keyword
MENU ▼
Read by QxMD icon Read
search

Network protein function prediction

keyword
https://www.readbyqxmd.com/read/28812049/importance-of-adiponectin-activity-in-the-pathogenesis-of-alzheimer-s-disease
#1
REVIEW
Masaaki Waragai, Gilbert Ho, Yoshiki Takamatsu, Kazunari Sekiyama, Shuei Sugama, Takato Takenouchi, Eliezer Masliah, Makoto Hashimoto
A recent study suggested that insulin resistance may play a central role in the pathogenesis of Alzheimer's disease (AD). In this regard, it is of note that upregulation of plasma adiponectin (APN), a benign adipokine that sensitizes the insulin receptor signaling pathway and suppresses inflammation, has recently been associated with the severities of amyloid deposits and cognitive deficits in the elderly, suggesting that APN may enhance the risk of AD. These results are unanticipated because AD has been linked to type II diabetes and other metabolic disorders in which hypoadiponectinemia has been firmly established, and because APN ameliorated neuropathological features in a mouse model of neurodegeneration...
August 2017: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/28807238/unravelling-the-complexity-of-signalling-networks-in-cancer-a-review-of-the-increasing-role-for-computational-modelling
#2
REVIEW
John Garland
Cancer induction is a highly complex process involving hundreds of different inducers but whose eventual outcome is the same. Clearly, it is essential to understand how signalling pathways and networks generated by these inducers interact to regulate cell behaviour and create the cancer phenotype. While enormous strides have been made in identifying key networking profiles, the amount of data generated far exceeds our ability to understand how it all "fits together". The number of potential interactions is astronomically large and requires novel approaches and extreme computation methods to dissect them out...
September 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28802167/induction-of-senescence-in-cancer-cells-by-5-aza-2-deoxycytidine-bioinformatics-and-experimental-insights-to-its-targets
#3
Jayarani F Putri, Nashi Widodo, Kazuichi Sakamoto, Sunil C Kaul, Renu Wadhwa
5'-Aza-2'-deoxycytidine (5-Aza-dC) is a demethylating drug that causes genome-wide hypomethylation resulting in the expression of several tumor suppressor genes causing growth arrest of cancer cells. Cancer is well established as a multifactorial disease and requires multi-module therapeutics. Search for new drugs and their approval by FDA takes a long time. Keeping this in view, research on new functions of FDA-approved anticancer drugs is desired to expand the list of multi-module functioning drugs for cancer therapy...
August 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28797096/prediction-of-n-linked-glycosylation-sites-using-position-relative-features-and-statistical-moments
#4
Muhammad Aizaz Akmal, Nouman Rasool, Yaser Daanial Khan
Glycosylation is one of the most complex post translation modification in eukaryotic cells. Almost 50% of the human proteome is glycosylated as glycosylation plays a vital role in various biological functions such as antigen's recognition, cell-cell communication, expression of genes and protein folding. It is a significant challenge to identify glycosylation sites in protein sequences as experimental methods are time taking and expensive. A reliable computational method is desirable for the identification of glycosylation sites...
2017: PloS One
https://www.readbyqxmd.com/read/28796060/candidate-genes-investigation-for-severe-nonalcoholic-fatty-liver-disease-based-on-bioinformatics-analysis
#5
Shan Qi, Changhong Wang, Chunfu Li, Pu Wang, Minghui Liu
BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver condition worldwide. However, its etiology and fundamental pathophysiology for the disease process are poorly understood. In this study, we thus used bioinformatics to identify candidate genes potentially causative of severe NAFLD. METHODS: Gene expression profile data GSE49541 were downloaded from the Gene Expression Omnibus database. Tissues samples from 32 severe and 40 mild NAFLD patients were evaluated to identify differentially expressed genes (DEGs) between the 2 groups, followed by analyses of Gene Ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes pathways...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28796037/functional-prediction-of-mir-3144-5p-in-human-cardiac-myocytes-based-on-transcriptome-sequencing-and-bioinformatics
#6
Lei Ruan, Yi Yang, Yi Huang, Ling Ding, Cuntai Zhang, Xiaofen Wu
BACKGROUND: RAN guanine nucleotide release factor (RANGRF) encoding protein MOG1 plays an important role in cardiac arrhythmia, so we intended to investigate the regulatory miRNA of RANGRF and explore its potential regulatory mechanism in arrhythmogenesis. METHODS: Based on bioinformatic analysis, miR-3144-5p was predicted to be a regulatory miRNA of RANGRF, which were then validated through a dual-luciferase reporter plasmid assay. Subsequently, the expression level of miR-3144-5p in human cardiac myocytes (HCMs) was detected, followed by cell transfection with miR-3144-5p mimics...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28795686/hdl-and-atherosclerotic-cardiovascular-disease-genetic-insights-into-complex-biology
#7
REVIEW
Robert S Rosenson, H Bryan Brewer, Philip J Barter, Johan L M Björkegren, M John Chapman, Daniel Gaudet, Daniel Seung Kim, Eric Niesor, Kerry-Anne Rye, Frank M Sacks, Jean-Claude Tardif, Robert A Hegele
Plasma levels of HDL cholesterol (HDL-C) predict the risk of cardiovascular disease at the epidemiological level, but a direct causal role for HDL in cardiovascular disease remains controversial. Studies in animal models and humans with rare monogenic disorders link only particular HDL-associated mechanisms with causality, including those mechanisms related to particle functionality rather than cholesterol content. Mendelian randomization studies indicate that most genetic variants that affect a range of pathways that increase plasma HDL-C levels are not usually associated with reduced risk of cardiovascular disease, with some exceptions, such as cholesteryl ester transfer protein variants...
August 10, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/28793249/network-based-genomic-analysis-of-human-oligodendrocyte-progenitor-differentiation
#8
Suyog U Pol, Jessie J Polanco, Richard A Seidman, Melanie A O'Bara, Hani J Shayya, Karen C Dietz, Fraser J Sim
Impaired human oligodendrocyte progenitor cell (hOPC) differentiation likely contributes to failed remyelination in multiple sclerosis. The characterization of molecular pathways that regulate hOPC differentiation will provide means to induce remyelination. In this study, we determined the gene expression profile of PDGFαR(+) hOPCs during initial oligodendrocyte commitment. Weighted gene coexpression network analysis was used to define progenitor and differentiation-specific gene expression modules and functionally important hub genes...
August 8, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28790346/gaussian-network-model-can-be-enhanced-by-combining-solvent-accessibility-in-proteins
#9
Hua Zhang, Tao Jiang, Guogen Shan, Shiqi Xu, Yujie Song
Gaussian network model (GNM), regarded as the simplest and most representative coarse-grained model, has been widely adopted to analyze and reveal protein dynamics and functions. Designing a variation of the classical GNM, by defining a new Kirchhoff matrix, is the way to improve the residue flexibility modeling. We combined information arising from local relative solvent accessibility (RSA) between two residues into the Kirchhoff matrix of the parameter-free GNM. The undetermined parameters in the new Kirchhoff matrix were estimated by using particle swarm optimization...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28782718/merging-in-silico-and-in-vitro-salivary-protein-complex-partners-using-the-string-database-a-tutorial
#10
Karla Tonelli Bicalho Crosara, Eduardo Buozi Moffa, Yizhi Xiao, Walter Luiz Siqueira
Protein-protein interaction is a common physiological mechanism for protection and actions of proteins in an organism. The identification and characterization of protein-protein interactions in different organisms is necessary to better understand their physiology and to determine their efficacy. In a previous in vitro study using mass spectrometry, we identified 43 proteins that interact with histatin 1. Six previously documented interactors were confirmed and 37 novel partners were identified. In this tutorial, we aimed to demonstrate the usefulness of the STRING database for studying protein-protein interactions...
August 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28778080/using-molecular-functional-networks-to-manifest-connections-between-obesity-and-obesity-related-diseases
#11
Jialiang Yang, Jing Qiu, Kejing Wang, Lijuan Zhu, Jingjing Fan, Deyin Zheng, Xiaodi Meng, Jiasheng Yang, Lihong Peng, Yu Fu, Dahan Zhang, Shouneng Peng, Haiyun Huang, Yi Zhang
Obesity is a primary risk factor for many diseases such as certain cancers. In this study, we have developed three algorithms including a random-walk based method OBNet, a shortest-path based method OBsp and a direct-overlap method OBoverlap, to reveal obesity-disease connections at protein-interaction subnetworks corresponding to thousands of biological functions and pathways. Through literature mining, we also curated an obesity-associated disease list, by which we compared the methods. As a result, OBNet outperforms other two methods...
July 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28775366/microrna-143-and-145-modulate-the-phenotype-of-synovial-fibroblasts-in-rheumatoid-arthritis
#12
Bong-Ki Hong, Sungyong You, Seung-Ah Yoo, Dohyun Park, Daehee Hwang, Chul-Soo Cho, Wan-Uk Kim
Fibroblast-like synoviocytes (FLSs) constitute a major cell subset of rheumatoid arthritis (RA) synovia. Dysregulation of microRNAs (miRNAs) has been implicated in activation and proliferation of RA-FLSs. However, the functional association of various miRNAs with their targets that are characteristic of the RA-FLS phenotype has not been globally elucidated. In this study, we performed microarray analyses of miRNAs and mRNAs in RA-FLSs and osteoarthritis FLSs (OA-FLSs), simultaneously, to validate how dysregulated miRNAs may be associated with the RA-FLS phenotype...
August 4, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28775330/enriching-traditional-protein-protein-interaction-networks-with-alternative-conformations-of-proteins
#13
Farideh Halakou, Emel Sen Kilic, Engin Cukuroglu, Ozlem Keskin, Attila Gursoy
Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling...
August 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28771719/the-aberrantly-expressed-long-noncoding-rna-in-the-substantia-nigra-and-corpus-striatum-of-nrf2-knockout-mice
#14
Jian Liu, Yali Xu, Yunxiao Kang, Shanhu Cao, Geming Shi, Huixian Cui, Shaoguang Sun, Lei Wang
Nuclear factor erythroid 2 like 2 (Nrf2) functions as a neuroprotective agent in Parkinson's disease (PD). The present study aimed to investigate the key long noncoding RNAs (lncRNAs) correlated with Nrf2, which might provide valuable information for the exploration of pathogenesis of PD. The lncRNA and mRNA expression profiling of substantia nigra and corpus striatum of Nrf2 (-/-) mice model was obtained from microarray analysis. The animal experiments conducted for this study were approved by the ethics committee of Hebei Medical University...
August 3, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28765971/identification-of-key-genes-and-pathways-in-parkinson-s-disease-through-integrated-analysis
#15
Jingru Wang, Yining Liu, Tuanzhi Chen
Parkinson's disease (PD) is a progressive, degene-rative neurological disease, typically characterized by tremors and muscle rigidity. The present study aimed to identify differe-ntially expressed genes (DEGs) between patients with PD and healthy patients, and clarify their association with additional biological processes that may regulate factors that lead to PD. An integrated analysis of publicly available Gene Expression Omnibus datasets of PD was performed. DEGs were identified between PD and normal blood samples...
July 31, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28765929/characterization-and-predicted-role-of-microrna-expression-profiles-associated-with-early-childhood-obesity
#16
Shengrong Ouyang, Renqiao Tang, Zhuo Liu, Feifei Ma, Yuanyuan Li, Jianxin Wu
MicroRNAs (miRNAs) are implicated in the pathogenesis of obesity. The aim of the present study was to characterize the miRNA profile associated with early childhood obesity in peripheral blood mononuclear cells (PBMCs). A total of 12 children (6 obese and 6 lean controls) aged 36 months old to 48 months old were recruited. The miRNA expression profile from PBMCs was detected using the multiplexed NanoString nCounter system. Bioinformatics was employed to detect target genes and miRNA‑regulated biological function...
July 31, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28765921/mir-198-induced-upregulation-of-livin-may-be-associated-with-the-prognosis-and-contribute-to-the-oncogenesis-of-lung-adenocarcinoma
#17
Yicheng Liang, Hetan Wang, Yuanyuan Sun, Sheng Chen, Haoyou Wang, Rong Huang, Xinyi Zhao, Weineng Fu, Chunlu Yang
Livin, a member of the inhibitor of apoptosis protein (IAP) family, is expressed at a high level in lung adenocarcinoma and influences the progression of cancer, and its response to chemotherapy and radiotherapy. Aberrant microRNA (miRNA) expression has also been associated with cancer initiation and development. However, the clinical significance of Livin and its relationship with miRNAs in lung adenocarcinoma are still unclear. In the present study, the expression level of Livin in 90 pairs of lung adenocarcinoma and their adjacent tissues were detected by immunohistochemistry staining...
August 1, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28763201/tracking-reactive-water-and-hydrogen-bonding-networks-in-photosynthetic-oxygen-evolution
#18
Bridgette A Barry, Udita Brahmachari, Zhanjun Guo
In oxygenic photosynthesis, photosystem II (PSII) converts water to molecular oxygen through four photodriven oxidation events at a Mn4CaO5 cluster. A tyrosine, YZ (Y161 in the D1 polypeptide), transfers oxidizing equivalents from an oxidized, primary chlorophyll donor to the metal center. Calcium or its analogue, strontium, is required for activity. The Mn4CaO5 cluster and YZ are predicted to be hydrogen bonded in a water-containing network, which involves amide carbonyl groups, amino acid side chains, and water...
August 1, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28759592/pcsf-an-r-package-for-network-based-interpretation-of-high-throughput-data
#19
Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
With the recent technological developments a vast amount of high-throughput data has been profiled to understand the mechanism of complex diseases. The current bioinformatics challenge is to interpret the data and underlying biology, where efficient algorithms for analyzing heterogeneous high-throughput data using biological networks are becoming increasingly valuable. In this paper, we propose a software package based on the Prize-collecting Steiner Forest graph optimization approach. The PCSF package performs fast and user-friendly network analysis of high-throughput data by mapping the data onto a biological networks such as protein-protein interaction, gene-gene interaction or any other correlation or coexpression based networks...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28759171/identification-of-potential-crucial-genes-associated-with-early-onset-pre-eclampsia-via-a-microarray-analysis
#20
Yifei Ma, Hongmei Lin, Hong Zhang, Xiu'e Song, Huili Yang
AIM: This study aimed to identify potential key genes related to early-onset pre-eclampsia (EOPET), and to obtain a better understanding of the molecular mechanisms of this disease. METHODS: The microarray dataset GSE44711 was obtained from the Gene Expression Omnibus, including eight chorionic villi samples from EOPET placentas and eight normal controls. The differentially expressed genes (DEG) were identified using the LIMMA package, and their potential functions were predicted by Gene Ontology (GO) enrichment analysis...
May 2017: Journal of Obstetrics and Gynaecology Research
keyword
keyword
6571
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"