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Network gene function prediction

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https://www.readbyqxmd.com/read/29158991/ndufa4l2-is-associated-with-clear-cell-renal-cell-carcinoma-malignancy-and-is-regulated-by-elk1
#1
Lei Wang, Zhiqiang Peng, Kaizhen Wang, Yijun Qi, Ying Yang, Yue Zhang, Xinyuan An, Shudong Luo, Junfang Zheng
Background: Clear cell renal cell carcinoma (ccRCC) is the most common and lethal cancer of the adult kidney. However, its pathogenesis has not been fully understood till now, which hinders the therapeutic development of ccRCC. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) was found to be upregulated and play an important role in ccRCC. We aimed to further investigate the underlying mechanisms by which NDUFA4L2 exerted function and its expression level was upregulated...
2017: PeerJ
https://www.readbyqxmd.com/read/29156814/screening-circular-rna-expression-patterns-following-focal-cerebral-ischemia-in-mice
#2
Cuiying Liu, Chencheng Zhang, Jian Yang, Xiaokun Geng, Huishan Du, Xunming Ji, Heng Zhao
Circular RNAs (circRNAs) have been demonstrated to act as microRNA (miRNA) sponges and they play important roles in regulating gene expression through a circRNA-miRNA-gene pathway. The specific roles of circRNAs in the pathogenesis of cerebral ischemia, however, are still unclear. Thus, the aim of this study is to determine circRNA expression profiles in the ischemic brain after stroke, which was induced by 45 min of transient middle cerebral artery occlusion (MCAO). The results from the circRNA microarrays revealed that 1027 circRNAs were significantly altered 48 hours after reperfusion in the ischemic brain compared with the sham group...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156709/using-molecular-functional-networks-to-manifest-connections-between-obesity-and-obesity-related-diseases
#3
Jialiang Yang, Jing Qiu, Kejing Wang, Lijuan Zhu, Jingjing Fan, Deyin Zheng, Xiaodi Meng, Jiasheng Yang, Lihong Peng, Yu Fu, Dahan Zhang, Shouneng Peng, Haiyun Huang, Yi Zhang
Obesity is a primary risk factor for many diseases such as certain cancers. In this study, we have developed three algorithms including a random-walk based method OBNet, a shortest-path based method OBsp and a direct-overlap method OBoverlap, to reveal obesity-disease connections at protein-interaction subnetworks corresponding to thousands of biological functions and pathways. Through literature mining, we also curated an obesity-associated disease list, by which we compared the methods. As a result, OBNet outperforms other two methods...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156009/discovering-cancer-vulnerabilities-using-high-throughput-micro-rna-screening
#4
Iva Nikolic, Benjamin Elsworth, Eoin Dodson, Sunny Z Wu, Cathryn M Gould, Pieter Mestdagh, Glenn M Marshall, Lisa G Horvath, Kaylene J Simpson, Alexander Swarbrick
Micro-RNAs (miRNAs) are potent regulators of gene expression and cellular phenotype. Each miRNA has the potential to target hundreds of transcripts within the cell thus controlling fundamental cellular processes such as survival and proliferation. Here, we exploit this important feature of miRNA networks to discover vulnerabilities in cancer phenotype, and map miRNA-target relationships across different cancer types. More specifically, we report the results of a functional genomics screen of 1280 miRNA mimics and inhibitors in eight cancer cell lines, and its presentation in a sophisticated interactive data portal...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29154475/identification-and-analysis-of-a-key-long-non-coding-rnas-lncrnas-associated-module-reveal-functional-lncrnas-in-cardiac-hypertrophy
#5
Jian Zhang, Chenchen Feng, Chao Song, Bo Ai, Xuefeng Bai, Yuejuan Liu, Xuecang Li, Jianmei Zhao, Shengshu Shi, Xin Chen, Xiaojie Su, Chunquan Li
Cardiac hypertrophy (CH) is a common disease that originates from long-term heart pressure overload and finally leads to heart failure. Recently, long non-coding RNAs (lncRNAs) have attracted attention because they have broad and crucial functions in regulating complex biological processes. Some studies had found that lncRNAs play vital roles in complex cardiovascular diseases. However, the function and mechanism of lncRNAs in CH have not been elucidated. In our study, to investigate the potential roles of lncRNAs in CH, the Cardiac Hypertrophy-associated LncRNAs-Protein coding genes Network (CHLPN) was constructed by integrating gene microarray re-annotation and subpathway enrichment analyses...
November 20, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29152649/identification-of-key-genes-in-glioma-cpg-island-methylator-phenotype-via-network-analysis-of-gene-expression-data
#6
Lijuan Bo, Bo Wei, Zhanfeng Wang, Daliang Kong, Zheng Gao, Zhuang Miao
Gene expression data were analysed using bioinformatic tools to demonstrate molecular mechanisms underlying the glioma CpG island methylator phenotype (CIMP). A gene expression data set (accession no. GSE30336) was downloaded from Gene Expression Omnibus, including 36 CIMP+ and 16 CIMP- glioma samples. Differential analysis was performed for CIMP+ vs. CIMP‑ samples using the limma package in R. Functional enrichment analysis was subsequently conducted for differentially expressed genes (DEGs) using Database for Annotation, Visualization and Integration Discovery...
October 19, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29151698/circulating-mirnas-as-biomarkers-for-severe-acute-pancreatitis-associated-with-acute-lung-injury
#7
Xiao-Guang Lu, Xin Kang, Li-Bin Zhan, Li-Min Kang, Zhi-Wei Fan, Li-Zhi Bai
AIM: To identify circulating micro (mi)RNAs as biological markers for prediction of severe acute pancreatitis (SAP) with acute lung injury (ALI). METHODS: Twenty-four serum samples were respectively collected and classified as SAP associated with ALI and SAP without ALI, and the miRNA expression profiles were determined by microarray analysis. These miRNAs were validated by quantitative reverse transcription-polymerase chain reaction, and their putative targets were predicted by the online software TargetScan, miRanda and PicTar database...
November 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29145121/role-of-acid-alkali-treatment-in-primary-sludge-anaerobic-fermentation-insights-into-microbial-community-structure-functional-shifts-and-metabolic-output-by-high-throughput-sequencing
#8
Xiao Huang, Wenyi Dong, Hongjie Wang, Yangyang Feng
This study aimed to investigate the effect of acid- or alkali-treatment on volatile fatty acids (VFAs) production and microbiological mechanism during primary sludge anaerobic fermentation. Seven fermentation experiments were conducted at different pH (3-12). Results showed that the optimal pH was 10 for accumulation of VFAs. High-throughput sequencing results indicated that acid and alkali treatment could inhibit Erysipelotrichaceae_UCG-004 and norank_p_Aminicenantes, instead of promoting Pseudomonas and Tissierella at acidic and alkaline condition, respectively...
November 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29144390/rna-sequencing-and-coexpression-analysis-reveal-key-genes-involved-in-%C3%AE-linolenic-acid-biosynthesis-in-perilla-frutescens-seed
#9
Tianyuan Zhang, Chi Song, Li Song, Zhiwei Shang, Sen Yang, Dong Zhang, Wei Sun, Qi Shen, Degang Zhao
Perillafrutescen is used as traditional food and medicine in East Asia. Its seeds contain high levels of α-linolenic acid (ALA), which is important for health, but is scarce in our daily meals. Previous reports on RNA-seq of perilla seed had identified fatty acid (FA) and triacylglycerol (TAG) synthesis genes, but the underlying mechanism of ALA biosynthesis and its regulation still need to be further explored. So we conducted Illumina RNA-sequencing in seven temporal developmental stages of perilla seeds...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29143332/accurate-prediction-and-elucidation-of-drug-resistance-based-on-the-robust-and-reproducible-chemoresponse-communities
#10
Enyu Dai, Jing Wang, Feng Yang, Xu Zhou, Qian Song, Shuyuan Wang, Xuexin Yu, Dianming Liu, Qian Yang, Hong Dai, Wei Jiang, Hong Ling
Selecting the available treatment for each cancer patient from genomic context is a core goal of precision medicine, but innovative approaches with mechanism interpretation and improved performance are still highly needed. Through utilizing in vitro chemotherapy response data coupled with gene and miRNA expression profiles, we applied a network-based approach that identified markers not as individual molecules but as functional groups extracted from the integrated transcription factor and miRNA regulatory network...
November 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29143172/identification-of-key-genes-and-construction-of-microrna-mrna-regulatory-networks-in-bladder-smooth-muscle-cell-response-to-mechanical-stimuli-using-microarray-expression-profiles-and-bioinformatics-analysis
#11
Liao Peng, De-Yi Luo
PURPOSE: To identify keys genes and elucidate miRNA-mRNA regulatory networks in Bladder smooth muscle cell (BSMC) response to mechanical stimuli. METHODS: Human BSMCs, seeded on a silicone membrane, were subjected to mechanical stretch or without stretch. Microarray was used to analyze the differential expression of mRNAs and miRNAs between human BSMCs under mechanical stretch and control static control group. Differentially expressed genes(DEGs) and miRNAs (DEMs) in these two groups were identified...
November 15, 2017: World Journal of Urology
https://www.readbyqxmd.com/read/29138682/mir-128-is-implicated-in-stress-responses-by-targeting-mafg-in-skeletal-muscle-cells
#12
Rocco Caggiano, Fabio Cattaneo, Ornella Moltedo, Giovanni Esposito, Cinzia Perrino, Bruno Trimarco, Rosario Ammendola, Raffaella Faraonio
MAFG (v-Maf avian musculoaponeurotic fibrosarcoma oncogene homolog G) is a bZIP-type transcriptional regulator that belongs to the small MAF (sMAFs) protein family. By interacting with other bZIP transcription factors, sMAFs can form homo- and heterodimers governing either repressive or activating transcriptional functions. As heterodimeric partner of Nrf2, MAFG positively influences the ARE-dependent antioxidant/xenobiotic pathways, at least in condition of a correct MAFG:Nrf2 balance. MicroRNAs (miRs) participate to different regulatory networks being involved as fine-tuning regulators of gene expression...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/29138518/predicted-molecular-targets-and-pathways-for-germacrone-curdione-and-furanodiene-in-the-treatment-of-breast-cancer-using-a-bioinformatics-approach
#13
Qi Kong, Yong Ma, Jie Yu, Xiuping Chen
Germacrone, curdione, and furanodiene have been shown to be useful in the treatment of breast cancer but the pharmacological mechanism of action is unclear. In this paper, we explored a new method to study the molecular network and function of Traditional Chinese Medicine (TCM) herbs and their corresponding ingredients with bioinformatics tools, including PubChem Compound Database, BATMAN-TCM, SystemsDock, Coremine Medical, Gene ontology, and KEGG. Eleven targeted genes/proteins, 4 key pathways, and 10 biological processes were identified to participate in the mechanism of action in treating breast cancer with germacrone, curdione, and furanodiene...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138116/in-silico-identification-of-genes-involved-in-chronic-metabolic-acidosis
#14
Ishfaq A Sheikh, Adeel Malik, Sameera F M AlBasri, Mohd A Beg
AIMS: Chronic metabolic acidosis (CMA) refers to increased plasma acidity due to disturbed acid-base equilibrium in human body. CMA leads to many dysfunctions including disorders of intestinal metabolism and barrier functions. The human body responds to these intestinal dysfunctions by creating a compensatory mechanism at genomic level in intestinal epithelial cells. This study was to identify the molecular pathways involved in metabolic dysfunction and compensatory adaptations in intestinal epithelium during CMA...
November 11, 2017: Life Sciences
https://www.readbyqxmd.com/read/29137225/circular-rna-expression-profile-and-potential-function-of-hsa_circrna_101238-in-human-thoracic-aortic-dissection
#15
Meisheng Zou, Chixiong Huang, Xinzhong Li, Xiang He, Yanmei Chen, Wangjun Liao, Yulin Liao, Jie Sun, Ze Liu, Lintao Zhong, Jianping Bin
Objective: To assess the circular RNAs (circRNAs) expression profile and explore the potential functions in human thoracic aortic dissection (TAD). Methods: The differentially expressed circRNAs profiles of the aortic segments between human type A TAD patients (n=3) and age-matched normal donors (NA; n=3) were analyzed using the Arraystar human circRNAs microarray. Quantitative real-time PCR was used to validate the expression pattern of circRNAs, parental genes, and hsa-miR-320a; Western blotting confirmed MMP9 expression with additional samples...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29132315/comprehensive-genomic-analysis-of-the-cngc-gene-family-in-brassica-oleracea-novel-insights-into-synteny-structures-and-transcript-profiles
#16
Kaleem U Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A Almoneafy, Raqeeb Ullah, Xue-Liang Ren, Qing-Yao Shu
BACKGROUND: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. RESULTS: In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29132026/integrated-omics-analysis-of-root-preferred-genes-across-diverse-rice-varieties-including-japonica-and-indica-cultivars
#17
Sunok Moon, Anil Kumar Nalini Chandran, Yun-Shil Gho, Sun-A Park, Sung-Ryul Kim, Yo-Han Yoo, Ki-Hong Jung
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles...
October 26, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29129810/discerning-molecular-interactions-a-comprehensive-review-on-biomolecular-interaction-databases-and-network-analysis-tools
#18
REVIEW
Sravan Kumar Miryala, Anand Anbarasu, Sudha Ramaiah
Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge...
November 9, 2017: Gene
https://www.readbyqxmd.com/read/29129807/the-long-noncoding-rna-expression-profiles-of-paroxysmal-atrial-fibrillation-identified-by-microarray-analysis
#19
Ying Su, Long Li, Sheng Zhao, Yunan Yue, Shuixiang Yang
BACKGROUND: Long noncoding RNAs (lncRNAs) represent a novel class of noncoding RNAs that are involved in a variety of biological processes and human diseases. Recent evidence suggested that lncRNAs were associated with cardiac disorders. However, the roles of lncRNAs in paroxysmal atrial fibrillation (PAF) remain elusive. The purpose of the present study was to identify differentially expressed lncRNAs in PAF and predict their potential functions. METHODS: Between May 2014 and December 2015, a total of 67 patients, including 34 patients with PAF and 33 patients without PAF were recruited in this study...
November 9, 2017: Gene
https://www.readbyqxmd.com/read/29126713/turmeric-curcuma-longa-mirnas-and-their-regulating-targets-are-involved-in-development-and-secondary-metabolite-pathways
#20
Noopur Singh, Ashok Sharma
Turmeric has been used as a therapeutic herb over centuries in traditional medicinal systems due to the presence of several secondary metabolite compounds. microRNAs are known to regulate gene expression at the post-transcriptional level by transcriptional cleavage or translation repression. miRNAs have been demonstrated to play an active role in secondary metabolism regulation. The present work was focused on the identification of the miRNAs involved in the regulation of secondary metabolite and development process of turmeric...
November 7, 2017: Comptes Rendus Biologies
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