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https://www.readbyqxmd.com/read/28919414/changes-in-related-circular-rnas-following-er%C3%AE-knockdown-and-the-relationship-to-rbmsc-osteogenesis
#1
Xiaoyun Li, Bojia Peng, Xiaofeng Zhu, Panpan Wang, Yingquan Xiong, Hengrui Liu, Kehuan Sun, Haixia Wang, Ling Ou, Zhidi Wu, Xiaoguang Liu, Haibin He, Shu Mo, Xunqian Peng, Ya Tian, Ronghua Zhang, Li Yang
Recently, several studies have indicated that circular RNAs (circRNAs) play significant roles in various disease; however, Little is known about the chronology of estrogen receptor beta (ERβ) deficiency and altered circRNA expression, or their relationship with osteogenesis. Herein, we show through western-blot and quantitative real-time PCR assays, that when ERβ is silenced, the expression of osteogenesis-related proteins and mRNAs were down-regulated. We then performed RNA-Seq to analyze differential circRNA expression between the control and ERβ knockdown group...
September 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28919164/integrated-analysis-of-microrna-and-gene-expression-profiles-reveals-a-functional-regulatory-module-associated-with-liver-fibrosis
#2
Wei Chen, Wenshan Zhao, Aiting Yang, Anjian Xu, Huan Wang, Min Cong, Tianhui Liu, Ping Wang, Hong You
BACKGROUND: Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation have important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. METHODS: The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28919162/mir-101-1-expression-pattern-in-qinchuan-cattle-and-its-role-in-the-regulation-of-cell-differentiation
#3
Jiyao Wu, Dandan He, Binglin Yue, Chunlei Zhang, Xingtang Fang, Hong Chen
MiRNAs have emerged as key regulators of skeletal muscle development, but the knowledge of miRNAs in the molecular network of muscle development remains poorly understood. In this study, we designed to examine the biological function of bovine-miR-101-1. The bovine miR-101-1 was detected in the skeletal muscle of fetal, calf and adult cattle. Its abundance was significantly higher in the skeletal muscle of calf cattle than that in fetal and adult cattle. In the course of C2C12 myoblast differentiation, the expression of miR-101-1 gradually increased...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28916800/alternative-splicing-complexity-contributes-to-genetic-improvement-of-drought-resistance-in-the-rice-maintainer-huhan2b
#4
Haibin Wei, Qiaojun Lou, Kai Xu, Ming Yan, Hui Xia, Xiaosong Ma, Xinqiao Yu, Lijun Luo
Water-saving and drought-resistantce rice (WDR) breeding practices have greatly increased grain yield and drought resistance. To study the genetic basis of adaptation to drought, transcriptome sequences from the WDR maintainer line HuHan2B and the recurrent parent HanFengB were analyzed for alternative splicing (AS) complexity. Intron retention, the dominant AS type, accounted for 42% of the observed AS events. Differential expression analysis revealed transcripts were preferentially expressed in different varieties and conditions...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28915785/seed-maturation-associated-transcriptional-programs-and-regulatory-networks-underlying-genotypic-difference-in-seed-dormancy-and-size-weight-in-wheat-triticum-aestivum-l
#5
Yuji Yamasaki, Feng Gao, Mark C Jordan, Belay T Ayele
BACKGROUND: Maturation forms one of the critical seed developmental phases and it is characterized mainly by programmed cell death, dormancy and desiccation, however, the transcriptional programs and regulatory networks underlying acquisition of dormancy and deposition of storage reserves during the maturation phase of seed development are poorly understood in wheat. The present study performed comparative spatiotemporal transcriptomic analysis of seed maturation in two wheat genotypes with contrasting seed weight/size and dormancy phenotype...
September 16, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28912564/transcriptome-analysis-of-developing-lens-reveals-abundance-of-novel-transcripts-and-extensive-splicing-alterations
#6
Rajneesh Srivastava, Gungor Budak, Soma Dash, Salil A Lachke, Sarath Chandra Janga
Lens development involves a complex and highly orchestrated regulatory program. Here, we investigate the transcriptomic alterations and splicing events during mouse lens formation using RNA-seq data from multiple developmental stages, and construct a molecular portrait of known and novel transcripts. We show that the extent of novelty of expressed transcripts decreases significantly in post-natal lens compared to embryonic stages. Characterization of novel transcripts into partially novel transcripts (PNTs) and completely novel transcripts (CNTs) (novelty score ≥ 70%) revealed that the PNTs are both highly conserved across vertebrates and highly expressed across multiple stages...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911111/combinatorial-ensemble-mirna-target-prediction-of-co-regulation-networks-with-non-prediction-data
#7
Jason A Davis, Sita J Saunders, Martin Mann, Rolf Backofen
MicroRNAs (miRNAs) are key regulators of cell-fate decisions in development and disease with a vast array of target interactions that can be investigated using computational approaches. For this study, we developed metaMIR, a combinatorial approach to identify miRNAs that co-regulate identified subsets of genes from a user-supplied list. We based metaMIR predictions on an improved dataset of human miRNA-target interactions, compiled using a machine-learning-based meta-analysis of established algorithms. Simultaneously, the inverse dataset of negative interactions not likely to occur was extracted to increase classifier performance, as measured using an expansive set of experimentally validated interactions from a variety of sources...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28902459/exome-sequences-of-multiplex-multigenerational-families-reveal-schizophrenia-risk-loci-with-potential-implications-for-neurocognitive-performance
#8
Mark Z Kos, Melanie A Carless, Juan Peralta, Joanne E Curran, Ellen E Quillen, Marcio Almeida, August Blackburn, Lucy Blondell, David R Roalf, Michael F Pogue-Geile, Ruben C Gur, Harald H H Göring, Vishwajit L Nimgaonkar, Raquel E Gur, Laura Almasy
Schizophrenia is a serious mental illness, involving disruptions in thought and behavior, with a worldwide prevalence of about one percent. Although highly heritable, much of the genetic liability of schizophrenia is yet to be explained. We searched for susceptibility loci in multiplex, multigenerational families affected by schizophrenia, targeting protein-altering variation with in silico predicted functional effects. Exome sequencing was performed on 136 samples from eight European-American families, including 23 individuals diagnosed with schizophrenia or schizoaffective disorder...
September 13, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28901494/molecular-mechanisms-of-pathogenesis-in-hepatocellular-carcinoma-revealed-by-rna%C3%A2-sequencing
#9
Yao Liu, Zhe Yang, Feng Du, Qiao Yang, Jie Hou, Xiaohong Yan, Yi Geng, Yaning Zhao, Hua Wang
The present study aimed to explore the underlying molecular mechanisms of hepatocellular carcinoma (HCC). RNA‑sequencing profiles GSM629264 and GSM629265, from the GSE25599 data set, were downloaded from the Gene Expression Omnibus database and processed by quality evaluation. GSM629264 and GSM629265 were from HCC and adjacent non‑cancerous tissues, respectively. TopHat software was used for alignment analysis, followed by the detection of novel splicing sites. In addition, the Cufflinks software package was used to analyze gene expressions, and the Cuffdiff program was used to screen for differently expressed genes (DEGs) and differentially expressed splicing variants...
September 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28899343/genome-wide-gene-expression-analysis-in-the-placenta-from-fetus-with-trisomy-21
#10
Ji Hyae Lim, You Jung Han, Hyun Jin Kim, Dong Wook Kwak, So Yeon Park, Sun-Hee Chun, Hyun Mee Ryu
BACKGROUND: We performed whole human genome expression analysis in placenta tissue (normal and T21) samples in order to investigate gene expression into the pathogenesis of trisomy 21 (T21) placenta. We profiled the whole human genome expression of placental samples from normal and T21 fetuses using the GeneChip Human Genome U133 plus 2.0 array. Based on these data, we predicted the functions of differentially expressed genes using bioinformatics tools. RESULTS: A total of 110 genes had different expression patterns in the T21 placentas than they did in the normal placentas...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28895406/identification-of-potential-key-genes-associated-with-diffuse-large-b-cell-lymphoma-based-on-microarray-gene-expression-profiling
#11
X Luo, F Shi, H Qiu, Y Tong, X Gao
The study aimed to screen potential key genes, and their targeted miRNAs and transcription factors (TFs) that were related to diffuse large B-cell lymphoma (DLBCL), and explore potential therapeutic targets for the progression of DLBCL. Dataset GSE56315 extracted from human tonsils was downloaded from Gene Expression Omnibus. Limma package was used to identify differential expression genes (DEG) between DLBCL and normal human tonsils samples, and the function and pathway enrichment analyses were performed. Then, functional interaction (FI) networks analyses of DEGs were implemented, and modules were extracted...
September 12, 2017: Neoplasma
https://www.readbyqxmd.com/read/28895405/screening-key-mirnas-for-human-hepatocellular-carcinoma-based-on-mirna-mrna-functional-synergistic-network
#12
C Zhang, H Du
The safety of miRNAs has been proven and the prophylactic use of miRNA-based approaches may be foreseen for patients with hepatocellular carcinoma (HCC). However, the underlying regulatory mechanism of miRNAs in HCC has not been fully clarified. Using bioinformatic analyses, we compared data of miRNA and mRNA expression profiling of HCC from Gene Expression Omnibus (GEO) database, respectively. Differentially expressed miRNAs and differentially expressed genes (DEGs) were identified. Based on the miRTarBase predictions, the miRNA-dependent regulatory network was constructed...
September 12, 2017: Neoplasma
https://www.readbyqxmd.com/read/28894971/identification-of-genes-associated-with-primary-open-angle-glaucoma-by-bioinformatics-approach
#13
Haiyan Qiu, Benhu Zhu, Shengrong Ni
PURPOSE: This study aimed to identify associated genes with primary open-angle glaucoma (POAG) and explore the potentially modular mechanism underlying POAG. METHODS: We downloaded gene expression profiles data GSE27276 from gene expression omnibus and identified differentially expressed genes between POAG patients and normal controls. Then, gene ontology analysis and kyoto encyclopedia of genes and genomes pathway enrichment were performed to predict the DEGs functions, followed with the construction, centrality analysis, and module mining of protein-protein interaction network...
September 11, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28894961/digital-soil-mapping-using-remote-sensing-indices-terrain-attributes-and-vegetation-features-in-the-rangelands-of-northeastern-iran
#14
Ebrahim Mahmoudabadi, Alireza Karimi, Gholam Hosain Haghnia, Adel Sepehr
Digital soil mapping has been introduced as a viable alternative to the traditional mapping methods due to being fast and cost-effective. The objective of the present study was to investigate the capability of the vegetation features and spectral indices as auxiliary variables in digital soil mapping models to predict soil properties. A region with an area of 1225 ha located in Bajgiran rangelands, Khorasan Razavi province, northeastern Iran, was chosen. A total of 137 sampling sites, each containing 3-5 plots with 10-m interval distance along a transect established based on randomized-systematic method, were investigated...
September 11, 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28894735/navigating-the-functional-landscape-of-transcription-factors-via-non-negative-tensor-factorization-analysis-of-medline-abstracts
#15
Sujoy Roy, Daqing Yun, Behrouz Madahian, Michael W Berry, Lih-Yuan Deng, Daniel Goldowitz, Ramin Homayouni
In this study, we developed and evaluated a novel text-mining approach, using non-negative tensor factorization (NTF), to simultaneously extract and functionally annotate transcriptional modules consisting of sets of genes, transcription factors (TFs), and terms from MEDLINE abstracts. A sparse 3-mode term × gene × TF tensor was constructed that contained weighted frequencies of 106,895 terms in 26,781 abstracts shared among 7,695 genes and 994 TFs. The tensor was decomposed into sub-tensors using non-negative tensor factorization (NTF) across 16 different approximation ranks...
2017: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/28892060/a-functional-genomics-predictive-network-model-identifies-regulators-of-inflammatory-bowel-disease
#16
Lauren A Peters, Jacqueline Perrigoue, Arthur Mortha, Alina Iuga, Won-Min Song, Eric M Neiman, Sean R Llewellyn, Antonio Di Narzo, Brian A Kidd, Shannon E Telesco, Yongzhong Zhao, Aleksandar Stojmirovic, Jocelyn Sendecki, Khader Shameer, Riccardo Miotto, Bojan Losic, Hardik Shah, Eunjee Lee, Minghui Wang, Jeremiah J Faith, Andrew Kasarskis, Carrie Brodmerkel, Mark Curran, Anuk Das, Joshua R Friedman, Yoshinori Fukui, Mary Beth Humphrey, Brian M Iritani, Nicholas Sibinga, Teresa K Tarrant, Carmen Argmann, Ke Hao, Panos Roussos, Jun Zhu, Bin Zhang, Radu Dobrin, Lloyd F Mayer, Eric E Schadt
A major challenge in inflammatory bowel disease (IBD) is the integration of diverse IBD data sets to construct predictive models of IBD. We present a predictive model of the immune component of IBD that informs causal relationships among loci previously linked to IBD through genome-wide association studies (GWAS) using functional and regulatory annotations that relate to the cells, tissues, and pathophysiology of IBD. Our model consists of individual networks constructed using molecular data generated from intestinal samples isolated from three populations of patients with IBD at different stages of disease...
September 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28889104/machine-learning-analysis-identifies-drosophilagrunge-atrophin-as-an-important-learning-and-memory-gene-required-for-memory-retention-and-social-learning
#17
Balint Z Kacsoh, Casey S Greene, Giovanni Bosco
High throughput experiments are becoming increasingly common, and scientists must balance hypothesis driven experiments with genome wide data acquisition. We sought to predict novel genes involved in Drosophila learning and long-term memory from existing public high-throughput data. We performed an analysis using PILGRM, which analyzes public gene expression compendia using machine learning. We evaluated the top prediction alongside genes involved in learning and memory in IMP, an interface for functional relationship networks...
September 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28882624/network-pharmacology-analysis-of-the-anti-cancer-pharmacological-mechanisms-of-ganoderma-lucidum-extract-with-experimental-support-using-hepa1-6-bearing-c57-bl-6-mice
#18
Ruo-Lin Zhao, Yu-Min He
ETHNOPHARMACOLOGICAL RELEVANCE: Ganoderma lucidum (GL) is an oriental medical fungus, which was used to prevent and treat many diseases. Previously, the effective components of Ganoderma lucidum extract (GLE) were extracted from two kinds of GL, Ganoderma lucidum (Leyss. Ex Fr.) Karst. and Ganoderma sinense Zhao, Xu et Zhang, which have been used for adjuvant anti-cancer clinical therapy for more than 20 years. However, its concrete active components and its regulation mechanisms on tumor are unclear...
September 4, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28879530/correlation-analyses-revealed-global-microrna-mrna-expression-associations-in-human-peripheral-blood-mononuclear-cells
#19
Lan Wang, Jiang Zhu, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Xiao-Wei Zhu, Wei Xia, Fang-Fei Xie, Pei He, Peng-Fei Bing, Ying-Hua Qiu, Xiang Lin, Xin Lu, Lei Zhang, Neng-Jun Yi, Yong-Hong Zhang, Shu-Feng Lei
MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study...
September 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28878756/analysis-of-microbial-functions-in-the-rhizosphere-using-a-metabolic-network-based-framework-for-metagenomics-interpretation
#20
Shany Ofaim, Maya Ofek-Lalzar, Noa Sela, Jiandong Jinag, Yechezkel Kashi, Dror Minz, Shiri Freilich
Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups...
2017: Frontiers in Microbiology
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