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https://www.readbyqxmd.com/read/29785561/reptb-a-gene-ontology-based-drug-repurposing-approach-for-tuberculosis
#1
Anurag Passi, Neeraj Kumar Rajput, David J Wild, Anshu Bhardwaj
Tuberculosis (TB) is the world's leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes...
May 21, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29784056/biomarker-micrornas-for-prostate-cancer-metastasis-screened-with-a-network-vulnerability-analysis-model
#2
Yuxin Lin, Feifei Chen, Li Shen, Xiaoyu Tang, Cui Du, Zhandong Sun, Huijie Ding, Jiajia Chen, Bairong Shen
BACKGROUND: Prostate cancer (PCa) is a fatal malignant tumor among males in the world and the metastasis is a leading cause for PCa death. Biomarkers are therefore urgently needed to detect PCa metastatic signature at the early time. MicroRNAs are small non-coding RNAs with the potential to be biomarkers for disease prediction. In addition, computer-aided biomarker discovery is now becoming an attractive paradigm for precision diagnosis and prognosis of complex diseases. METHODS: In this study, we identified key microRNAs as biomarkers for predicting PCa metastasis based on network vulnerability analysis...
May 21, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29781401/screening-of-prognostic-risk-micrornas-for-acute-myeloid-leukemia
#3
Hai-Yan Gao, Wei Wang, Xin-Guo Luo, Yong-Fang Jiang, Xin He, Ping Xu, Xi Chen, Xiao-Yun Li
OBJECTIVES: This study aimed to investigate the risk miRNAs (microRNAs) for AML (acute myeloid leukemia) prognosis and related regulatory mechanisms. METHODS: MiRNA and gene expression data, as well as clinical data of 176 patients were first downloaded from TCGA. Then miRNAs and genes significantly affecting the survival time based on KM survival curve were identified using Log Rank test. Next, COX proportional-hazard regression analysis was performed to screen the risk miRNAs (P-value < 0...
May 19, 2018: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/29775159/bioinformatics-functional-analysis-of-let-7a-mir-34a-and-mir-199a-b-reveals-novel-insights-into-immune-system-pathways-and-cancer-hallmarks-for-hepatocellular-carcinoma
#4
Bangly Soliman, Ahmed Salem, Mohamed Ghazy, Nourhan Abu-Shahba, Mahmoud El Hefnawi
Let-7a, miR-34a, and miR-199 a/b have gained a great attention as master regulators for cellular processes. In particular, these three micro-RNAs act as potential onco-suppressors for hepatocellular carcinoma. Bioinformatics can reveal the functionality of these micro-RNAs through target prediction and functional annotation analysis. In the current study, in silico analysis using innovative servers (miRror Suite, DAVID, miRGator V3.0, GeneTrail) has demonstrated the combinatorial and the individual target genes of these micro-RNAs and further explored their roles in hepatocellular carcinoma progression...
May 2018: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29772236/identification-and-characterization-of-circular-rnas-in-rapid-atrial-pacing-dog-atrial-tissue
#5
Wenfeng Shangguan, Xue Liang, Wen Shi, Tong Liu, Manman Wang, Guangping Li
Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs, and participating in the process of many diseases. However, the expression and functions of circRNAs in Rapid atrial pacing (RAP) dog atrial tissue still unknown. 12 canines were randomly assigned to control and pacing group. RAP at 500 beats per minute was maintained 14 days in the pacing group. The expression characterization of circRNAs were revealed by high-throughput sequencing. We totally predicted 15,990 circRNAs in dog atrial tissues...
May 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29772009/ptra-a-reporter-system-for-monitoring-the-intracellular-dynamics-of-gene-expression
#6
Sabine G Wagner, Martin Ziegler, Hannes Löwe, Andreas Kremling, Katharina Pflüger-Grau
The presence of standardised tools and methods to measure and represent accurately biological parts and functions is a prerequisite for successful metabolic engineering and crucial to understand and predict the behaviour of synthetic genetic circuits. Many synthetic gene networks are based on transcriptional circuits, thus information on transcriptional and translational activity is important for understanding and fine-tuning the synthetic function. To this end, we have developed a toolkit to analyse systematically the transcriptional and translational activity of a specific synthetic part in vivo...
2018: PloS One
https://www.readbyqxmd.com/read/29768346/abnormally-high-expression-of-pold1-mcm2-and-plk4-promotes-relapse-of-acute-lymphoblastic-leukemia
#7
Sheng Li, Chengzhong Wang, Weikai Wang, Weidong Liu, Guiqin Zhang
This study aimed to explore the underlying mechanism of relapsed acute lymphoblastic leukemia (ALL).Datasets of GSE28460 and GSE18497 were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between diagnostic and relapsed ALL samples were identified using Limma package in R, and a Venn diagram was drawn. Next, functional enrichment analyses of co-regulated DEGs were performed. Based on the String database, protein-protein interaction network and module analyses were also conducted...
May 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29767230/competing-endogenous-rna-regulatory-network-in-papillary-thyroid-carcinoma
#8
Shouhua Chen, Xiaobin Fan, He Gu, Lili Zhang, Wenhua Zhao
The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis...
May 11, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29765519/long-noncoding-rnas-are-associated-with-metabolic-and-cellular-processes-in-the-jejunum-mucosa-of-pre-weaning-calves-in-response-to-different-diets
#9
Rosemarie Weikard, Frieder Hadlich, Harald M Hammon, Doerte Frieten, Caroline Gerbert, Christian Koch, Georg Dusel, Christa Kuehn
Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome. Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves' intestinal mucosa...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29764394/comprehensive-analysis-of-coding-lncrna-gene-co-expression-network-uncovers-conserved-functional-lncrnas-in-zebrafish
#10
Wen Chen, Xuan Zhang, Jing Li, Shulan Huang, Shuanglin Xiang, Xiang Hu, Changning Liu
BACKGROUND: Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing. RESULTS: We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29763751/integration-of-summary-data-from-gwas-and-eqtl-studies-identified-novel-causal-bmd-genes-with-functional-predictions
#11
Xiang-He Meng, Xiang-Ding Chen, Jonathan Greenbaum, Qin Zeng, Sheng-Lan You, Hong-Mei Xiao, Li-Jun Tan, Hong-Wen Deng
PURPOSE: Osteoporosis is a common global health problem characterized by low bone mineral density (BMD) and increased risk of fracture. Genome-wide association studies (GWAS) have identified >100 genetic loci associated with BMD. However, the functional genes responsible for most associations remain largely unknown. We conducted an innovative summary statistic data-based Mendelian randomization (SMR) analysis to identify novel causal genes associated with BMD and explored their potential functional significance...
May 12, 2018: Bone
https://www.readbyqxmd.com/read/29760811/global-dna-methylation-changes-spanning-puberty-are-near-predicted-estrogen-responsive-genes-and-enriched-for-genes-involved-in-endocrine-and-immune-processes
#12
Emma E Thompson, Jessie Nicodemus-Johnson, Kyung Won Kim, James E Gern, Daniel J Jackson, Robert F Lemanske, Carole Ober
Background: The changes that occur during puberty have been implicated in susceptibility to a wide range of diseases later in life, many of which are characterized by sex-specific differences in prevalence. Both genetic and environmental factors have been associated with the onset or delay of puberty, and recent evidence has suggested a role for epigenetic changes in the initiation of puberty as well. Objective: To identify global DNA methylation changes that arise across the window of puberty in girls and boys...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29760609/identification-of-potential-crucial-genes-and-construction-of-microrna-mrna-negative-regulatory-networks-in-osteosarcoma
#13
Yue Pan, Lingyun Lu, Junquan Chen, Yong Zhong, Zhehao Dai
Background: This study aimed to identify potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma by comprehensive bioinformatics analysis. Methods: Data of gene expression profiles (GSE28424) and miRNA expression profiles (GSE28423) were downloaded from GEO database. The differentially expressed genes (DEGs) and miRNAs (DEMIs) were obtained by R Bioconductor packages. Functional and enrichment analyses of selected genes were performed using DAVID database...
2018: Hereditas
https://www.readbyqxmd.com/read/29760555/comprehensive-analysis-of-a-long-noncoding-rna-associated-competing-endogenous-rna-network-in-colorectal-cancer
#14
Qiaowei Fan, Bingrong Liu
Purpose: This study was aimed to develop a lncRNA-associated competing endogenous RNA (ceRNA) network to provide further understanding of the ceRNA regulatory mechanism and pathogenesis in colorectal cancer (CRC). Patients and methods: Expression profiles of mRNAs, lncRNAs, and miRNAs, and clinical information for CRC patients were obtained from The Cancer Genome Atlas. The differentially expressed mRNAs, lncRNAs, and miRNAs (referred to as "DEmRNAs", "DElncRNAs", and "DEmiRNAs", respectively) were screened out between 539 CRC samples and 11 normal samples...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29758261/annotating-diseases-using-human-phenotype-ontology-improves-prediction-of-disease-associated-long-non-coding-rnas
#15
Duc-Hau Le, Lan T M Dao
Recently, many long non-coding RNAs (lncRNAs) have been identified and their biological function has been characterized; however, our understanding of their underlying molecular mechanisms related to disease is still limited. To overcome the limitation in experimentally identifying disease-lncRNA associations, computational methods have been proposed as a powerful tool to predict such associations. These methods are usually based on the similarities between diseases or lncRNAs since it was reported that similar diseases are associated with functionally similar lncRNAs...
May 11, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29751546/genome-wide-identification-and-analysis-of-arabidopsis-sodium-proton-antiporter-nhx-and-human-sodium-proton-exchanger-nhe-homologs-in-sorghum-bicolor
#16
P Hima Kumari, S Anil Kumar, Katam Ramesh, Palakolanu Sudhakar Reddy, M Nagaraju, A Bhanu Prakash, Trushar Shah, Ashley Henderson, Rakesh K Srivastava, G Rajasheker, A Chitikineni, Rajeev K Varshney, P Rathnagiri, M Lakshmi Narasu, P B Kavi Kishor
Na⁺ transporters play an important role during salt stress and development. The present study is aimed at genome-wide identification, in silico analysis of sodium-proton antiporter (NHX) and sodium-proton exchanger (NHE)-type transporters in Sorghum bicolor and their expression patterns under varied abiotic stress conditions. In Sorghum , seven NHX and nine NHE homologs were identified. Amiloride (a known inhibitor of Na⁺/H⁺ exchanger activity) binding motif was noticed in both types of the transporters...
May 3, 2018: Genes
https://www.readbyqxmd.com/read/29749550/microarray%C3%A2-based-bioinformatics-analysis-of-the-prospective-target-gene-network-of-key-mirnas-influenced-by-long-non%C3%A2-coding-rna-pvt1-in-hcc
#17
Yu Zhang, Wei-Jia Mo, Xiao Wang, Tong-Tong Zhang, Yuan Qin, Han-Lin Wang, Gang Chen, Dan-Ming Wei, Yi-Wu Dang
The long non‑coding RNA (lncRNA) PVT1 plays vital roles in the tumorigenesis and development of various types of cancer. However, the potential expression profiling, functions and pathways of PVT1 in HCC remain unknown. PVT1 was knocked down in SMMC‑7721 cells, and a miRNA microarray analysis was performed to detect the differentially expressed miRNAs. Twelve target prediction algorithms were used to predict the underlying targets of these differentially expressed miRNAs. Bioinformatics analysis was performed to explore the underlying functions, pathways and networks of the targeted genes...
May 2, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29749517/identification-of-a-5%C3%A2-lncrna-signature%C3%A2-based-risk-scoring-system-for-survival-prediction-in-colorectal-cancer
#18
Liqiang Gu, Jun Yu, Qing Wang, Bin Xu, Liechen Ji, Lin Yu, Xipeng Zhang, Hui Cai
The present study aimed to investigate potential prognostic long noncoding RNAs (lncRNAs) associated with colorectal cancer (CRC). An mRNA‑seq dataset obtained from The Cancer Genome Atlas was employed to identify the differentially expressed lncRNAs (DELs) between CRC patients with good and poor prognoses. Subsequently, univariate and multivariate Cox regression analyses were conducted to analyze the prognosis‑associated lncRNAs among all DELs. In addition, a risk scoring system was developed according to the expression levels of the prognostic lncRNAs, which was then applied to a training set and an independent testing set...
May 3, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29749503/a-gene-interaction-network%C3%A2-based-method-to-measure-the-common-and-heterogeneous-mechanisms-of-gynecological-cancer
#19
Mingyuan Wang, Liping Li, Jinglan Liu, Jinjin Wang
Gynecological malignancies are a leading cause of mortality in the female population. The present study intended to identify the association between three severe types of gynecological cancer, specifically ovarian cancer, cervical cancer and endometrial cancer, and to identify the connective driver genes, microRNAs (miRNAs) and biological processes associated with these types of gynecological cancer. In the present study, individual driver genes for each type of cancer were identified using integrated analysis of multiple microarray data...
May 3, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29745859/detecting-complexes-from-edge-weighted-ppi-networks-via-genes-expression-analysis
#20
Zehua Zhang, Jian Song, Jijun Tang, Xinying Xu, Fei Guo
BACKGROUND: Identifying complexes from PPI networks has become a key problem to elucidate protein functions and identify signal and biological processes in a cell. Proteins binding as complexes are important roles of life activity. Accurate determination of complexes in PPI networks is crucial for understanding principles of cellular organization. RESULTS: We propose a novel method to identify complexes on PPI networks, based on different co-expression information...
April 24, 2018: BMC Systems Biology
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