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Network protein function prediction

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https://www.readbyqxmd.com/read/28629469/a-putative-molecular-network-associated-with-colon-cancer-metastasis-constructed-from-microarray-data
#1
Songtao Chu, Haipeng Wang, Miao Yu
BACKGROUND: This study aimed to identify the potential molecular network associated with colon cancer metastasis. METHODS: A gene expression profile dataset (GSE40367) downloaded from Gene Expression Omnibus was used to identify and compare differentially expressed genes (DEGs) between primary colon adenocarcinoma tissues and matched tissue samples of liver metastases of colon adenocarcinoma. After the functional analysis of the DEGs, their protein-protein interactions (PPIs) were analyzed, and the transcription factors (TFs) and microRNAs (miRNAs) that regulated these DEGs were predicted...
June 19, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28623591/predicting-transcription-factor-binding-sites-and-their-cognate-transcription-factors-using-gene-expression-data
#2
Chun-Ping Yu, Wen-Hsiung Li
A transcription factor (TF) is a DNA binding protein that targets specific binding-sites (TFBSs) to regulate the transcript levels of its downstream genes. Thus, identifying the TF-TFBS pairs is a pivotal step in understanding the function of TFs and the regulatory network in an organism. Here, we describe two methods for predicting the TFBS of a given TF and for predicting the cognate TF of a given TFBS from a set of strongly co-expressed genes, using time-course transcriptome data of maize developing leaves...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623581/analysis-of-a-plant-transcriptional-regulatory-network-using-transient-expression-systems
#3
Sara Díaz-Triviño, Yuchen Long, Ben Scheres, Ikram Blilou
In plant biology, transient expression systems have become valuable approaches used routinely to rapidly study protein expression, subcellular localization, protein-protein interactions, and transcriptional activity prior to in vivo studies. When studying transcriptional regulation, luciferase reporter assays offer a sensitive readout for assaying promoter behavior in response to different regulators or environmental contexts and to confirm and assess the functional relevance of predicted binding sites in target promoters...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28620443/pattern-recognition-for-predictive-preventive-and-personalized-medicine-in-cancer
#4
REVIEW
Tingting Cheng, Xianquan Zhan
Predictive, preventive, and personalized medicine (PPPM) is the hot spot and future direction in the field of cancer. Cancer is a complex, whole-body disease that involved multi-factors, multi-processes, and multi-consequences. A series of molecular alterations at different levels of genes (genome), RNAs (transcriptome), proteins (proteome), peptides (peptidome), metabolites (metabolome), and imaging characteristics (radiome) that resulted from exogenous and endogenous carcinogens are involved in tumorigenesis and mutually associate and function in a network system, thus determines the difficulty in the use of a single molecule as biomarker for personalized prediction, prevention, diagnosis, and treatment for cancer...
March 2017: EPMA Journal
https://www.readbyqxmd.com/read/28618433/crestal-sinus-augmentation-with-recombinant-human-bone-morphogenetic-protein-2-clinical-and-radiographic-outcomes-of-2-year-pilot-trial
#5
Ulrike Kuchler, Claudia M Rudelstorfer, Barbara Barth, Gabor Tepper, Dominika Lidinsky, Patrick Heimel, Georg Watzek, Reinhard Gruber
PURPOSE: Recombinant human bone morphogenetic protein 2 (rhBMP-2) together with an absorbable collagen carrier (ACS) was approved for augmentation of the maxillary sinus prior to implant placement. The original registration trial was based on a lateral window approach. Clinical outcomes of crestal sinus augmentation with rhBMP-2 have not been reported so far. MATERIALS AND METHODS: An uncontrolled pilot trial in which seven patients with a residual maxillary height below 5 mm were enrolled to receive crestal sinus augmentation with rhBMP-2/ACS was conducted...
June 14, 2017: International Journal of Oral & Maxillofacial Implants
https://www.readbyqxmd.com/read/28615003/3d-deep-convolutional-neural-networks-for-amino-acid-environment-similarity-analysis
#6
Wen Torng, Russ B Altman
BACKGROUND: Central to protein biology is the understanding of how structural elements give rise to observed function. The surfeit of protein structural data enables development of computational methods to systematically derive rules governing structural-functional relationships. However, performance of these methods depends critically on the choice of protein structural representation. Most current methods rely on features that are manually selected based on knowledge about protein structures...
June 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28607455/discovering-overlapped-protein-complexes-from-weighted-ppi-networks-by-removing-inter-module-hubs
#7
A M A Maddi, Ch Eslahchi
Detecting known protein complexes and predicting undiscovered protein complexes from protein-protein interaction (PPI) networks help us to understand principles of cell organization and its functions. Nevertheless, the discovery of protein complexes based on experiment still needs to be explored. Therefore, computational methods are useful approaches to overcome the experimental limitations. Nevertheless, extraction of protein complexes from PPI network is often nontrivial. Two major constraints are large amount of noise and ignorance of occurrence time of different interactions in PPI network...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28601573/upregulation-of-cyclin-b1-plays-potential-roles-in-the-invasiveness-of-pituitary-adenomas
#8
Peng Zhao, Pengfei Zhang, Wei Hu, Hongyun Wang, Guoqiang Yu, Zhuang Wang, Chuzhong Li, Jiwei Bai, Yazhuo Zhang
Predicting aggressive or malignant behavior of pituitary adenomas (PAs) remains challenging. Aberrant expression of cyclin B1 (CCNB1) occurred in various tumors including PAs. Our study was aimed to explore its roles in the development of PAs aggressiveness. According to the integrated analysis, the expression of CCNB1 was evaluated. Following bioinformatics analysis was performed to uncover the pathways CCNB1 involved in and the upstream transcriptional regulation factors. The mRNA expression of CCNB1 was verified by qRT-PCR...
June 7, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28598986/computational-analysis-of-multimorbidity-between-asthma-eczema-and-rhinitis
#9
Daniel Aguilar, Mariona Pinart, Gerard H Koppelman, Yvan Saeys, Martijn C Nawijn, Dirkje S Postma, Mübeccel Akdis, Charles Auffray, Stéphane Ballereau, Marta Benet, Judith García-Aymerich, Juan Ramón González, Stefano Guerra, Thomas Keil, Manolis Kogevinas, Bart Lambrecht, Nathanael Lemonnier, Erik Melen, Jordi Sunyer, Rudolf Valenta, Sergi Valverde, Magnus Wickman, Jean Bousquet, Baldo Oliva, Josep M Antó
BACKGROUND: The mechanisms explaining the co-existence of asthma, eczema and rhinitis (allergic multimorbidity) are largely unknown. We investigated the mechanisms underlying multimorbidity between three main allergic diseases at a molecular level by identifying the proteins and cellular processes that are common to them. METHODS: An in silico study based on computational analysis of the topology of the protein interaction network was performed in order to characterize the molecular mechanisms of multimorbidity of asthma, eczema and rhinitis...
2017: PloS One
https://www.readbyqxmd.com/read/28596505/progressive-modulation-of-the-human-olfactory-bulb-transcriptome-during-alzheimer%C3%A2-s-disease-evolution-novel-insights-into-the-olfactory-signaling-across-proteinopathies
#10
Mercedes Lachen-Montes, María Victoria Zelaya, Víctor Segura, Joaquín Fernández-Irigoyen, Enrique Santamaría
Alzheimer´s disease (AD) is characterized by progressive dementia, initially presenting olfactory dysfunction. Despite the olfactory bulb (OB) is the first central structure of the olfactory pathway, we lack a complete molecular characterization of the transcriptional events that occurs in this olfactory area during AD progression. To address this gap in knowledge, we have assessed the genome-wide expression in postmortem OBs from subjects with varying degree of AD pathology. A stage-dependent deregulation of specific pathways was observed, revealing transmembrane transport, and neuroinflammation as part of the functional modules that are disrupted across AD grading...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28588641/the-significant-pathways-and-genes-underlying-the-colon-cancer-treatment-by-the-traditional-chinese-medicine-phy906
#11
Ziyuan Su, Changyu Zhou, Shaoyou Qin, Erna Jia, Zhenting Wu
BACKGROUND: We attempted to explore the molecular mechanism underlying PHY906 intervention of colon cancer. METHODS: The microarray data of tumors treated by PHY906 and PBS alone were downloaded from the public Gene Expression Omnibus database. The dataset was further analyzed for the differentially expressed genes (DEGs) and their related biological functions were analyzed, followed by function and pathways. Protein-protein interaction (PPI) network was constructed and the significant nodes were screened by network centralities and then the significant modules analysis...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28587194/cross-kingdom-regulation-of-putative-mirnas-derived-from-happy-tree-in-cancer-pathway-a-systems-biology-approach
#12
Dinesh Kumar, Swapnil Kumar, Garima Ayachit, Shivarudrappa B Bhairappanavar, Afzal Ansari, Priyanka Sharma, Subhash Soni, Jayashankar Das
MicroRNAs (miRNAs) are well-known key regulators of gene expression primarily at the post-transcriptional level. Plant-derived miRNAs may pass through the gastrointestinal tract, entering into the body fluid and regulate the expression of endogenous mRNAs. Camptotheca acuminata, a highly important medicinal plant known for its anti-cancer potential was selected to investigate cross-kingdom regulatory mechanism and involvement of miRNAs derived from this plant in cancer-associated pathways through in silico systems biology approach...
June 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28586048/modeling-osteosarcoma-progression-by-measuring-the-connectivity-dynamics-using-an-inference-of-multiple-differential-modules-algorithm
#13
Bin Liu, Zhi Zhang, E-Nuo Dai, Jia-Xin Tian, Jiang-Ze Xin, Liang Xu
Understanding the dynamic changes in connectivity of molecular pathways is important for determining disease prognosis. Thus, the current study used an inference of multiple differential modules (iMDM) algorithm to identify the connectivity changes of sub‑network to predict the progression of osteosarcoma (OS) based on the microarray data of OS at four Huvos grades. Initially, multiple differential co‑expression networks (M‑DCNs) were constructed, and weight values were assigned for each edge, followed by detection of seed genes in M‑DCNs according to the topological properties...
June 6, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28586047/identification-and-functional-analysis-of-the-risk-micrornas-associated-with-cerebral-low-grade-glioma-prognosis
#14
Xinrui Liu, Bin Song, Shanji Li, Nan Wang, Hongfa Yang
Low-grade gliomas (LGGs) are associated with neurological disability. The present study used microRNA (miRNA) expression profiles to identify risk miRNAs for potential prognosis of cerebral LGGs. miRNA expression profiles and clinical data from 408 patients with cerebral LGGs were obtained from the Cancer Genome Atlas database. Risk miRNAs were identified by plotting Kaplan‑Meier curves and Cox proportional hazard regression analysis with the survival and KMsurv packages in R. A regulatory network of miRNA‑targets was constructed, followed by gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis using the Database for Annotation, Visualization and Integrated Discovery...
June 6, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28585144/weighted-gene-co-expression-network-analysis-of-gene-modules-for-the-prognosis-of-esophageal-cancer
#15
Cong Zhang, Qian Sun
Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas (TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time...
June 2017: Journal of Huazhong University of Science and Technology. Medical Sciences
https://www.readbyqxmd.com/read/28584099/genome-wide-use-of-high-and-low-affinity-tbrain-transcription-factor-binding-sites-during-echinoderm-development
#16
Gregory A Cary, Alys M Cheatle Jarvela, Rene D Francolini, Veronica F Hinman
Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). Although cis-regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low-affinity, secondary binding motif. The primary, high-affinity motif is conserved. To date, however, no genome-wide comparisons have been performed to provide an unbiased assessment of the evolution of GRNs between these taxa, and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28581477/inter-organ-signalling-by-hrg-7-promotes-systemic-haem-homeostasis
#17
Jason Sinclair, Katherine Pinter, Tamika Samuel, Simon Beardsley, Xiaojing Yuan, Jianbing Zhang, Kevin Meng, Sijung Yun, Michael Krause, Iqbal Hamza
Growing evidence in vertebrates predicts that cellular haem levels in animals are maintained not only by a cell's internal capacity for haem synthesis in a cell-autonomous manner, but also by an inter-organ haem trafficking network through cell-non-autonomous regulation. Using Caenorhabditis elegans, a genetically and optically amenable animal model for visualizing haem-dependent signalling, we show that HRG-7, a protein with homology to aspartic proteases, mediates inter-organ signalling between the intestine and extra-intestinal tissues...
June 5, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28571639/longitudinal-outcomes-of-patients%C3%A2-with%C3%A2-single-ventricle-after%C3%A2-the%C3%A2-fontan%C3%A2-procedure
#18
Andrew M Atz, Victor Zak, Lynn Mahony, Karen Uzark, Nicholas D'agincourt, David J Goldberg, Richard V Williams, Roger E Breitbart, Steven D Colan, Kristin M Burns, Renee Margossian, Heather T Henderson, Rosalind Korsin, Bradley S Marino, Kaitlyn Daniels, Brian W McCrindle
BACKGROUND: Multicenter longitudinal objective data for survival into adulthood of patients who have undergone Fontan procedures are lacking. OBJECTIVES: This study sought to describe transplant-free survival and explore relationships between laboratory measures of ventricular performance and functional status over time. METHODS: Exercise testing, echocardiography, B-type natriuretic peptide, functional health assessment, and medical history abstraction were repeated 9...
June 6, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28562633/bioinformatics-identification-and-transcript-profile-analysis-of-the-mitogen-activated-protein-kinase-gene-family-in-the-diploid-woodland-strawberry-fragaria-vesca
#19
Wei Wei, Zhuangzhuang Chai, Yinge Xie, Kuan Gao, Mengyuan Cui, Ying Jiang, Jiayue Feng
Mitogen-activated protein kinases (MAPKs) play essential roles in mediating biotic and abiotic stress responses in plants. However, the MAPK gene family in strawberry has not been systematically characterized. Here, we performed a genome-wide survey and identified 12 MAPK genes in the Fragaria vesca genome. Protein domain analysis indicated that all FvMAPKs have typical protein kinase domains. Sequence alignments and phylogenetic analysis classified the FvMAPK genes into four different groups. Conserved motif and exon-intron organization supported the evolutionary relationships inferred from the phylogenetic analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28555214/the-maximum-penalty-criterion-for-ridge-regression-application-to-the-calibration-of-the-force-constant-in-elastic-network-models
#20
Yves Dehouck, Ugo Bastolla
Tikhonov regularization, or ridge regression, is a popular technique to deal with collinearity in multivariate regression. We unveil a formal analogy between ridge regression and statistical mechanics, where the objective function is comparable to a free energy, and the ridge parameter plays the role of temperature. This analogy suggests two novel criteria for selecting a suitable ridge parameter: specific-heat (Cv) and maximum penalty (MP). We apply these fits to evaluate the relative contributions of rigid-body and internal fluctuations, which are typically highly collinear, to crystallographic B-factors...
May 30, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
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