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Microarray gene expression meta-analysis

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https://www.readbyqxmd.com/read/29774565/local-and-systemic-regulation-of-psii-efficiency-in-triticale-infected-by-the-hemibiotrophic-pathogen-microdochium-nivale
#1
Mateusz Dyda, Iwona Wąsek, Mirosław Tyrka, Maria Wędzony, Magdalena Szechyńska-Hebda
Microdochium nivale is a fungal pathogen that causes yield losses of cereals during winter. Cold hardening under light conditions induces genotype-dependent resistance of a plant to infection. We aim to show how photosystem II (PSII) regulation contributes to plant resistance. Using mapping population of triticale doubled haploid lines, three M. nivale strains and different infection assays, we demonstrate that plants that maintain a higher maximum quantum efficiency of PSII show less leaf damage upon infection...
May 17, 2018: Physiologia Plantarum
https://www.readbyqxmd.com/read/29758295/systematic-bioinformatic-approaches-reveal-novel-gene-expression-signatures-associated-with-acquired-resistance-to-egfr-targeted-therapy-in-lung-cancer
#2
Marjan Mojtabavi Naeini, Manoochehr Tavassoli, Kamran Ghaedi
OBJECTIVES: Human non-small cell lung cancer (NSCLC) that harbors activating mutations in epidermal growth factor receptor (EGFR) initially responds to treatment with EGFR tyrosine kinase inhibitors (TKIs) such as gefitinib and erlotinib but eventually tumor cells acquire resistance. To date, several gene expression profiles have been reported in TKIs-resistant EGFR-mutant NSCLC. The objective of this study is to identify robust gene expression signatures, biological processes, and promising overcoming targets for TKIs-resistant EGFR-mutant NSCLC...
May 11, 2018: Gene
https://www.readbyqxmd.com/read/29725421/expression-of-bcl-2-is-a-favorable-prognostic-biomarker-in-lung-squamous-cell-carcinoma
#3
Changjiang Feng, Jiaqi Wu, Fan Yang, Mangtang Qiu, Shuofeng Hu, Saisai Guo, Jin Wu, Xiaomin Ying, Jun Wang
Lung squamous cell carcinoma (LUSC) is the second major type of lung cancer globally. The majority of patients with LUSC are clinically diagnosed at the advanced stages, thus it is urgent to identify suitable prognostic markers for LUSC. B-cell lymphoma 2 (Bcl-2) has been widely studied in non-small cell lung cancer (NSCLC). However, the prognostic role of Bcl-2 in NSCLC remains conflicting and controversial, particularly for LUSC. Although certain studies have been performed to identify the prognostic value of Bcl-2, to the best of our knowledge, no study has investigated the prognostic role of Bcl-2 in LUSC specifically...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29688366/biodataome-a-collection-of-uniformly-preprocessed-and-automatically-annotated-datasets-for-data-driven-biology
#4
Kleanthi Lakiotaki, Nikolaos Vorniotakis, Michail Tsagris, Georgios Georgakopoulos, Ioannis Tsamardinos
Biotechnology revolution generates a plethora of omics data with an exponential growth pace. Therefore, biological data mining demands automatic, 'high quality' curation efforts to organize biomedical knowledge into online databases. BioDataome is a database of uniformly preprocessed and disease-annotated omics data with the aim to promote and accelerate the reuse of public data. We followed the same preprocessing pipeline for each biological mart (microarray gene expression, RNA-Seq gene expression and DNA methylation) to produce ready for downstream analysis datasets and automatically annotated them with disease-ontology terms...
January 1, 2018: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29625265/network-based-meta-analysis-in-the-identification-of-biomarkers-for-papillary-thyroid-cancer
#5
Hengqiang Zhao, Hehe Li
Papillary thyroid carcinoma (PTC) has been increasing across the world with incomplete understanding of its pathogenesis. We aimed to investigate gene alterations and biomarkers contributing to PTC development. A total of five eligible microarray datasets including 94 PTC and 81 normal thyroid samples were included to identify gene expression signatures. Using integrative meta-analysis of expression data (INMEX) program, we identified a total of 2699 differentially expressed genes (DEGs) (1333 overexpressed and 1366 underexpressed genes) in PTC relative to normal thyroid samples...
April 3, 2018: Gene
https://www.readbyqxmd.com/read/29617451/integrative-multi-platform-meta-analysis-of-gene-expression-profiles-in-pancreatic-ductal-adenocarcinoma-patients-for-identifying-novel-diagnostic-biomarkers
#6
Antonio Irigoyen, Cristina Jimenez-Luna, Manuel Benavides, Octavio Caba, Javier Gallego, Francisco Manuel Ortuño, Carmen Guillen-Ponce, Ignacio Rojas, Enrique Aranda, Carolina Torres, Jose Prados
Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases can be a hard task when working with heterogeneous datasets. Expression data are strongly influenced by technology, sample preparation processes, and/or labeling methods. The proliferation of different microarray platforms for measuring gene expression increases the need to develop models able to compare their results, especially when different technologies can lead to signal values that vary greatly. Integrative meta-analysis can significantly improve the reliability and robustness of DEG detection...
2018: PloS One
https://www.readbyqxmd.com/read/29587635/genome-wide-transcriptional-analyses-in-anopheles-mosquitoes-reveal-an-unexpected-association-between-salivary-gland-gene-expression-and-insecticide-resistance
#7
Alison T Isaacs, Henry D Mawejje, Sean Tomlinson, Daniel J Rigden, Martin J Donnelly
BACKGROUND: To combat malaria transmission, the Ugandan government has embarked upon an ambitious programme of indoor residual spraying (IRS) with a carbamate class insecticide, bendiocarb. In preparation for this campaign, we characterized bendiocarb resistance and associated transcriptional variation among Anopheles gambiae s.s. mosquitoes from two sites in Uganda. RESULTS: Gene expression in two mosquito populations displaying some resistance to bendiocarb (95% and 79% An...
March 27, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29567998/system-wide-coordinates-of-higher-order-functions-in-host-pathogen-environment-upon-mycobacterium-tuberculosis-infection
#8
P V Parvati Sai Arun, Sravan Kumar Miryala, Aarti Rana, Sreenivasulu Kurukuti, Yusuf Akhter, Sailu Yellaboina
Molecular signatures and their interactions behind the successful establishment of infection of Mycobacterium tuberculosis (Mtb) inside macrophage are largely unknown. In this work, we present an inter-system scale atlas of the gene expression signatures, their interactions and higher order gene functions of macrophage-Mtb environment at the time of infection. We have carried out large-scale meta-analysis of previously published gene expression microarray studies andhave identified a ranked list of differentially expressed genes and their higher order functions in intracellular Mtb as well as the infected macrophage...
March 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29552153/-in-silico-analysis-identifies-crisp3-as-a-potential-peripheral-blood-biomarker-for-multiple-myeloma-from-data-modeling-to-validation-with-rt-pcr
#9
Dong Leng, Ran Miao, Xiaoxi Huang, Ying Wang
Octamer-binding protein 2 (Oct2) binds to the ATGCAAAT octamer on the IgH enhancer and stimulates IgH expression in human multiple myeloma (MM). Cysteine-rich secreted protein 3 (CRISP3) possesses the ATGCAAAT sequence and thus is activated by Oct2 in mouse B cells, suggesting that CRISP3 may be activated in and be a potential biomarker for MM. The present study involved a meta-analysis of the gene expression profiling data of human MM peripheral blood. Significantly expressed genes were analyzed on merged super array microarray data and selected sample data with significantly expressed genes were additionally analyzed by principal component analysis and Bayesian probit regression...
April 2018: Oncology Letters
https://www.readbyqxmd.com/read/29504232/morphological-and-transcriptomic-analyses-reveal-three-discrete-primary-stages-of-postembryonic-development-in-the-common-fire-salamander-salamandra-salamandra
#10
Eugenia Sanchez, Eliane Küpfer, Daniel J Goedbloed, Arne W Nolte, Tim Lüddecke, Stefan Schulz, Miguel Vences, Sebastian Steinfartz
The postembryonic development of amphibians has been characterized as divided into three predominant periods, hereafter named primary developmental stages: premetamorphosis (PreM), prometamorphosis (ProM), metamorphic climax (Meta), and completion of metamorphosis (PostM), largely based on examination of anuran development. Here, we categorized the postembryonic development of larvae of a poisonous fire salamander (Salamandra salamandra) by integrating morphology and gene expression (transcriptomic) data. Morphological analysis revealed three distinct clusters suggestive of PreM, ProM, and Meta, which were confirmed in parallel by microarray-derived gene expression analysis...
March 2018: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/29503661/identification-of-shared-molecular-signatures-indicate-the-susceptibility-of-endometriosis-to-multiple-sclerosis
#11
Amit Katiyar, Sujata Sharma, Tej P Singh, Punit Kaur
Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29487289/meta-and-cross-species-analyses-of-insulin-resistance-based-on-gene-expression-datasets-in-human-white-adipose-tissues
#12
Junghyun Jung, Go Woon Kim, Woosuk Lee, Changsoo Mok, Sung Hyun Chung, Wonhee Jang
Ample evidence indicates that insulin resistance (IR) is closely related to white adipose tissue (WAT), but the underlying mechanisms of IR pathogenesis are still unclear. Using 352 microarray datasets from seven independent studies, we identified a meta-signature which comprised of 1,413 genes. Our meta-signature was also enriched in overall WAT in in vitro and in vivo IR models. Only 12 core enrichment genes were consistently enriched across all IR models. Among the meta-signature, we identified a drug signature made up of 211 genes with expression levels that were co-regulated by thiazolidinediones and metformin using cross-species analysis...
February 27, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29470489/integration-of-machine-learning-and-meta-analysis-identifies-the-transcriptomic-bio-signature-of-mastitis-disease-in-cattle
#13
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/29436659/cholangiocarcinoma%C3%A2-associated-genes-identified-by-integrative-analysis-of-gene-expression-data
#14
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...
April 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29434863/identification-of-common-key-genes-in-breast-lung-and-prostate-cancer-and-exploration-of-their-heterogeneous-expression
#15
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/29424253/molecular-hydrogen-upregulates-heat-shock-response-and-collagen-biosynthesis-and-downregulates-cell-cycles-meta-analyses-of-gene-expression-profiles
#16
Hiroshi Nishiwaki, Mikako Ito, Shuto Negishi, Sayaka Sobue, Masatoshi Ichihara, Kinji Ohno
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-analysed gene expression profiles modulated by molecular hydrogen. 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. We used two categories of meta-analysis methods: the cross-platform method and the conventional meta-analysis method (Fisher's method)...
March 20, 2018: Free Radical Research
https://www.readbyqxmd.com/read/29394946/clinical-value-of-mir-198-5p-in-lung-squamous-cell-carcinoma-assessed-using-microarray-and-rt-qpcr
#17
Yue-Ya Liang, Jia-Cheng Huang, Rui-Xue Tang, Wen-Jie Chen, Peng Chen, Wei-Luan Cen, Ke Shi, Li Gao, Xiang Gao, An-Gui Liu, Xiao-Tong Peng, Gang Chen, Su-Ning Huang, Ye-Ying Fang, Yong-Yao Gu
BACKGROUND: To examine the clinical value of miR-198-5p in lung squamous cell carcinoma (LUSC). METHODS: Gene Expression Omnibus (GEO) microarray datasets were used to explore the miR-198-5p expression and its diagnostic value in LUSC. Real-time reverse transcription quantitative polymerase chain reaction was used to evaluate the expression of miR-198-5p in 23 formalin-fixed, paraffin-embedded (FFPE) LUSC tissues and corresponding non-cancerous tissues. The correlation between miR-198-5p expression and clinic pathological features was assessed...
February 2, 2018: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29393467/expression-level-and-potential-target-pathways-of-mir-1-3p-in-colorectal-carcinoma-based-on-645-cases-from-9-microarray-datasets
#18
Jie-Yu Wang, Jia-Cheng Huang, Gang Chen, Dan-Ming Wei
For the purpose of demonstrating the clinical value and unraveling the molecular mechanisms of micro RNA (miR)-1-3p in colorectal carcinoma (CRC), the present study collected expression and diagnostic data from Gene Expression Omnibus (GEO), ArrayExpress and existing literature to conduct meta‑analyses and diagnostic tests. Furthermore, the potential targets of miR‑1‑3p were attained from datasets that transfected miR‑1‑3p into CRC cells, online prediction databases and differentially expressed genes from The Cancer Genome Atlas and literature...
April 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29371945/-bicd1-expression-as-a-potential-biomarker-for-prognosis-and-predicting-response-to-therapy-in-patients-with-glioblastomas
#19
Shang-Pen Huang, Yu-Chan Chang, Qie Hua Low, Alexander T H Wu, Chi-Long Chen, Yuan-Feng Lin, Michael Hsiao
There is variation in the survival and therapeutic outcome of patients with glioblastomas (GBMs). Therapy resistance is an important challenge in the treatment of GBM patients. The aim of this study was to identify Temozolomide (TMZ) related genes and confirm their clinical relevance. The TMZ-related genes were discovered by analysis of the gene-expression profiling in our cell-based microarray. Their clinical relevance was verified by in silico meta-analysis of the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) datasets...
December 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/29328493/meta-analysis-of-mrna-expression-profiles-to-identify-differentially-expressed-genes-in-lung-adenocarcinoma-tissue-from-smokers-and-non-smokers
#20
Xiaona He, Cheng Zhang, Chao Shi, Quqin Lu
Compared to other types of lung cancer, lung adenocarcinoma patients with a history of smoking have a poor prognosis during the treatment of lung cancer. How lung adenocarcinoma-related genes are differentially expressed between smoker and non-smoker patients has yet to be fully elucidated. We performed a meta-analysis of four publicly available microarray datasets related to lung adenocarcinoma tissue in patients with a history of smoking using R statistical software. The top 50 differentially expressed genes (DEGs) in smoking vs...
March 2018: Oncology Reports
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