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https://www.readbyqxmd.com/read/28224024/topological-and-functional-analysis-of-nonalcoholic-steatohepatitis-through-protein-interaction-mapping
#1
Hamid Asadzadeh-Aghdaee, Vahid Mansouri, Ali Asghar Peyvandi, Fathollah Moztarzadeh, Farshad Okhovatian, Farhad Lahmi, Reza Vafaee, Mohammad Reza Zali
AIM: The corresponding proteins are important for network mapping since the interaction analysis can provide a new interpretation about disease underlying mechanisms as the aim of this study. BACKGROUD: Nonalcoholic steatohepatitis (NASH) is one of the main causes of liver disease in the world. It has been known with many susceptible proteins that play essential role in its pathogenesis. METHODS: In this paper, protein-protein interaction (PPI) network analysis of fatty liver disease retrieved from STRING db by the application of Cytoscape Software...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28224023/evaluation-of-liver-cirrhosis-and-hepatocellular-carcinoma-using-protein-protein-interaction-networks
#2
Mohammad Javad Ehsani Ardakani, Akram Safaei, Afsaneh Arefi Oskouie, Hesam Haghparast, Mehrdad Haghazali, Hamid Mohaghegh Shalmani, Hassan Peyvandi, Nosratollah Naderi, Mohammad Reza Zali
AIM: In the current study, we analysised only the articles that investigate serum proteome profile of cirrhosis patients or HCC patients versus healthy controls. BACKGROUND: Increased understanding of cancer biology has enabled identification of molecular events that lead to the discovery of numerous potential biomarkers in diseases. Protein-protein interaction networks is one of aspect that could elevate the understanding level of molecular events and protein connections that lead to the identification of genes and proteins associated with diseases...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28224022/introduction-of-inflammatory-bowel-disease-biomarkers-panel-using-protein-protein-interaction-ppi-network-analysis
#3
Hamid Asadzadeh-Aghdaee, Shabnam Shahrokh, Mohsen Norouzinia, Mostafa Hosseini, Aliasghar Keramatinia, Mostafa Jamalan, Bijan Naghibzadeh, Ali Sadeghi, Somayeh Jahani Sherafat, Mohammad Reza Zali
AIM: In the present study, a protein-protein interaction network construction is conducted for IBD. BACKGROUND: Inflammatory bowel diseases as serious chronic gastrointestinal disorders attracted many molecular investigations. Diverse molecular information is present for IBD. However, these molecular findings are not highlighted based on interactome analysis. On the other hand, PPI network analysis is a powerful method for study of molecular interactions in the protein level that provide useful information for highlighting the desired key proteins...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28222782/identification-of-mirna-mrna-crosstalk-in-cd4-t-cells-during-hiv-1-infection-by-integrating-transcriptome-analyses
#4
Qibin Liao, Jin Wang, Zenglin Pei, Jianqing Xu, Xiaoyan Zhang
BACKGROUND: HIV-1-infected long-term nonprogressors (LTNPs) are characterized by infection with HIV-1 more than 7-10 years, but keeping high CD4(+) T cell counts and low viral load in the absence of antiretroviral treatment, while loss of CD4(+) T cells and high viral load were observed in the most of HIV-1-infected individuals with chronic progressors (CPs) However, the mechanisms of different clinical outcomes in HIV-1 infection needs to be further resolved. METHODS: To identify microRNAs (miRNAs) and their target genes related to distinct clinical outcomes in HIV-1 infection, we performed the integrative transcriptome analyses in two series GSE24022 and GSE6740 by GEO2R, R, TargetScan, miRDB, and Cytoscape softwares...
February 21, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28199418/analysis-of-long-noncoding-rna-and-mrna-using-rna-sequencing-during-the-differentiation-of-intramuscular-preadipocytes-in-chicken
#5
Tao Zhang, Xiangqian Zhang, Kunpeng Han, Genxi Zhang, Jinyu Wang, Kaizhou Xie, Qian Xue, Xiaomei Fan
Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison...
2017: PloS One
https://www.readbyqxmd.com/read/28191039/elevated-transcriptional-levels-of-aldolase-a-aldoa-associates-with-cell-cycle-related-genes-in-patients-with-nsclc-and-several-solid-tumors
#6
Fan Zhang, Jie-Diao Lin, Xiao-Yu Zuo, Yi-Xuan Zhuang, Chao-Qun Hong, Guo-Jun Zhang, Xiao-Jiang Cui, Yu-Kun Cui
BACKGROUND: Aldolase A (ALDOA) is one of the glycolytic enzymes primarily found in the developing embryo and adult muscle. Recently, a new role of ALDOA in several cancers has been proposed. However, the underlying mechanism remains obscure and inconsistent. In this study, we tried to investigate ALDOA-associated (AA) genes using available microarray datasets to help elucidating the role of ALDOA in cancer. RESULTS: In the dataset of patients with non-small-cell lung cancer (NSCLC, E-GEOD-19188), 3448 differentially expressed genes (DEGs) including ALDOA were identified, in which 710 AA genes were found to be positively associated with ALDOA...
2017: BioData Mining
https://www.readbyqxmd.com/read/28165644/hif1a-gene-polymorphisms-and-human-diseases-graphical-review-of-97-association-studies
#7
REVIEW
I Gladek, J Ferdin, S Horvat, G A Calin, T Kunej
Hypoxia-inducible factors (HIFs) belong to a family of transcription factors (TF) responsive to a low O2 availability, which is often a characteristic feature of solid tumors. The alpha subunit of the HIF heterodimer is O2 -sensitive, and once stabilized in hypoxia, it functions as a master regulator of various genes involved in hypoxia pathway. Changes in the HIF1A (hypoxia inducible factor 1, alpha subunit) nucleotide sequence or expression has been shown to be associated with development of several diseases...
February 6, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28158465/a-cytoscape-app-for-motif-enumeration-with-ismags
#8
Thomas Van Parys, Ine Melckenbeeck, Maarten Houbraken, Pieter Audenaert, Didier Colle, Mario Pickavet, Piet Demeester, Yves Van de Peer
No abstract text is available yet for this article.
February 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28158294/deep-proteome-mapping-of-wm-266-4-human-metastatic-melanoma-cells-from-oncogenic-addiction-to-druggable-targets
#9
Eumorphia G Konstantakou, Athanassios D Velentzas, Athanasios K Anagnostopoulos, Zoi I Litou, Ourania A Konstandi, Aikaterini F Giannopoulou, Ema Anastasiadou, Gerassimos E Voutsinas, George Th Tsangaris, Dimitrios J Stravopodis
Cutaneous melanoma is a malignant tumor of skin melanocytes that are pigment-producing cells located in the basal layer (stratum basale) of epidermis. Accumulation of genetic mutations within their oncogenes or tumor-suppressor genes compels melanocytes to aberrant proliferation and spread to distant organs of the body, thereby resulting in severe and/or lethal malignancy. Metastatic melanoma's heavy mutational load, molecular heterogeneity and resistance to therapy necessitate the development of novel biomarkers and drug-based protocols that target key proteins involved in perpetuation of the disease...
2017: PloS One
https://www.readbyqxmd.com/read/28155725/moro-a-cytoscape-app-for-relationship-analysis-between-modularity-and-robustness-in-large-scale-biological-networks
#10
Cong-Doan Truong, Tien-Dzung Tran, Yung-Keun Kwon
BACKGROUND: Although there have been many studies revealing that dynamic robustness of a biological network is related to its modularity characteristics, no proper tool exists to investigate the relation between network dynamics and modularity. RESULTS: Accordingly, we developed a novel Cytoscape app called MORO, which can conveniently analyze the relationship between network modularity and robustness. We employed an existing algorithm to analyze the modularity of directed graphs and a Boolean network model for robustness calculation...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155685/sig2grn-a-software-tool-linking-signaling-pathway-with-gene-regulatory-network-for-dynamic-simulation
#11
Fan Zhang, Runsheng Liu, Jie Zheng
BACKGROUND: Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. In this work, we present Sig2GRN, a Cytoscape plugin that is able to simulate time-course gene expression data given the user-defined external stimuli to the signaling pathways. METHODS: A generalized logical model is used in modeling the upstream signaling pathways. Then a Boolean model and a thermodynamics-based model are employed to predict the downstream changes in gene expression based on the simulated dynamics of transcription factors in signaling pathways...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155194/regulatory-network-analysis-of-epstein-barr-virus-identifies-functional-modules-and-hub-genes-involved-in-infectious-mononucleosis
#12
Mansour Poorebrahim, Ali Salarian, Saeideh Najafi, Mohammad Foad Abazari, Maryam Nouri Aleagha, Mohammad Nasr Dadras, Seyed Mohammad Jazayeri, Atousa Ataei, Vahdat Poortahmasebi
Epstein-Barr virus (EBV) is the most common cause of infectious mononucleosis (IM) and establishes lifetime infection associated with a variety of cancers and autoimmune diseases. The aim of this study was to develop an integrative gene regulatory network (GRN) approach and overlying gene expression data to identify the representative subnetworks for IM and EBV latent infection (LI). After identifying differentially expressed genes (DEGs) in both IM and LI gene expression profiles, functional annotations were applied using gene ontology (GO) and BiNGO tools, and construction of GRNs, topological analysis and identification of modules were carried out using several plugins of Cytoscape...
February 2, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28150241/functional-interaction-network-construction-and-analysis-for-disease-discovery
#13
Guanming Wu, Robin Haw
Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150233/tutorial-on-protein-ontology-resources
#14
Cecilia N Arighi, Harold Drabkin, Karen R Christie, Karen E Ross, Darren A Natale
The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence variants, and post-translationally modified forms), and protein complexes. PRO defines classes of proteins and protein complexes, both species-specific and species nonspecific, and indicates their relationships in a hierarchical framework, supporting accurate protein annotation at the appropriate level of granularity, analyses of protein conservation across species, and semantic reasoning...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28138311/specific-networks-of-plasma-acute-phase-reactants-are-associated-with-the-severity-of-chronic-obstructive-pulmonary-disease-a-case-control-study
#15
Elena Arellano-Orden, Carmen Calero-Acuña, Juan Antonio Cordero, María Abad-Arranz, Verónica Sánchez-López, Eduardo Márquez-Martín, Francisco Ortega-Ruiz, José Luis López-Campos
Objectives. A detailed understanding of the intricate relationships between different acute phase reactants (APRs) in chronic obstructive pulmonary disease (COPD) can shed new light on its clinical course. In this case-control study, we sought to identify the interaction networks of a number of plasma APRs in COPD, with a special focus on their association with disease severity. Methods. COPD cases and healthy smoking controls (3:1 ratio) were recruited in our outpatient pulmonary clinic. Cardiopulmonary exercise testing was used to rule out the presence of ischemic heart disease...
2017: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/28122780/biopaxviz-a-cytoscape-application-for-the-visual-exploration-of-metabolic-pathway-evolution
#16
Fotis E Psomopoulos, Dimitrios M Vitsios, Shakuntala Baichoo, Christos A Ouzounis
: BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway...
January 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28122019/cynetsvm-a-cytoscape-app-for-cancer-biomarker-identification-using-network-constrained-support-vector-machines
#17
Xu Shi, Sharmi Banerjee, Li Chen, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
One of the important tasks in cancer research is to identify biomarkers and build classification models for clinical outcome prediction. In this paper, we develop a CyNetSVM software package, implemented in Java and integrated with Cytoscape as an app, to identify network biomarkers using network-constrained support vector machines (NetSVM). The Cytoscape app of NetSVM is specifically designed to improve the usability of NetSVM with the following enhancements: (1) user-friendly graphical user interface (GUI), (2) computationally efficient core program and (3) convenient network visualization capability...
2017: PloS One
https://www.readbyqxmd.com/read/28121923/identifying-key-stage-specific-genes-and-transcription-factors-for-gastric-cancer-based-on-rna-sequencing-data
#18
Yan Wang
BACKGROUND: To identify gastric cancer (GC)-associated genes and transcription factors (TFs) using RNA-sequencing (RNA-seq) data of Asians. MATERIALS AND METHODS: The RNA-seq data (GSE36968) were downloaded from Gene Expression Omnibus database, including 6 noncancerous gastric tissue samples, 5 stage I GC samples, 5 stage II GC samples, 8 stage III GC samples, and 6 stage IV GC samples. The gene expression values in each sample were calculated using Cuffdiff. Following, stage-specific genes were identified by 1-way analysis of variance and hierarchical clustering analysis...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28120235/identifying-key-genes-associated-with-hirschsprung-s-disease-based-on-bioinformatics-analysis-of-rna-sequencing-data
#19
Wei-Kang Pan, Ya-Fei Zhang, Hui Yu, Ya Gao, Bai-Jun Zheng, Peng Li, Chong Xie, Xin Ge
BACKGROUND: Hirschsprung's disease (HSCR) is a type of megacolon induced by deficiency or dysfunction of ganglion cells in the distal intestine and is associated with developmental disorders of the enteric nervous system. To explore the mechanisms of HSCR, we analyzed the RNA-sequencing data of the expansion and the narrow segments of colon tissues separated from children with HSCR. METHODS: RNA-sequencing of the expansion segments and the narrow segments of colon tissues isolated from children with HSCR was performed...
January 25, 2017: World Journal of Pediatrics: WJP
https://www.readbyqxmd.com/read/28111234/transcriptomic-signatures-for-ovulation-in-vertebrates
#20
Dong Teng Liu, Michael S Brewer, Shixi Chen, Wanshu Hong, Yong Zhu
The central roles of luteinizing hormone (LH), progestin and their receptors for initiating ovulation have been well established. However, signaling pathways and downstream targets such as proteases that are essential for the rupture of follicular cells are still unclear. Recently, we found anovulation in nuclear progestin receptor (Pgr) knockout (Pgr-KO) zebrafish, which offers a new model for examining genes and pathways that are important for ovulation and fertility. In this study, we examined expression of all transcripts using RNA-Seq in preovulatory follicular cells collected following the final oocyte maturation, but prior to ovulation, from wild-type (WT) or Pgr-KO fish...
January 19, 2017: General and Comparative Endocrinology
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