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Network protein function prediction

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https://www.readbyqxmd.com/read/29781401/screening-of-prognostic-risk-micrornas-for-acute-myeloid-leukemia
#1
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
#2
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/29772009/ptra-a-reporter-system-for-monitoring-the-intracellular-dynamics-of-gene-expression
#3
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
#4
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/29766490/emotional-hyper-reactivity-and-cardiometabolic-risk-in-remitted-bipolar-patients-a-machine-learning-approach
#5
A A Dargél, F Roussel, S Volant, B Etain, R Grant, J-M Azorin, K M'Bailara, F Bellivier, T Bougerol, J-P Kahn, P Roux, V Aubin, P Courtet, M Leboyer, F Kapczinski, C Henry
OBJECTIVE: Remitted bipolar disorder (BD) patients frequently present with chronic mood instability and emotional hyper-reactivity, associated with poor psychosocial functioning and low-grade inflammation. We investigated emotional hyper-reactivity as a dimension for characterization of remitted BD patients, and clinical and biological factors for identifying those with and without emotional hyper-reactivity. METHOD: A total of 635 adult remitted BD patients, evaluated in the French Network of Bipolar Expert Centers from 2010-2015, were assessed for emotional reactivity using the Multidimensional Assessment of Thymic States...
May 15, 2018: Acta Psychiatrica Scandinavica
https://www.readbyqxmd.com/read/29760609/identification-of-potential-crucial-genes-and-construction-of-microrna-mrna-negative-regulatory-networks-in-osteosarcoma
#6
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/29757353/development-and-evaluation-of-a-deep-learning-model-for-protein-ligand-binding-affinity-prediction
#7
Marta M Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki
Motivation: Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has recently gained considerable attention as it allows the model to "learn" to extract features that are relevant for the task at hand. Results: We have developed a novel deep neural network estimating the binding affinity of ligand-receptor complexes...
May 10, 2018: Bioinformatics
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
#8
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/29749517/identification-of-a-5%C3%A2-lncrna-signature%C3%A2-based-risk-scoring-system-for-survival-prediction-in-colorectal-cancer
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/29741786/reconstruction-and-analysis-of-the-aberrant-lncrna-mirna-mrna-network-based-on-competitive-endogenous-rna-in-cesc
#12
Jukun Song, Aizhu Ye, Enli Jiang, Xinhai Yin, Zhu Chen, Guohui Bai, Yu Zhou, Jianguo Liu
A growing body of studies has demonstrated that long non-coding RNA (lncRNA) are regarded as the primary section of the ceRNA network. This is thought to be the case owing to its regulation of protein-coding gene expression by functioning as miRNA sponges. However, functional roles and regulatory mechanisms of lncRNA-mediated ceRNA in cervical squamous cell carcinoma (CESC), as well as their use for potential prediction of CESC prognosis, remains unknown. The aberrant expression profiles of mRNA, lncRNA, and miRNA of 306 cervical squamous cancer tissues and three adjacent cervical tissues were obtained from the TCGA database...
May 9, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29740518/enzynet-enzyme-classification-using-3d-convolutional-neural-networks-on-spatial-representation
#13
Afshine Amidi, Shervine Amidi, Dimitrios Vlachakis, Vasileios Megalooikonomou, Nikos Paragios, Evangelia I Zacharaki
During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank (PDB) has increased more than 15-fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence, however, is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function...
2018: PeerJ
https://www.readbyqxmd.com/read/29740493/bioinformatic-analysis-and-prediction-of-the-function-and-regulatory-network-of-long-non-coding-rnas-in-hepatocellular-carcinoma
#14
Ming-Rong Cao, Ze-Ping Han, Ji-Ming Liu, Yu-Guang Li, Yu-Bing Lv, Jia-Bin Zhou, Jin-Hua He
Computational analysis and bioinformatics have significantly advanced the ability of researchers to process and analyze biological data. Molecular data from human and model organisms may facilitate drug target validation and identification of biomarkers with increased predictive accuracy. The aim of the present study was to investigate the function of long non-coding RNAs (lncRNAs) in hepatocellular carcinoma (HCC) using online databases, and to predict their regulatory mechanism. HCC-associated lncRNAs, their downstream transcription factors and microRNAs (miRNAs/miRs), as well as the HCC-associated target genes, were identified using online databases...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29739397/integrative-analyses-of-genes-and-microrna-expressions-in-human-trisomy-21-placentas
#15
Ji Hyae Lim, You Jung Han, Hyun Jin Kim, Moon Young Kim, So Yeon Park, Youl-Hee Cho, Hyun Mee Ryu
BACKGROUND: The most frequent chromosomal aneuploidy is trisomy 21 (T21) that is caused by an extra copy of chromosome 21. The imbalance of whole genome including genes and microRNAs contributes to the various phenotypes of T21. However, the integrative association between genes and microRNAs in the T21 placenta has yet to be determined. METHODS: We analyzed the expressions of genes and microRNAs in the whole genomes of chorionic villi cells from normal and T21 human fetal placentas based on our prior studies...
May 9, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29739327/potential-molecular-mechanisms-of-overgrazing-induced-dwarfism-in-sheepgrass-leymus-chinensis-analyzed-using-proteomic-data
#16
Weibo Ren, Jihong Xie, Xiangyang Hou, Xiliang Li, Huiqin Guo, Ningning Hu, Lingqi Kong, Jize Zhang, Chun Chang, Zinian Wu
BACKGROUND: This study was designed to reveal potential molecular mechanisms of long-term overgrazing-induced dwarfism in sheepgrass (Leymus chinensis). METHODS: An electrospray ionisation mass spectrometry system was used to generate proteomic data of dwarf sheepgrass from a long-term overgrazed rangeland and normal sheepgrass from a long-term enclosed rangeland. Differentially expressed proteins (DEPs) between dwarf and normal sheepgrass were identified, after which their potential functions and interactions with each other were predicted...
May 8, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29734798/the-disordered-c-terminus-of-yeast-hsf1-contains-a-cryptic-low-complexity-amyloidogenic-region
#17
Jordi Pujols, Jaime Santos, Irantzu Pallarès, Salvador Ventura
Response mechanisms to external stress rely on networks of proteins able to activate specific signaling pathways to ensure the maintenance of cell proteostasis. Many of the proteins mediating this kind of response contain intrinsically disordered regions, which lack a defined structure, but still are able to interact with a wide range of clients that modulate the protein function. Some of these interactions are mediated by specific short sequences embedded in the longer disordered regions. Because the physicochemical properties that promote functional and abnormal interactions are similar, it has been shown that, in globular proteins, aggregation-prone and binding regions tend to overlap...
May 6, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29726930/functional-variants-in-tbx2-are-associated-with-a-syndromic-cardiovascular-and-skeletal-developmental-disorder
#18
Ning Liu, Kelly Schoch, Xi Luo, Loren Pena, Venkata Hemanjani Bhavana, Mary K Kukolich, Sarah Stringer, Zöe Powis, Kelly Radtke, Cameron Mroske, Kristen Deak, Marie T McDonald, Allyn McConkie-Rosell, M Louise Markert, Peter G Kranz, Nicholas Stong, Anna C Need, David Bick, Michelle D Amaral, Elizabeth A Worthey, Shawn Levy, Michael F Wangler, Hugo J Bellen, Shashi Vandana, Shinya Yamamoto
The seventeen genes of the T-box family are transcriptional regulators that are involved in all stages of embryonic development, including craniofacial, brain, heart, skeleton and immune system. Malformation syndromes have been linked to many of the T-box genes. For example, haploinsufficiency of TBX1 is responsible for many structural malformations in DiGeorge syndrome caused by a chromosome 22q11.2 deletion. We report four individuals with an overlapping spectrum of craniofacial dysmorphisms, cardiac anomalies, skeletal malformations, immune deficiency, endocrine abnormalities and developmental impairments, reminiscent of DiGeorge syndrome, who are heterozygotes for TBX2 variants...
May 2, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29725597/data-mining-mycobacterium-tuberculosis-pathogenic-gene-transcription-factors-and-their-regulatory-network-nodes
#19
Guangxin Yuan, Yu Bai, Yuhang Zhang, Guangyu Xu
Tuberculosis (TB) is one of the deadliest infectious diseases worldwide. In Mycobacterium tuberculosis , changes in gene expression are highly variable and involve many genes, so traditional single-gene screening of M. tuberculosis targets has been unable to meet the needs of clinical diagnosis. In this study, using the National Center for Biotechnology Information (NCBI) GEO Datasets, whole blood gene expression profile data were obtained in patients with active pulmonary tuberculosis. Linear model-experience Bayesian statistics using the Limma package in R combined with t -tests were applied for nonspecific filtration of the expression profile data, and the differentially expressed human genes were determined...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29724313/-analysis-of-differentially-expressed-genes-and-the-interaction-network-between-acute-and-chronic-idiopathic-thrombocytopenic-purpura-in-children
#20
Xiao Mei Ren, Qi Ling Liu, Bao Xin, Rong Qiang Zhang
Objective To analyze the differentially expressed genes and key proteins in T cells between acute and chronic idiopathic thrombocytopenic purpura (ITP) in children and provide the basis for the prevention and therapies of this disease. Methods Microarray gene chip data from T cells of children with acute or chronic ITP were downloaded from the GEO Database. The gene expression profiles,gene function,and protein interaction network were analyzed by R,QOE,Networkanalyst,GCBI,and GenClip. Results The gene expression profiles between these two groups were significantly different...
April 28, 2018: Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
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