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Tissue specific gene network

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https://www.readbyqxmd.com/read/29330297/characterization-and-evidence-of-the-mir-888-cluster-as-a-novel-cancer-network-in-prostate
#1
Tsuyoshi Hasegawa, Garrison Glavich, Mary Pahuski, Aleena M Short, Oliver John Semmes, Lifang Yang, Vitold Galkin, Richard R Drake, Aurora Esquela-Kerscher
Prostate cancer afflicts 1 in 7 men and is the second leading cause of male cancer-related deaths in the United States. MicroRNAs (miRNAs), an extensive class of ~22 nucleotide non-coding RNAs, are often aberrantly expressed in tissues and fluids from prostate cancer patients but the mechanism of how specific miRNAs regulate prostate tumorigenesis and metastasis are poorly understood. Here, miR-888 was identified as a novel prostate factor that promotes proliferation and migration. miR-888 resides within a genomic cluster of 7 miRNA genes (mir-892c, mir-890, mir-888, mir-892a, mir-892b, mir-891b, mir-891a) on human chromosome Xq27...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#2
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29323241/integrative-approach-using-liver-and-duodenum-rna-seq-data-identifies-candidate-genes-and-pathways-associated-with-feed-efficiency-in-pigs
#3
Yuliaxis Ramayo-Caldas, Maria Ballester, Juan Pablo Sánchez, Olga González-Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, David Torrallardona, Raquel Quintanilla
This study aims identifying candidate genes and pathways associated with feed efficiency (FE) in pigs. Liver and duodenum transcriptomes of 37 gilts showing high and low residual feed intake (RFI) were analysed by RNA-Seq. Gene expression data was explored through differential expression (DE) and weighted gene co-expression network analyses. DE analysis revealed 55 and 112 differentially regulated genes in liver and duodenum tissues, respectively. Clustering genes according to their connectivity resulted in 23 (liver) and 25 (duodenum) modules of genes with a co-expression pattern...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322794/integrated-analysis-of-the-rna-seq-data-of-liver-hepatocellular-carcinoma
#4
H Xue, L Luo, Y T Yao, L L Wei, S P Deng, X L Huang
The present study aimed to explore the genetic changes involved in the liver hepatocellular carcinoma (HCC) development. The RNA-Seq data of 212 HCC tissue samples and 50 normal tissue samples were downloaded using TCGA-Assembler. A total of 4 subgroups were obtained, and 4167, 6279, 5379, and 2548 DEGs were screened in group 1, group 2, group 3, and group 4, respectively. Enrichment analysis found that cell cycle, metabolism, and translation related terms were the most significantly changed functions and pathways...
2018: Neoplasma
https://www.readbyqxmd.com/read/29320577/genome-wide-profiling-of-the-piwi-interacting-rna-mrna-regulatory-networks-in-epithelial-ovarian-cancers
#5
Garima Singh, Jyoti Roy, Pratiti Rout, Bibekanand Mallick
PIWI-interacting (piRNAs), ~23-36 nucleotide-long small non-coding RNAs (sncRNAs), earlier believed to be germline-specific, have now been identified in somatic cells, including cancer cells. These sncRNAs impact critical biological processes by fine-tuning gene expression at post-transcriptional and epigenetic levels. The expression of piRNAs in ovarian cancer, the most lethal gynecologic cancer is largely uncharted. In this study, we investigated the expression of PIWILs by qRT-PCR and western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prevalent epithelial ovarian cancer subtypes, serous and endometrioid by small RNA sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29312749/circular-rnas-in-thoracic-diseases
#6
REVIEW
Fan Yang, Ping Zhu, Jintao Guo, Xiang Liu, Sheng Wang, Guoxin Wang, Wen Liu, Shupeng Wang, Nan Ge
Circular RNAs (circRNAs) are a class of noncoding RNAs with continuous, covalently closed circular structures. Investigators have shown previously that circRNAs are regulators of gene expression in mammals. These tissue-specific transcripts are produced primarily by exonic or intronic sequences of housekeeping genes. Several biosynthetic models have been proposed for circRNAs, and consensus is lacking. CircRNAs are widely expressed in the cytoplasm and highly conserved, what is more, unlike other noncoding RNAs, circRNAs are relatively stable...
December 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29311280/an-algu-regulated-antisense-transcript-encoded-within-the-pseudomonas-syringae-fleq-gene-has-a-positive-effect-on-motility
#7
Eric Markel, Hollie Dalenberg, Caroline L Monteil, Boris A Vinatzer, Bryan Swingle
Production of bacterial flagella is controlled by a multi-tiered regulatory system that coordinates expression of 40-50 subunits and ordered assembly of these elaborate structures. Flagellar expression is environmentally controlled, presumably to optimize the benefits and liabilities of having these organelles with cell growth and survival. We recently reported a global survey of AlgU-dependent regulation and binding in Pseudomonas syringae pv. tomato DC3000 that included evidence for strong down-regulation of many flagellar and chemotaxis motility genes...
January 8, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29309507/segreg-a-database-for-human-specifically-expressed-genes-and-their-regulations-in-cancer-and-normal-tissue
#8
Qin Tang, Qiong Zhang, Yao Lv, Ya-Ru Miao, An-Yuan Guo
Human specifically expressed genes (SEGs) usually serve as potential biomarkers for disease diagnosis and treatment. However, the regulation underlying their specific expression remains to be revealed. In this study, we constructed SEG regulation database (SEGreg; available at http://bioinfo.life.hust.edu.cn/SEGreg) for showing SEGs and their transcription factors (TFs) and microRNA (miRNA) regulations under different physiological conditions, which include normal tissue, cancer tissue and cell line. In total, SEGreg collected 6387, 1451, 4506 and 5320 SEGs from expression profiles of 34 cancer types and 55 tissues of The Cancer Genome Atlas, Cancer Cell Line Encyclopedia, Human Body Map and Genotype-Tissue Expression databases/projects, respectively...
January 3, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29307754/physical-constraints-in-cell-fate-specification-a-case-in-point-microgravity-and-phenotypes-differentiation
#9
REVIEW
Maria Grazia Masiello, Roberto Verna, Alessandra Cucina, Mariano Bizzarri
Data obtained by studying mammalian cells in absence of gravity strongly support the notion that cell fate specification cannot be understood according to the current molecular model. A paradigmatic case in point is provided by studying cell populations growing in absence of gravity. When the physical constraint (gravity) is 'experimentally removed', cells spontaneously allocate into two morphologically different phenotypes. Such phenomenon is likely enacted by the intrinsic stochasticity, which, in turn, is successively 'canalized' by a specific gene regulatory network...
January 4, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29305255/comparative-analysis-of-gene-expression-in-maternal-peripheral-blood-and-monocytes-during-spontaneous-preterm-labor
#10
Alison G Paquette, Oksana Shynlova, Mark Kibschull, Nathan D Price, Stephen J Lye
BACKGROUND: Preterm birth is the leading cause of newborn death worldwide, and is associated with significant cognitive and physiological challenges in later life. There is a pressing need to define the mechanisms that initiate spontaneous preterm labor , and for development of novel clinical biomarkers to identify high-risk pregnancies. Most preterm birth studies utilize fetal tissues, and there is limited understanding of the transcriptional changes that occur in mothers undergoing spontaneous preterm labor...
January 2, 2018: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29303984/transcription-factor-and-lncrna-regulatory-networks-identify-key-elements-in-lung-adenocarcinoma
#11
Dan Li, William Yang, Jialing Zhang, Jack Y Yang, Renchu Guan, Mary Qu Yang
Lung cancer is the second most commonly diagnosed carcinoma and is the leading cause of cancer death. Although significant progress has been made towards its understanding and treatment, unraveling the complexities of lung cancer is still hampered by a lack of comprehensive knowledge on the mechanisms underlying the disease. High-throughput and multidimensional genomic data have shed new light on cancer biology. In this study, we developed a network-based approach integrating somatic mutations, the transcriptome, DNA methylation, and protein-DNA interactions to reveal the key regulators in lung adenocarcinoma (LUAD)...
January 5, 2018: Genes
https://www.readbyqxmd.com/read/29302752/the-role-of-the-circadian-clock-system-in-physiology
#12
REVIEW
Violetta Pilorz, Charlotte Helfrich-Förster, Henrik Oster
Life on earth is shaped by the 24-h rotation of our planet around its axes. To adapt behavior and physiology to the concurring profound but highly predictable changes, endogenous circadian clocks have evolved that drive 24-h rhythms in invertebrate and vertebrate species. At the molecular level, circadian clocks comprised a set of clock genes organized in a system of interlocked transcriptional-translational feedback loops. A ubiquitous network of cellular central and peripheral tissue clocks coordinates physiological functions along the day through activation of tissue-specific transcriptional programs...
January 4, 2018: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/29300920/simultaneous-inference-of-phenotype-associated-genes-and-relevant-tissues-from-gwas-data-via-bayesian-integration-of-multiple-tissue-specific-gene-networks
#13
Mengmeng Wu, Zhixiang Lin, Shining Ma, Ting Chen, Rui Jiang, Wing Hung Wong
Although genome-wide association studies (GWAS) have successfully identified thousands of genomic loci associated with hundreds of complex traits in the past decade, the debate about such problems as missing heritability and weak interpretability has been appealing for effective computational methods to facilitate the advanced analysis of the vast volume of existing and anticipated genetic data. Towards this goal, gene-level integrative GWAS analysis with the assumption that genes associated with a phenotype tend to be enriched in biological gene sets or gene networks has recently attracted much attention, due to such advantages as straightforward interpretation, less multiple testing burdens, and robustness across studies...
December 29, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/29298665/analysis-of-microarrays-of-mir-34a-and-its-identification-of-prospective-target-gene-signature-in-hepatocellular-carcinoma
#14
Fang-Hui Ren, Hong Yang, Rong-Quan He, Jing-Ning Lu, Xing-Gu Lin, Hai-Wei Liang, Yi-Wu Dang, Zhen-Bo Feng, Gang Chen, Dian-Zhong Luo
BACKGROUND: Currently, some studies have demonstrated that miR-34a could serve as a suppressor of several cancers including hepatocellular carcinoma (HCC). Previously, we discovered that miR-34a was downregulated in HCC and involved in the tumorigenesis and progression of HCC; however, the mechanism remains unclear. The purpose of this study was to estimate the expression of miR-34a in HCC by applying the microarray profiles and analyzing the predicted targets of miR-34a and their related biological pathways of HCC...
January 3, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29297292/repositioning-drugs-by-targeting-network-modules-a-parkinson-s-disease-case-study
#15
Zongliang Yue, Itika Arora, Eric Y Zhang, Vincent Laufer, S Louis Bridges, Jake Y Chen
BACKGROUND: Much effort has been devoted to the discovery of specific mechanisms between drugs and single targets to date. However, as biological systems maintain homeostasis at the level of functional networks robustly controlling the internal environment, such networks commonly contain multiple redundant mechanisms designed to counteract loss or perturbation of a single member of the network. As such, investigation of therapeutics that target dysregulated pathways or processes, rather than single targets, may identify agents that function at a level of the biological organization more relevant to the pathology of complex diseases such as Parkinson's Disease (PD)...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29295970/construction-and-comprehensive-analysis-for-dysregulated-long-non-coding-rna-lncrna-associated-competing-endogenous-rna-cerna-network-in-gastric-cancer
#16
Fengxi Li, Chuiguo Huang, Qian Li, Xianghua Wu
Long non-coding RNA (lncRNA) is a kind of non-coding RNA with transcripts more than 200 bp in length. LncRNA can interact with the miRNA as a competing endogenous RNA (ceRNA) to regulate the expression of target genes, which play a significant role in the initiation and progression of tumors. In this study, we explored the functional roles and regulatory mechanisms of lncRNAs as ceRNAs in gastric cancer, and their potential implications for prognosis. The lncRNAs, miRNAs, and mRNAs expression profiles of 375 gastric cancer tissues and 32 non-tumor gastric tissues were downloaded from The Cancer Genome Atlas (TCGA) database...
January 3, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29286097/identification-of-key-genes-associated-with-congenital-heart-defects-in-embryos-of-diabetic-mice
#17
Nan Lin, Yan Cai, Linlin Zhang, Yahang Chen
Maternal diabetes has been reported to be a critical factor for congenital heart defects (CHD) in offspring. The present study aimed to screen the key genes that may be involved in CHD in offspring of diabetic mothers. The present study obtained the gene expression profile of GSE32078, including three embryonic heart tissue samples at embryonic day 13.5 (E13.5), three embryonic heart tissue samples at embryonic day 15.5 (E15.5) from diabetic mice and their respective controls from normal mice. The cut‑off criterion of P<0...
December 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29285254/microrna-co-expression-networks-exhibit-increased-complexity-in-pancreatic-ductal-compared-to-vater-s-papilla-adenocarcinoma
#18
Tommaso Mazza, Massimiliano Copetti, Daniele Capocefalo, Caterina Fusilli, Tommaso Biagini, Massimo Carella, Antonio De Bonis, Nicola Mastrodonato, Ada Piepoli, Valerio Pazienza, Evaristo Maiello, Fabio Francesco di Mola, Pierluigi di Sebastiano, Angelo Andriulli, Francesca Tavano
MiRNA expression abnormalities in adenocarcinoma arising from pancreatic ductal system (PDAC) and Vater's papilla (PVAC) could be associated with distinctive pathologic features and clinical cancer behaviours. Our previous miRNA expression profiling data on PDAC (n=9) and PVAC (n=4) were revaluated to define differences/similarities in miRNA expression patterns. Afterwards, in order to uncover target genes and core signalling pathways regulated by specific miRNAs in these two tumour entities, miRNA interaction networks were wired for each tumour entity, and experimentally validated target genes underwent pathways enrichment analysis...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29284660/the-modern-resource-genome-wide-binding-profiles-for-hundreds-of-drosophila-and-caenorhabditis-elegans-transcription-factors
#19
Michelle M Kudron, Alec Victorsen, Louis Gevirtzman, LaDeana W Hillier, William W Fisher, Dionne Vafeados, Matt Kirkey, Ann S Hammonds, Jeffery Gersch, Haneen Ammouri, Martha L Wall, Jennifer Moran, David Steffen, Matt Szynkarek, Samantha Seabrook-Sturgis, Nader Jameel, Madhura Kadaba, Jaeda Patton, Robert Terrell, Mitch Corson, Timothy J Durham, Soo Park, Swapna Samanta, Mei Han, Jinrui Xu, Koon-Kiu Yan, Susan E Celniker, Kevin P White, Lijia Ma, Mark Gerstein, Valerie Reinke, Robert Waterston
In order to develop a catalog of regulatory sites in two major model organisms, Drosophilia melanogaster and Caenorhabditis elegans, the modERN consortium has systematically assayed the binding sites of transcription factors (TFs). Combined with data produced by our predecessor, modENCODE, we now have data for 262 TFs identifying 1.23M sites in the fly genome and 217 TFs identifying 0.67M sites in the worm genome. Because sites from different TFs are often overlapping and tightly clustered, they fall into 91,011 and 59,150 regions in the fly and worm, respectively, and these binding sites span as little as 8...
December 28, 2017: Genetics
https://www.readbyqxmd.com/read/29284399/profiling-the-onset-of-somatic-embryogenesis-in-arabidopsis
#20
E Magnani, J M Jiménez-Gómez, L Soubigou-Taconnat, L Lepiniec, E Fiume
BACKGROUND: Totipotency is the ability of a cell to regenerate a whole organism. Plant somatic embryogenesis (SE) is a remarkable example of totipotency because somatic cells reverse differentiation, respond to an appropriate stimulus and initiate embryo development. Although SE is an ideal system to investigate de-differentiation and differentiation, we still lack a deep molecular understanding of the phenomenon due to experimental restraints. RESULTS: We applied the INTACT method to specifically isolate the nuclei of those cells undergoing SE among the majority of non-embryogenic cells that make up a callus...
December 29, 2017: BMC Genomics
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