingsong Tian
Thyroid cancer (TC) is the most common endocrine malignancy, with an incidence continuing to grow every year. Although thyroid cancer as a whole is generally indolent and relatively easy to treat, some subtypes carry a higher rate of metastasis and cancer-related mortality. A growing number of studies have focused on the dysregulation of miRNAs in TC. However, differences in methods make comparison of gene profiling data difficult. A meta-analysis of published studies comparing miRNA expression data of invasive thyroid carcinoma with paired non-invasive tumors or normal tissues was performed by searching the literature for "invasion", "thyroid cancer", and "miRNA"...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29434863/identification-of-common-key-genes-in-breast-lung-and-prostate-cancer-and-exploration-of-their-heterogeneous-expression
#10
Richa K Makhijani, Shital A Raut, Hemant J Purohit
Cancer is one of the leading causes of mortality worldwide, and in particular, breast cancer in women, prostate cancer in men, and lung cancer in both women and men. The present study aimed to identify a common set of genes which may serve as indicators of important molecular and cellular processes in breast, prostate and lung cancer. Six microarray gene expression profile datasets [GSE45827, GSE48984, GSE19804, GSE10072, GSE55945 and GSE26910 (two datasets for each cancer)] and one RNA-Seq expression dataset (GSE62944 including all three cancer types), were downloaded from the Gene Expression Omnibus database...
February 2018: Oncology Letters
https://www.readbyqxmd.com/read/29432976/epigenomic-and-genomic-landscape-of-drosophila-melanogaster-heterochromatic-genes
#11
Parna Saha, Divya Tej Sowpati, Rakesh K Mishra
Heterochromatin is associated with transcriptional repression. In contrast, several genes in the pericentromeric regions of Drosophila melanogaster are dependent on this heterochromatic environment for their expression. Here we present a comprehensive analysis of the epigenetic landscape of heterochromatic genes across all the developmental stages of Drosophila using the available histone modification and expression data from modENCODE. We find that heterochromatic genes exhibit combinations of active and inactive histone marks that correspond to their level of expression during development...
February 9, 2018: Genomics
https://www.readbyqxmd.com/read/29427123/clinical-utility-of-rt-pcr-in-assessing-her-2-gene-expression-versus-traditional-ihc-and-fish-in-breast-cancer-patients
#12
Moushumi Suryavanshi, Anurag Mehta, Jiten Jaipuria, Dushyant Kumar, Gayatri Vishwakarma, Manoj Kumar Panigrahi, Haristuti Verma, Mumtaz Saifi, Sanjeev Sharma, Simran Tandon, D C Doval, Bhudev C Das
BACKGROUND: IHC and FISH are used for categorizing HER 2 status in breast cancer at the protein and DNA level, respectively. HER 2 expression at the RNA level is quantitative, cheaper, easier to standardize and free from interobserver variation. METHODS: 115 consecutive patients were tested by IHC, FISH and RT-PCR (test cohort). Assuming FISH result to be the response variable, ROC curves for RT-PCR ratio were analyzed to label HER 2 negative, equivocal and positive cases as RT-PCR score 1, 2 and 3, respectively...
February 9, 2018: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/29426835/transcriptome-analysis-and-prognosis-of-aldh-isoforms-in-human-cancer
#13
Peter Mu-Hsin Chang, Che-Hong Chen, Chi-Chun Yeh, Hsueh-Ju Lu, Tze-Tze Liu, Ming-Huang Chen, Chun-Yu Liu, Alexander T H Wu, Muh-Hwa Yang, Shyh-Kuan Tai, Daria Mochly-Rosen, Chi-Ying F Huang
Overexpression of ALDH is associated with cancer stem-like features and poor cancer prognosis. High ALDH activity has been observed in cancer stem-like cells. There are a total of 19 human ALDH isoforms, all of which are associated with reducing oxidative stress and protecting cells from damage. However, it is unknown whether all ALDHs are associated with poor cancer prognosis and which ones play a significant role in cancer progression. In this study, we used RNA sequencing data from The Cancer Genome Atlas (TCGA) to evaluate the differential expression of 19 ALDH isoforms in 5 common human cancers...
February 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29424253/molecular-hydrogen-upregulates-heat-shock-response-and-collagen-biosynthesis-and-downregulates-cell-cycles-%C3%A2-meta-analyses-of-gene-expression-profiles
#14
Hiroshi Nishiwaki, Mikako Ito, Shuto Negishi, Sayaka Sobue, Masatoshi Ichihara, Kinji Ohno
BACKGROUND: Molecular hydrogen exerts its effect on multiple pathologies, including oxidative stress, inflammation, and apoptosis. However, its molecular mechanisms have not been fully elucidated. In order to explore the effects of molecular hydrogen, we meta-analyzed gene expression profiles modulated by molecular hydrogen. METHODS: We performed microarray analysis of the mouse liver with or without drinking hydrogen water. We also integrated two previously reported microarray datasets of the rat liver into meta-analyses...
February 9, 2018: Free Radical Research
https://www.readbyqxmd.com/read/29422604/genome-wide-meta-analysis-identifies-five-new-susceptibility-loci-for-pancreatic-cancer
#15
Alison P Klein, Brian M Wolpin, Harvey A Risch, Rachael Z Stolzenberg-Solomon, Evelina Mocci, Mingfeng Zhang, Federico Canzian, Erica J Childs, Jason W Hoskins, Ashley Jermusyk, Jun Zhong, Fei Chen, Demetrius Albanes, Gabriella Andreotti, Alan A Arslan, Ana Babic, William R Bamlet, Laura Beane-Freeman, Sonja I Berndt, Amanda Blackford, Michael Borges, Ayelet Borgida, Paige M Bracci, Lauren Brais, Paul Brennan, Hermann Brenner, Bas Bueno-de-Mesquita, Julie Buring, Daniele Campa, Gabriele Capurso, Giulia Martina Cavestro, Kari G Chaffee, Charles C Chung, Sean Cleary, Michelle Cotterchio, Frederike Dijk, Eric J Duell, Lenka Foretova, Charles Fuchs, Niccola Funel, Steven Gallinger, J Michael M Gaziano, Maria Gazouli, Graham G Giles, Edward Giovannucci, Michael Goggins, Gary E Goodman, Phyllis J Goodman, Thilo Hackert, Christopher Haiman, Patricia Hartge, Manal Hasan, Peter Hegyi, Kathy J Helzlsouer, Joseph Herman, Ivana Holcatova, Elizabeth A Holly, Robert Hoover, Rayjean J Hung, Eric J Jacobs, Krzysztof Jamroziak, Vladimir Janout, Rudolf Kaaks, Kay-Tee Khaw, Eric A Klein, Manolis Kogevinas, Charles Kooperberg, Matthew H Kulke, Juozas Kupcinskas, Robert J Kurtz, Daniel Laheru, Stefano Landi, Rita T Lawlor, I-Min Lee, Loic LeMarchand, Lingeng Lu, Núria Malats, Andrea Mambrini, Satu Mannisto, Roger L Milne, Beatrice Mohelníková-Duchoňová, Rachel E Neale, John P Neoptolemos, Ann L Oberg, Sara H Olson, Irene Orlow, Claudio Pasquali, Alpa V Patel, Ulrike Peters, Raffaele Pezzilli, Miquel Porta, Francisco X Real, Nathaniel Rothman, Ghislaine Scelo, Howard D Sesso, Gianluca Severi, Xiao-Ou Shu, Debra Silverman, Jill P Smith, Pavel Soucek, Malin Sund, Renata Talar-Wojnarowska, Francesca Tavano, Mark D Thornquist, Geoffrey S Tobias, Stephen K Van Den Eeden, Yogesh Vashist, Kala Visvanathan, Pavel Vodicka, Jean Wactawski-Wende, Zhaoming Wang, Nicolas Wentzensen, Emily White, Herbert Yu, Kai Yu, Anne Zeleniuch-Jacquotte, Wei Zheng, Peter Kraft, Donghui Li, Stephen Chanock, Ofure Obazee, Gloria M Petersen, Laufey T Amundadottir
In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 × 10-8). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PANDoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36...
February 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29421442/rage-may-act-as-a-tumour-suppressor-to-regulate-lung-cancer-development
#16
Shuangshuang Wu, Liping Mao, Yan Li, Yuan Yin, Weiwei Yuan, Yujia Chen, Wenlong Ren, Xiao Lu, Yue Li, Lei Chen, Bo Chen, Wei Xu, Tian Tian, Yihua Lu, Liying Jiang, Xun Zhuang, Minjie Chu, Jianqing Wu
Although the correlation of the RAGE rs2070600 polymorphism and cancer risk has been confirmed, detailed studies with functional and experimental evaluations are lacking. In this study, we first aimed to examine whether this polymorphism is associated with cancer risk based on the latest published data, and consistent with previous meta-analyses, a significant association between the rs2070600 polymorphism and cancer risk was observed (A versus G: OR = 1.25; 95% CI = 1.12-1.40). In additional stratified analyses based on cancer type, rs2070600 was significantly associated with an increased risk of lung cancer (A versus G: OR = 1...
February 5, 2018: Gene
https://www.readbyqxmd.com/read/29420797/octopus-toolkit-a-workflow-to-automate-mining-of-public-epigenomic-and-transcriptomic-next-generation-sequencing-data
#17
Taemook Kim, Hogyu David Seo, Lothar Hennighausen, Daeyoup Lee, Keunsoo Kang
Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository...
February 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29408621/integrated-analysis-of-gene-expression-signatures-associated-with-colon-cancer-from-three-datasets
#18
Ping Gao, Miao He, Chunling Zhang, Changhui Geng
PURPOSE: The present study aimed to elucidate the pathogenesis of colon cancer and identify genes associated with tumor development. METHODS: Three datasets, two (GSE74602 and GSE44861) from the Gene Expression Omnibus database and RNA-Seq colon cancer data from The Cancer Genome Atlas data portal, were downloaded. These three datasets were grouped using a meta-analysis approach, and differentially expressed genes (DEGs) were identified between colon tumor samples and adjacent normal samples...
February 3, 2018: Gene
https://www.readbyqxmd.com/read/29408173/pten-in-kidney-cancer-a-review-and-meta-analysis
#19
REVIEW
Wan-Cai Que, Hong-Qiang Qiu, Yu Cheng, Mao-Bai Liu, Chao-Yang Wu
BACKGROUND: Kidney cancer is one of the most common cancers in the USA causing 14,400 deaths per year. The phosphatase and tensin homolog (PTEN) has been extensively documented as a tumor suppresser gene in cancer. However, there is unclear evidence for its clinicopathological and prognostic role in kidney cancer. METHODS: A systematic review of literature assessing PTEN expression and clinical outcome in patients with kidney cancer. Web of Science, PubMed, Embase, and Chinese databases were searched for collecting for the eligible studies providing sufficient information...
February 2, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29404214/gene-based-association-study-for-lipid-traits-in-diverse-cohorts-implicates-bace1-and-sidt2-regulation-in-triglyceride-levels
#20
Angela Andaleon, Lauren S Mogil, Heather E Wheeler
Plasma lipid levels are risk factors for cardiovascular disease, a leading cause of death worldwide. While many studies have been conducted on lipid genetics, they mainly focus on Europeans and thus their transferability to diverse populations is unclear. We performed SNP- and gene-level genome-wide association studies (GWAS) of four lipid traits in cohorts from Nigeria and the Philippines and compared them to the results of larger, predominantly European meta-analyses. Two previously implicated loci met genome-wide significance in our SNP-level GWAS in the Nigerian cohort, rs34065661 in CETP associated with HDL cholesterol (P = 9...
2018: PeerJ
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