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Network protein function prediction

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https://www.readbyqxmd.com/read/28449114/neuro-symbolic-representation-learning-on-biological-knowledge-graphs
#1
Mona Alshahrani, Mohammed Asif Khan, Omar Maddouri, Akira R Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf
Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28446508/enrichment-of-pik3-akt-mtor-pathway-activation-in-hepatic-metastases-from-breast-cancer
#2
Mariaelena Pierobon, Corrine Ramos, Shukmei Wong, K Alex Hodge, Jessica Aldrich, Sara A Byron, Stephen P Anthony, Nicholas J Robert, Donald W Northfelt, Mohammad Jahanzeb, Linda Vocila, Julia D Wulfkuhle, Guido Gambara, Rosa Isela Gallagher, Bryant Dunetz, Nicholas Hoke, Ting Dong, David W Craig, Massimo Cristofanilli, Brian Leyland Jones, Lance Liotta, Joyce A O'Shaughnessy, John D Carpten, Emanuel F Petricoin
Purpose: Little is known about the molecular signatures associated with specific metastatic sites in breast cancer. Using comprehensive multi-omic molecular profiling, we assessed whether alterations or activation of the PI3K-AKT-mTOR pathway is associated with specific sites of breast cancer metastasis. <p>Experimental Design: NGS-based whole exome sequencing was coupled with Reverse Phase Protein Microarray (RPPA) functional signaling network analysis to explore the PI3K-AKT-mTOR axis in 32 pretreated breast cancer metastases...
April 26, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28445636/disposable-autonomous-device-for-rapid-swab-to-result-diagnosis-of-influenza
#3
Shichu Huang, Koji Abe, Steven Bennett, Tinny Liang, Paula D Ladd, Lindsay Yokobe, Caitlin E Anderson, Kamal Shah, Josh Bishop, Mike Purfield, Peter C Kauffman, Sai Paul, AnneMarie E Welch, Bonnie Strelitz, Kristin Follmer, Kelsey Pullar, Luis Sanchez-Erebia, Emily Gerth-Guyette, Gonzalo J Domingo, Eileen Klein, Janet A Englund, Elain Fu, Paul Yager
A prototype of a self-contained, automated, disposable device for chemically-amplified protein-based detection of influenza virus from nasal swab specimens was developed and evaluated in a clinical setting. The device required only simple specimen manipulation without any dedicated instrumentation or specialized training by the operator for interpretation. The device was based on a sandwich immunoassay for influenza virus nucleoprotein; it used an enzyme-labeled antibody and a chromogenic substrate to provide an amplified visible signal, in a two-dimensional paper network format...
April 26, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28444616/genome-wide-identification-of-grain-filling-genes-regulated-by-the-ossmf1-transcription-factor-in-rice
#4
Joung Sug Kim, Songhwa Chae, Kyong Mi Jun, Yoon-Mok Pahk, Tae-Ho Lee, Pil Joong Chung, Yeon-Ki Kim, Baek Hie Nahm
BACKGROUND: Spatial- and temporal-specific expression patterns are primarily regulated at the transcriptional level by gene promoters. Therefore, it is important to identify the binding motifs of transcription factors to better understand the networks associated with embryogenesis. RESULTS: Here, we used a protein-binding microarray (PBM) to identify the binding motifs of OsSMF1, which is a basic leucine zipper transcription factor involved in the regulation of rice seed maturation...
December 2017: Rice
https://www.readbyqxmd.com/read/28440408/identification-of-potential-gene-targets-in-systemic-vasculitis-using-dna-microarray-analysis
#5
Yiwen Feng, Miao Zheng, Shujie Gan, Lei Zhang, Zhong Wan, Yanping Zhang, Qin Qian, Jingdong Tang
The present study aimed to identify the involvement of critical genes in systemic vasculitis, to gain an improved understanding of the molecular circuity and to investigate novel potential gene targets for systemic vasculitis treatment. The dual‑color cDNA microarray data of GSE16945, consisting of peripheral mononuclear blood cell specimens from 13 patients with systemic vasculitis and 16 healthy controls, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened in systemic vasculitis compared with controls using BRB ArrayTools, followed by the construction of a protein‑protein interaction (PPI) network using the clusterProfiler package, and significant functional interaction (FI) module selection...
April 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28439950/protein-disulfide-isomerase-inhibition-synergistically-enhances-the-efficacy-of-sorafenib-for-hepatocellular-carcinoma
#6
Jae-Kyung Won, Su Jong Yu, Chae Young Hwang, Sung-Hwan Cho, Sang-Min Park, Kwangsoo Kim, Won-Mook Choi, Hyeki Cho, Eun Ju Cho, Jeong-Hoon Lee, Kyung Bun Lee, Yoon Jun Kim, Kyung-Suk Suh, Ja-June Jang, Chung Yong Kim, Jung-Hwan Yoon, Kwang-Hyun Cho
Sorafenib is the only approved targeted drug for hepatocellular carcinoma (HCC), but its effect on patients' survival gain is limited and varies over a wide range depending on patho-genetic conditions. Thus, enhancing the efficacy of sorafenib and finding a reliable predictive biomarker are crucial to achieve efficient control of HCCs. In this study, we employed a systems approach by combining transcriptome analysis of the mRNA changes in HCC cell lines in response to sorafenib with network analysis to investigate the action and resistance mechanism of sorafenib...
April 25, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28438123/small-rna-sequencing-reveals-a-role-for-sugarcane-mirnas-and-their-targets-in-response-to-sporisorium-scitamineum-infection
#7
Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo, Youxiong Que
BACKGROUND: Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing. RESULTS: The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28436483/itraq-based-proteomic-analysis-reveals-key-proteins-affecting-muscle-growth-and-lipid-deposition-in-pigs
#8
Zhixiu Wang, Peng Shang, Qinggang Li, Liyuan Wang, Yangzom Chamba, Bo Zhang, Hao Zhang, Changxin Wu
Growth rate and meat quality, two economically important traits in pigs, are controlled by multiple genes and biological pathways. In the present study, we performed a proteomic analysis of longissimus dorsi muscle from six-month-old pigs from two Chinese native mini-type breeds (TP and DSP) and two introduced western breeds (YY and LL) using isobaric tag for relative and absolute quantification (iTRAQ). In total, 4,815 peptides corresponding to 969 proteins were detected. Comparison of expression patterns between TP-DSP and YY-LL revealed 288 differentially expressed proteins (DEPs), of which 169 were up-regulated and 119 were down-regulated...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28434945/prognostic-biomarker-identification-through-integrating-the-gene-signatures-of-hepatocellular-carcinoma-properties
#9
Jialin Cai, Bin Li, Yan Zhu, Xuqian Fang, Mingyu Zhu, Mingjie Wang, Shupeng Liu, Xiaoqing Jiang, Jianming Zheng, XinXin Zhang, Peizhan Chen
Many molecular classification and prognostic gene signatures for hepatocellular carcinoma (HCC) patients have been established based on genome-wide gene expression profiling; however, their generalizability is unclear. Herein, we systematically assessed the prognostic effects of these gene signatures and identified valuable prognostic biomarkers by integrating these gene signatures. With two independent HCC datasets (GSE14520, N=242 and GSE54236, N=78), 30 published gene signatures were evaluated, and 11 were significantly associated with the overall survival (OS) of postoperative HCC patients in both datasets...
April 12, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28432981/hidden-markov-model-and-chapman-kolmogrov-for-protein-structures-prediction-from-images
#10
Md Sarwar Kamal, Linkon Chowdhury, Mohammad Ibrahim Khan, Amira S Ashour, João Manuel R S Tavares, Nilanjan Dey
Protein structure prediction and analysis are more significant for living organs to perfect asses the living organ functionalities. Several protein structure prediction methods use neural network (NN). However, the Hidden Markov model is more interpretable and effective for more biological data analysis compared to the NN. It employs statistical data analysis to enhance the prediction accuracy. The current work proposed a protein prediction approach from protein images based on Hidden Markov Model and Chapman Kolmogrov equation...
April 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28431521/a-reference-floral-transcriptome-of-sexual-and-apomictic-paspalum-notatum
#11
Juan Pablo A Ortiz, Santiago Revale, Lorena A Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc, Silvina C Pessino
BACKGROUND: Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. RESULTS: We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28431495/iron-regulated-small-rna-expression-as-neisseria-gonorrhoeae-fa-1090-transitions-into-stationary-phase-growth
#12
Lydgia A Jackson, Michael Day, Jennie Allen, Edgar Scott, David W Dyer
BACKGROUND: For most pathogens, iron (Fe) homeostasis is crucial for maintenance within the host and the ability to cause disease. The primary transcriptional regulator that controls intracellular Fe levels is the Fur (ferric uptake regulator) protein, which exerts its action on transcription by binding to a promoter-proximal sequence termed the Fur box. Fur-regulated transcriptional responses are often fine-tuned at the post-transcriptional level through the action of small regulatory RNAs (sRNAs)...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28430949/capturing-non-local-interactions-by-long-short-term-memory-bidirectional-recurrent-neural-networks-for-improving-prediction-of-protein-secondary-structure-backbone-angles-contact-numbers-and-solvent-accessibility
#13
Rhys Heffernan, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some "short to intermediate" non-local interactions...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#14
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#15
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28421415/a-tyrosine-residue-along-with-a-glutamic-acid-of-the-omega-like-loop-governs-the-beta-lactamase-activity-of-msmeg_4455-in-mycobacterium-smegmatis
#16
Ankita Bansal, Debasish Kar, Satya Deo Pandey, Ashok Matcha, N Ganesh Kumar, Soshina Nathan, Anindya S Ghosh
Mycobacterial beta-lactamases are involved in exerting beta-lactam resistance, though many of these proteins remain uncharacterized. Here, we have characterized MSMEG_4455 of Mycobacterium smegmatis as a beta-lactamase using molecular, biochemical and mutational techniques. To elucidate its nature in vivo and in vitro, and to predict its structure-function relationship in silico analysis is done. The MSMEG_4455 is cloned and expressed ectopically in a beta-lactamase deficient Escherichia coli mutant to establish the in vivo beta-lactamase like nature via minimum inhibitory concentration (MIC) determination...
April 19, 2017: Protein Journal
https://www.readbyqxmd.com/read/28420736/deciphering-the-regulatory-network-between-the-srebp-pathway-and-protein-secretion-in-neurospora-crassa
#17
Lina Qin, Vincent W Wu, N Louise Glass
Sterol regulatory element binding proteins (SREBPs) are conserved from yeast to mammalian cells and function in the regulation of sterol homeostasis. In fungi, the SREBP pathway has been implicated in the adaptation to hypoxia and in virulence. In Neurospora crassa and Trichoderma reesei, the SREBP pathway also negatively regulates protein secretion under lignocellulolytic conditions. Here we utilized global transcriptional profiling combined with genetic and physiological analyses to address the regulatory link between the SREBP pathway and protein secretion in N...
April 18, 2017: MBio
https://www.readbyqxmd.com/read/28415207/model-of-polar-auxin-transport-coupled-to-mechanical-forces-retrieves-robust-morphogenesis-along-the-arabidopsis-root
#18
J Roberto Romero-Arias, Valeria Hernández-Hernández, Mariana Benítez, Elena R Alvarez-Buylla, Rafael A Barrio
Stem cells are identical in many scales, they share the same molecular composition, DNA, genes, and genetic networks, yet they should acquire different properties to form a functional tissue. Therefore, they must interact and get some external information from their environment, either spatial (dynamical fields) or temporal (lineage). In this paper we test to what extent coupled chemical and physical fields can underlie the cell's positional information during development. We choose the root apical meristem of Arabidopsis thaliana to model the emergence of cellular patterns...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28413470/identification-of-genes-associated-with-the-effect-of-inflammation-on-the-neurotransmission-of-vascular-smooth-muscle-cell
#19
Shujie Gan, Shenlong Qiu, Yiwen Feng, Yanping Zhang, Qin Qian, Zhong Wan, Jingdong Tang
Vascular smooth muscle cell (VSMC) accumulation and hypertrophy are common in vascular disorders, and inflammation has a crucial role in the development of these diseases. To investigate the effect of inflammation on the neurotransmission of VSMC, bioinformatic analysis was performed, following next generation sequencing. Genes of lipopolysaccharide (LPS)-treated A7r5 cells and phosphate-buffered saline (PBS)-treated A7r5 cells were sequenced via next generation sequencing, and each assay was repeated three times...
April 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28412901/an-analysis-of-central-residues-between-ligand-bound-and-ligand-free-protein-structures-based-on-network-approach
#20
Amala Arumugam, Arnold Emerson Isacc
Depiction of protein structures as networks of interacting residues has enabled us to understand the structure and function of the protein. Previous investigations on closeness centrality have identified protein functional sites from three- dimensional structures. It is well recognized that ligand binding to a receptor protein induces a wide range of structural changes. An interesting question is, how central residues function during conformational changes triggered during ligand binding? The aim of this study is to comprehend at what extent central residues change during ligand binding to receptor proteins...
April 13, 2017: Protein and Peptide Letters
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