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miRNA prediction

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https://www.readbyqxmd.com/read/29054825/integrative-mrna-mirna-interaction-analysis-associate-with-immune-response-of-sea-cucumber-apostichopus-japonicus-based-on-transcriptome-database
#1
Xiaoxu Zhou, Yaqing Chang, Yaoyao Zhan, Xiuli Wang, Kai Lin
MicroRNAs (miRNAs) constitute a family of endogenous non-coding small RNAs that have been demonstrated to be the key effectors in mediating host-pathogen interactions. Additionally, high-throughput sequencing provides unexampled opportunities to identify the pathogenic mechanism underlying miRNAs. In the present study, the target genes of immune-related miRNAs (miR-31, miR-2008, miR-92a, miR-210 and miR-7) and specific miRNAs (miR-2004) in Echinodermata were predicted in silico and validated. Gene ontology (GO) analysis of the target genes of these six miRNAs were conducted to further understand the regulatory function in thehost immunity of Apostichopus japonicus (A...
October 17, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29053164/narrmda-negative-aware-and-rating-based-recommendation-algorithm-for-mirna-disease-association-prediction
#2
Lihong Peng, Yeqing Chen, Ning Ma, Xing Chen
An increasing amount of evidence indicates that microRNAs (miRNAs) are closely related to many important biological processes and play a significant role in various human diseases. More and more researchers have begun to seek effective methods to predict potential miRNA-disease associations. However, reliable computational methods to predict potential disease-related miRNAs are lacking. In this study, we developed a new miRNA-disease association prediction model called Negative-Aware and rating-based Recommendation algorithm for miRNA-Disease Association prediction (NARRMDA) based on the known miRNA-disease associations in the HMDD database, miRNA functional similarity, disease semantic similarity and Gaussian interaction profile kernel similarity...
October 20, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29052505/transcriptome-assembly-in-suaeda-aralocaspica-to-reveal-the-distinct-temporal-gene-mirna-alterations-between-the-dimorphic-seeds-during-germination
#3
Lei Wang, Hong-Ling Wang, Lan Yin, Chang-Yan Tian
BACKGROUND: Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mechanisms of Suaeda aralocaspica dimorphic seed germination, we applied RNA sequencing and small RNA sequencing for samples collected at three germination stages. RESULTS: A total of 79,414 transcripts were assembled using Trinity, of which 57...
October 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29051972/mir-96-5p-prevents-hepatic-stellate-cell-activation-by-inhibiting-autophagy-via-atg7
#4
Kangkang Yu, Ning Li, Qi Cheng, Jianming Zheng, Mengqi Zhu, Suxia Bao, Mingquan Chen, Guangfeng Shi
Activation of hepatic stellate cell (HSC), which is the main source of extracellular matrix, plays a pivotal role in liver fibrogenesis. Autophagy of hepatic stellate cell has been recently implicated in liver fibrosis, but the regulation of hepatic stellate cell autophagy during this process remains poorly understood. Here, we first identified miR-96-5p as an aberrantly expressed miRNA in fibrotic liver tissues. Next, we transfected miR-96-5p mimic into human hepatic stellate cell line LX-2 and observed decreased protein and mRNA levels of α-SMA and Col1A1...
October 19, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/29051527/micro-ribonucleic-acids-and-extracellular-vesicles-repertoire-in-the-spent-culture-media-is-altered-in-women-undergoing-in-vitro-fertilization
#5
Masood Abu-Halima, Sebastian Häusler, Christina Backes, Tobias Fehlmann, Claudia Staib, Sigrun Nestel, Irina Nazarenko, Eckart Meese, Andreas Keller
MicroRNAs (miRNAs) are class of small RNA molecules with major impact on gene regulation. We analyzed the potential of miRNAs secreted from pre-implantation embryos into the embryonic culture media as biomarkers to predict successful pregnancy. Using microarray analysis, we profiled the miRNome of the 56 spent culture media (SCM) after embryos transfer and found a total of 621 miRNAs in the SCM. On average, we detected 163 miRNAs in SCM of samples with failed pregnancies, but only 149 SCM miRNAs of embryos leading to pregnancies...
October 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29051037/serum-microrna-signature-predicts-response-to-high-dose-radiation-therapy-in-locally-advanced-non-small-cell-lung-cancer
#6
Yilun Sun, Peter G Hawkins, Nan Bi, Robert T Dess, Muneesh Tewari, Jason W D Hearn, James A Hayman, Gregory P Kalemkerian, Theodore S Lawrence, Randall K Ten Haken, Martha M Matuszak, Feng-Ming Kong, Shruti Jolly, Matthew J Schipper
PURPOSE: To assess the utility of circulating serum microRNAs (c-miRNAs) to predict response to high-dose radiation therapy for locally advanced non-small cell lung cancer (NSCLC). METHODS AND MATERIALS: Data from 80 patients treated from 2004 to 2013 with definitive standard- or high-dose radiation therapy for stages II-III NSCLC as part of 4 prospective institutional clinical trials were evaluated. Pretreatment serum levels of 62 miRNAs were measured by quantitative reverse transcription-polymerase chain reaction array...
September 4, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/29050943/mir-67-regulates-p-aeruginosa-avoidance-behavior-in-c-elegans
#7
Yi-Cheng Ma, Lu Zhang, Li-Li Dai, Rahat Ullah Khan, Cheng-Gang Zou
Pathogen avoidance behaviors are found throughout the animal kingdom and are important for animal's survival in nature. As a free-living nematode, C. elegans is exposed to a variety of microorganisms, including toxic or pathogenic bacteria, in soil. C. elegans can develop efficient avoidance responses to pathogenic bacteria to minimize the infection risk. However, the role of microRNAs (miRNAs) in pathogen avoidance in C. elegans remains unclear. In this report, we showed that the miRNA mir-67 was involved in a behavioral avoidance response to P...
October 16, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29050330/mir-196a2-and-lung-cancer-in-chinese-non-smoking-females-a-genetic-association-study-and-expression-analysis
#8
Zhihua Yin, Zhigang Cui, Yangwu Ren, Lingzi Xia, Hang Li, Baosen Zhou
BACKGROUND: The common polymorphism rs11614913 in miR-196a2 might be associated with lung cancer risk for non-smoking females in northeast China. METHODS: The genotypes of rs11614913 in miR-196a2 were determined by a case-control study including 1003 patients with lung cancer and 1003 healthy controls. The tissues were detected to assess the miRNA expression. Secondary structures of miR-196a2 were predicted. RESULTS: There was a significant association between miR-196a2 rs11614913 and lung cancer risk in Chinese non-smoking females...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050264/the-microrna-expression-signature-of-pancreatic-ductal-adenocarcinoma-by-rna-sequencing-anti-tumour-functions-of-the-microrna-216-cluster
#9
Keiichi Yonemori, Naohiko Seki, Tetsuya Idichi, Hiroshi Kurahara, Yusaku Osako, Keiichi Koshizuka, Takayuki Arai, Atsushi Okato, Yoshiaki Kita, Takaaki Arigami, Yuko Mataki, Yuko Kijima, Kosei Maemura, Shoji Natsugoe
We analysed the RNA sequence-based microRNA (miRNA) signature of pancreatic ductal adenocarcinoma (PDAC). Aberrantly expressed miRNAs were successfully identified in this signature. Using the PDAC signature, we focused on 4 clustered miRNAs, miR-216a-5p, miR-216a-3p, miR-216b-5p and miR-216b-3p on human chromosome 2p16.1. All members of the miR-216 cluster were significantly reduced in PDAC specimens. Ectopic expression of these miRNAs suppressed cancer cell aggressiveness, suggesting miR-216 cluster as anti-tumour miRNAs in PDAC cells...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050253/differential-expression-of-exosomal-mirnas-between-breast-cancer-patients-with-and-without-recurrence
#10
Aiko Sueta, Yutaka Yamamoto, Mai Tomiguchi, Takashi Takeshita, Mutsuko Yamamoto-Ibusuki, Hirotaka Iwase
BACKGROUND: Exosomal microRNAs (miRNAs) are promising candidate biomarkers for diagnosis or prognosis for breast cancer. We investigated the prognostic role of exosomal miRNAs in serum samples derived from patients with breast cancer and compared miRNA expression between serum and tumor tissues. METHODS: The miRNA profile derived from exosome between breast cancer patients with recurrence (n = 16) and without recurrence (n = 16) were compared by miRNA PCR array...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049183/identifying-key-genes-associated-with-acute-myocardial-infarction
#11
Ming Cheng, Shoukuan An, Junquan Li
BACKGROUND: This study aimed to identify key genes associated with acute myocardial infarction (AMI) by reanalyzing microarray data. METHODS: Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO database. After data preprocessing, genes without heterogeneity across different platforms were subjected to differential expression analysis between the AMI group and the control group using metaDE package. P < .05 was used as the cutoff for a differentially expressed gene (DEG)...
October 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29048659/microrna-520c-3p-negatively-regulates-emt-by-targeting-il-8-to-suppress-the-invasion-and-migration-of-breast-cancer
#12
Cui-Ping Tang, Han-Jing Zhou, Jian Qin, Yi Luo, Tao Zhang
Interleukin-8 (IL-8), which is secreted by cancer cells undergoing epithelial-mesenchymal transition (EMT), can promote EMT in adjacent epithelial-like cells. MicroRNAs (miRNAs/miRs) can affect the expression of target genes via binding to their 3'-untranslated regions (3'-UTRs), which may subsequently affect the biological behaviors of cancer cells. In our previous study, miR-520c-3p was predicted to directly target the 3'-UTR of IL-8. Therefore, the present study was carried out to investigate whether miR-520c-3p can interact with the IL-8 gene and regulate the EMT of breast cancer cells...
September 19, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29048632/microrna-1297-inhibits-metastasis-and-epithelial-mesenchymal-transition-by-targeting-aeg-1-in-cervical-cancer
#13
Zengyan Wang, Shanyang He, Peng Guo, Xu Guo, Jingxuan Zheng
Accumulating evidence has demonstrated that aberrant miRNAs contribute to cervical cancer (CC) development and progression. However, the roles of various miRNAs in CC remain to be determined. In the present study, we confirmed that a decreased miR-1297 expression was present in CC tissues and cell lines. Our clinical analysis revealed that the downregulated miR-1297 expression was significantly correlated with poor prognostic features including lymph node metastasis and lymphovascular space invasion. Moreover, we confirmed that miR-1297 was a novel independent prognostic marker for predicting the 5-year survival of CC patients...
September 20, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29048619/microrna-381-serves-as-a-prognostic-factor-and-inhibits-migration-and-invasion-in-non-small-cell-lung-cancer-by-targeting-lrh-1
#14
Chunyan Tian, Jun Li, Lili Ren, Ren Peng, Binbin Chen, Yumei Lin
Accumulating evidence has demonstrated that aberrant miRNAs were involved in carcinogenesis and tumor progression by regulating oncogenes or tumor suppressor expression. Dysregulation of miR-381 has been reported in different tumors. However, the clinical roles and underlying mechanism in non-small cell lung cancer (NSCLC) remains to be elucidated. We found the expression of miR-381 was significantly downregulated in both NSCLC tissues and cell lines. Clinical analysis revealed the reduced miR-381 was obviously associated with advanced TNM stage and lymph node metastasis...
September 14, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29048575/microrna-binding-site-polymorphisms-in-genes-involved-in-colorectal-cancer-etiopathogenesis-and-their-impact-on-disease-prognosis
#15
Michaela Schneiderova, Alessio Naccarati, Barbara Pardini, Fabio Rosa, Cornelia Di Gaetano, Katerina Jiraskova, Alena Opattova, Miroslav Levy, Karel Veskrna, Veronika Veskrnova, Tomas Buchler, Stefano Landi, Pavel Vodicka, Veronika Vymetalkova
According to the Vogelstein's model of colorectal carcinogenesis, genetic variations in highly penetrant genes may be involved in the colorectal cancer (CRC) pathogenesis. Similarly, aberrant function and/or altered expression of microRNAs (miRNAs) often occur in CRC. In this context, polymorphisms in miRNA-binding sites (miRSNPs) may affect miRNA/target gene interaction, resulting in differential mRNA/protein expression and increased susceptibility to common diseases. To explore this phenomenon, we have mined the 3' untranslated regions (3'UTRs) of genes known to be frequently mutated in CRC to search for miRSNPs and tested their association with CRC risk and clinical outcome...
October 17, 2017: Mutagenesis
https://www.readbyqxmd.com/read/29047327/integrative-testis-transcriptome-analysis-reveals-differentially-expressed-mirnas-and-their-mrna-targets-during-early-puberty-in-atlantic-salmon
#16
K O Skaftnesmo, R B Edvardsen, T Furmanek, D Crespo, E Andersson, L Kleppe, G L Taranger, J Bogerd, R W Schulz, A Wargelius
BACKGROUND: Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty negatively impacts animal welfare and growth. We hypothesize that certain miRNAs modulate mRNAs relevant for the initiation of puberty. To explore which miRNAs regulate mRNAs during initiation of puberty in salmon, we performed an integrated transcriptome analysis (miRNA and mRNA-seq) of salmon testis at three stages of development: an immature, long-term quiescent stage, a prepubertal stage just before, and a pubertal stage just after the onset of single cell proliferation activity in the testis...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29046688/global-analysis-of-small-rna-dynamics-during-seed-development-of-picea-glauca-and-arabidopsis-thaliana-populations-reveals-insights-on-their-evolutionary-trajectories
#17
Yang Liu, Yousry A El-Kassaby
While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18-24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29046684/novel-insights-into-mirna-regulation-of-storage-protein-biosynthesis-during-wheat-caryopsis-development-under-drought-stress
#18
Xin-Yu Chen, Yang Yang, Li-Ping Ran, Zhao-di Dong, Er-Jin Zhang, Xu-Run Yu, Fei Xiong
Drought stress is a significant abiotic stress factor that affects wheat yield and quality. MicroRNA (miRNA) plays an important role in regulating caryopsis development in response to drought stress. However, little is known about the expression characteristics of miRNAs and how they regulate protein accumulation in wheat caryopsis under drought stress. To address this, two small RNA libraries of wheat caryopsis under control and drought stress conditions were constructed and sequenced. A total of 125 miRNAs were identified in the two samples, of which 110 were known and 15 were novel...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29046142/the-roles-of-micrornas-in-regulating-chemotherapy-resistance-of-non-small-cell-lung-cancer
#19
Xiaoxuan Wei, Xiaoyan Shen, Yanchen Ren, Weidong Hu
Lung cancer is considered the leading cause of cancer death in the word. Among all lung cancer cases, non-small cell lung cancer (NSCLC) accounts for 85%. Currently, chemotherapy is still the major therapeutic method of lung cancer. However, chemoresistance is a serious obstacle in treating NSCLC. Up to now, many reports have suggested that microRNAs(miRNAs) could contribute to lung cancer cell chemosensitivity. MicroRNAs, a class of endogenous non-coding small RNAs, regulate gene expression by binding to their complementary target messenger RNAs, leading to mRNA degradation or translational suppression...
October 18, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/29045685/micrornas-and-complex-diseases-from-experimental-results-to-computational-models
#20
Xing Chen, Di Xie, Qi Zhao, Zhu-Hong You
Plenty of microRNAs (miRNAs) were discovered at a rapid pace in plants, green algae, viruses and animals. As one of the most important components in the cell, miRNAs play a growing important role in various essential and important biological processes. For the recent few decades, amounts of experimental methods and computational models have been designed and implemented to identify novel miRNA-disease associations. In this review, the functions of miRNAs, miRNA-target interactions, miRNA-disease associations and some important publicly available miRNA-related databases were discussed in detail...
October 17, 2017: Briefings in Bioinformatics
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