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Network protein function prediction

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https://www.readbyqxmd.com/read/29331040/jun-gal-cd74-and-c1qb-as-potential-indicator-for-neuropathic-pain
#1
Ji-An Yang, Jun-Min He, Jing-Min Lu, Li-Juan Ji
Neuropathic pain is a kind of pain caused by primary or secondary impairment or dysfunction of peripheral or central nervous system. Patients with neuropathic pain were often with poor clinical outcome. We screened the differentially expressed genes between sciatic nerve injury and dorsal root ganglion gene in the sham operation model. Microarray and the spared nerve injury module were used to explore the molecular mechanism of neuropathic pain by injuries and the differentially expressed genes (DEGs) were identified out...
January 13, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29330521/rgs7-is-recurrently-mutated-in-melanoma-and-promotes-migration-and-invasion-of-human-cancer-cells
#2
Nouar Qutob, Ikuo Masuho, Michal Alon, Rafi Emmanuel, Isadora Cohen, Antonella Di Pizio, Jason Madore, Abdel Elkahloun, Tamar Ziv, Ronen Levy, Jared J Gartner, Victoria K Hill, Jimmy C Lin, Yael Hevroni, Polina Greenberg, Alexandra Brodezki, Steven A Rosenberg, Mickey Kosloff, Nicholas K Hayward, Arie Admon, Masha Y Niv, Richard A Scolyer, Kirill A Martemyanov, Yardena Samuels
Analysis of 501 melanoma exomes revealed RGS7, which encodes a GTPase-accelerating protein (GAP), to be a tumor-suppressor gene. RGS7 was mutated in 11% of melanomas and was found to harbor three recurrent mutations (p.R44C, p.E383K and p.R416Q). Structural modeling of the most common recurrent mutation of the three (p.R44C) predicted that it destabilizes the protein due to the loss of an H-bond and salt bridge network between the mutated position and the serine and aspartic acid residues at positions 58 as 61, respectively...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330500/integration-of-gwas-pathway-and-network-analyses-reveals-novel-mechanistic-insights-into-the-synthesis-of-milk-proteins-in-dairy-cows
#3
Sara Pegolo, Núria Mach, Yuliaxis Ramayo-Caldas, Stefano Schiavon, Giovanni Bittante, Alessio Cecchinato
The quantities and proportions of protein fractions have notable effects on the nutritional and technological value of milk. Although much is known about the effects of genetic variants on milk proteins, the complex relationships among the set of genes and pathways regulating the different protein fractions synthesis and secretion into milk in dairy cows are still not completely understood. We conducted genome-wide association studies (GWAS) for milk nitrogen fractions in a cohort of 1,011 Brown Swiss cows, which uncovered 170 significant single nucleotide polymorphism (SNPs), mostly located on BTA6 and BTA11...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29328442/identification-of-differentially-expressed-genes-and-regulatory-relationships-in-huntington-s-disease-by-bioinformatics-analysis
#4
Xiaoyu Dong, Shuyan Cong
Huntington's disease (HD) is an inherited, progressive neurodegenerative disease caused by a CAG expansion in the huntingtin (HTT) gene; various dysfunctions of biological processes in HD have been proposed. However, at present the exact pathogenesis of HD is not fully understood. The present study aimed to explore the pathogenesis of HD using a computational bioinformatics analysis of gene expression. GSE11358 was downloaded from the Gene Expression Omnibus andthe differentially expressed genes (DEGs) in the mutant HTT knock‑in cell model STHdhQ111/Q111 were predicted...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328431/bioinformatic-analysis-of-gene-expression-profiling-of-intracranial-aneurysm
#5
Lijuan Bo, Bo Wei, Zhanfeng Wang, Chaohui Li, Zheng Gao, Zhuang Miao
Intracranial aneurysm (IA) is a severe clinical condition of primary concern and currently, there is no effective therapeutic reagent. The present study aimed to investigate the molecular mechanism of IA via bioinformatic analysis. Various gene expression profiles (GSE26969) were downloaded from the Gene Expression Omnibus database, including 3 IA and 3 normal superficial temporal artery samples. Firstly, the limma package in R language was used to identify differentially expressed genes (DEGs; P‑value <0...
December 29, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328410/cldn5-affects-lncrnas-acting-as-cerna-dynamics-contributing-to-regulating-blood%C3%A2-brain-barrier-permeability-in-tumor-brain-metastasis
#6
Shun-Chang Ma, Qi Li, Jia-Yi Peng, Jian-Long Zhouwen, Dai-Nan Zhang, Chuan-Bao Zhang, Wen-Guo Jiang, Wang Jia
The blood‑brain barrier (BBB) constitutes an efficient organization of tight junctions that limits the delivery of tumor to the brain. The principal tight junction protein in BBB is claudin‑5 (CLDN5), but its mechanism of action remains largely unknown. Long non‑coding RNAs (lncRNAs) are aberrantly expressed in many cancers, some lncRNAs play key roles in regulating BBB permeability and are involved in tumor brain metastasis. In particular, lncRNAs can function as competing endogenous RNAs (ceRNAs). Herein, we investigated whether ceRNA dysregulation is associated with alterations of the level of CLDN5 in human brain vascular endothelial hCMEC/D3 cells...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29328395/bioinformatic-identification-of-chemoresistance-associated-micrornas-in-breast-cancer-based-on-microarray-data
#7
Ya-Wen Wang, Weiguo Zhang, Rong Ma
Breast cancer is the most commonly diagnosed cancer among females, and chemoresistance constitutes a major clinical obstacle to the treatment of this disease. MicroRNAs (miRNAs) are related to human cancer development, progression and drug resistance. To identify breast cancer chemoresistance-associated miRNAs, miRNA microarray dataset GSE71142, including five chemoresistant breast cancer tissues and five chemosensitive tissues, was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DE-miRNAs) were obtained by t-test and the potential target genes were predicted by miRWalk2...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29328377/feature-genes-in-metastatic-breast-cancer-identified-by-metade-and-svm-classifier-methods
#8
Youlin Tuo, Ning An, Ming Zhang
The aim of the present study was to investigate the feature genes in metastatic breast cancer samples. A total of 5 expression profiles of metastatic breast cancer samples were downloaded from the Gene Expression Omnibus database, which were then analyzed using the MetaQC and MetaDE packages in R language. The feature genes between metastasis and non‑metastasis samples were screened under the threshold of P<0.05. Based on the protein‑protein interactions (PPIs) in the Biological General Repository for Interaction Datasets, Human Protein Reference Database and Biomolecular Interaction Network Database, the PPI network of the feature genes was constructed...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29327492/a-five-gene-signature-may-predict-sunitinib-sensitivity-and-serve-as-prognostic-biomarkers-for-renal-cell-carcinoma
#9
Yuan-Lei Chen, Guang-Ju Ge, Chao Qi, Huan Wang, Huai-Lan Wang, Li-Yang Li, Gong-Hui Li, Li-Qun Xia
Sunitinib resistance is, nowadays, the major challenge for advanced renal cell carcinoma patients. Illuminating the potential mechanisms and exploring effective strategies to overcome sunitinib resistance are highly desired. We constructed a reliable gene signature which may function as biomarkers for prediction of sunitinib sensitivity and clinical prognosis. The gene expression profiles were obtained from The Cancer Genome Atlas database. By performing GEO2R analysis, numerous differentially expressed genes (DEGs) were found to be associated with sunitinib resistance...
January 12, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29325119/mir-96-is-required-for-normal-development-of-the-auditory-hindbrain
#10
Tina Schlüter, Christina Berger, Elena Rosengauer, Pascal Fieth, Constanze Krohs, Kathy Ushakov, Karen P Steel, Karen B Avraham, Alexander Hartmann, Felix Felmy, Hans Gerd Nothwang
The peripheral deafness gene Mir96 is expressed in both the cochlea and central auditory circuits. To investigate whether it plays a role in the auditory system beyond the cochlea, we characterized homozygous Dmdo/Dmdo mice with a point mutation in miR-96. Anatomical analysis demonstrated a significant decrease in volume of auditory nuclei in Dmdo/Dmdo mice. This decrease resulted from decreased cell size. Non-auditory structures in the brainstem of Dmdo/Dmdo mice or auditory nuclei of the congenital deaf Cldn14-/- mice revealed no such differences...
January 9, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29322927/cpredictor3-0-detecting-protein-complexes-from-ppi-networks-with-expression-data-and-functional-annotations
#11
Ying Xu, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan
BACKGROUND: Effectively predicting protein complexes not only helps to understand the structures and functions of proteins and their complexes, but also is useful for diagnosing disease and developing new drugs. Up to now, many methods have been developed to detect complexes by mining dense subgraphs from static protein-protein interaction (PPI) networks, while ignoring the value of other biological information and the dynamic properties of cellular systems. RESULTS: In this paper, based on our previous works CPredictor and CPredictor2...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322790/integrated-network-analysis-to-identify-the-key-genes-transcription-factors-and-micrornas-involved-in-hepatocellular-carcinoma
#12
S Q Shi, J-J Ke, Q S Xu, W Q Wu, Y Y Wan
HCC (hepatocellular carcinoma), which can be induced by cirrhosis and viral hepatitis infection, is the most frequent form of liver cancer. This study is performed to investigate the mechanisms of HCC. GSE57957 was obtained from Gene Expression Omnibus database, including 39 HCC samples and 39 adjacent non-tumorous samples. The DEGs (differentially expressed genes) were screened using the limma package in R, and then were conducted with enrichment analysis using "BioCloud" platform. Using STRING database, WebGestalt tool, as well as ITFP and TRANSFAC databases, PPI (protein-protein interaction) pairs, miRNA (microRNA)-target pairs, and TF (transcription factor)-target pairs separately were predicted...
2018: Neoplasma
https://www.readbyqxmd.com/read/29321553/prediction-of-co-expression-genes-and-integrative-analysis-of-gene-microarray-and-proteomics-profile-of-keshan-disease
#13
Sen Wang, Rui Yan, Bin Wang, Peiru Du, Wuhong Tan, Mikko J Lammi, Xiong Guo
Keshan disease (KD) is a kind of endemic cardiomyopathy which has a high mortality. However, molecular mechanism in the pathogenesis of KD remains poorly understood. Serum samples were collected from 112 KD patients and 112 normal controls. Gene microarray was used to screen differently expressed genes. Genevestigator was applied to forecast co-expression genes of significant gene. iTRAQ proteomics analysis was used to verify significant genes and their co-expression genes. GO, COG, IPA and STRING were applied to undertake function categorization, pathway and network analysis separately...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320688/coevolutionary-landscape-of-kinase-family-proteins-sequence-probabilities-and-functional-motifs
#14
Allan Haldane, William F Flynn, Peng He, Ronald M Levy
The protein kinase catalytic domain is one of the most abundant domains across all branches of life. Although kinases share a common core function of phosphoryl-transfer, they also have wide functional diversity and play varied roles in cell signaling networks, and for this reason are implicated in a number of human diseases. This functional diversity is primarily achieved through sequence variation, and uncovering the sequence-function relationships for the kinase family is a major challenge. In this study we use a statistical inference technique inspired by statistical physics, which builds a coevolutionary "Potts" Hamiltonian model of sequence variation in a protein family...
January 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29320478/an-extracellular-network-of-arabidopsis-leucine-rich-repeat-receptor-kinases
#15
Elwira Smakowska-Luzan, G Adam Mott, Katarzyna Parys, Martin Stegmann, Timothy C Howton, Mehdi Layeghifard, Jana Neuhold, Anita Lehner, Jixiang Kong, Karin Grünwald, Natascha Weinberger, Santosh B Satbhai, Dominik Mayer, Wolfgang Busch, Mathias Madalinski, Peggy Stolt-Bergner, Nicholas J Provart, M Shahid Mukhtar, Cyril Zipfel, Darrell Desveaux, David S Guttman, Youssef Belkhadir
The cells of multicellular organisms receive extracellular signals using surface receptors. The extracellular domains (ECDs) of cell surface receptors function as interaction platforms, and as regulatory modules of receptor activation. Understanding how interactions between ECDs produce signal-competent receptor complexes is challenging because of their low biochemical tractability. In plants, the discovery of ECD interactions is complicated by the massive expansion of receptor families, which creates tremendous potential for changeover in receptor interactions...
January 10, 2018: Nature
https://www.readbyqxmd.com/read/29318668/vibrational-entropy-estimation-can-improve-binding-affinity-prediction-for-non-obligatory-protein-complexes
#16
Tatjana Škrbić, Stefano Zamuner, Rolando Hong, Flavio Seno, Alessandro Laio, Antonio Trovato
Predicting the binding affinity between protein monomers is of paramount importance for the understanding of thermodynamical and structural factors that guide the formation of a complex. Several numerical techniques have been developed for the calculation of binding affinities with different levels of accuracy. Approaches such as thermodynamic integration and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodologies which account for well defined physical interactions offer good accuracy but are computationally demanding...
January 10, 2018: Proteins
https://www.readbyqxmd.com/read/29317304/lncrna-and-mrna-integration-network-reconstruction-reveals-novel-key-regulators-in-esophageal-squamous-cell-carcinoma
#17
Shervin Alaei, Balal Sadeghi, Ali Najafi, Ali Masoudi-Nejad
Many experimental and computational studies have identified key protein coding genes in initiation and progression of esophageal squamous cell carcinoma (ESCC). However, the number of researches that tried to reveal the role of long non-coding RNAs (lncRNAs) in ESCC has been limited. LncRNAs are one of the important regulators of cancers which are transcribed dominantly in the genome and in various conditions. The main goal of this study was to use a systems biology approach to predict novel lncRNAs as well as protein coding genes associated with ESCC and assess their prognostic values...
January 6, 2018: Genomics
https://www.readbyqxmd.com/read/29309725/kdeep-protein-ligand-absolute-binding-affinity-prediction-via-3d-convolutional-neural-networks
#18
José Jiménez Luna, Miha Skalic, Gerard Martinez-Rosell, Gianni De Fabritiis
Accurately predicting protein-ligand binding affinities is an important problem in computational chemistry since it can substantially accelerate drug discovery for virtual screening and lead optimization. We propose here a fast machine-learning approach for predicting binding affinities using state-of-the-art 3D convolutional neural networks and compare this approach to other machine-learning and scoring methods using several diverse datasets. The results for the standard PDBbind (v.2016) core test-set are state-of-the-art with a Pearson's correlation coefficient of 0...
January 8, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29305979/target-gene-screening-and-evaluation-of-prognostic-values-in-non-small-cell-lung-cancers-by-bioinformatics-analysis
#19
Junjie Piao, Jie Sun, Yang Yang, Tiefeng Jin, Liyan Chen, Zhenhua Lin
BACKGROUND: Non-small cell lung cancer (NSCLC) is the major leading cause of cancer-related deaths worldwide. This study aims to explore molecular mechanism of NSCLC. METHODS: Microarray dataset was obtained from the Gene Expression Omnibus (GEO) database, and analyzed by using GEO2R. Functional and pathway enrichment analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Then, STRING, Cytoscape and MCODE were applied to construct the Protein-protein interaction (PPI) network and screen hub genes...
January 3, 2018: Gene
https://www.readbyqxmd.com/read/29302075/foxo1-a2m-and-tgf-%C3%AE-1-three-novel-genes-predicting-depression-in-gene-x-environment-interactions-are-identified-using-cross-species-and-cross-tissues-transcriptomic-and-mirnomic-analyses
#20
Annamaria Cattaneo, Nadia Cattane, Chiara Malpighi, Darina Czamara, Anna Suarez, Nicole Mariani, Eero Kajantie, Alessia Luoni, Johan G Eriksson, Jari Lahti, Valeria Mondelli, Paola Dazzan, Katri Räikkönen, Elisabeth B Binder, Marco A Riva, Carmine M Pariante
To date, gene-environment (GxE) interaction studies in depression have been limited to hypothesis-based candidate genes, since genome-wide (GWAS)-based GxE interaction studies would require enormous datasets with genetics, environmental, and clinical variables. We used a novel, cross-species and cross-tissues "omics" approach to identify genes predicting depression in response to stress in GxE interactions. We integrated the transcriptome and miRNome profiles from the hippocampus of adult rats exposed to prenatal stress (PNS) with transcriptome data obtained from blood mRNA of adult humans exposed to early life trauma, using a stringent statistical analyses pathway...
January 4, 2018: Molecular Psychiatry
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