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Network protein function prediction

Navadon Khunlertgit, Byung-Jun Yoon
BACKGROUND: Discovering robust markers for cancer prognosis based on gene expression data is an important yet challenging problem in translational bioinformatics. By integrating additional information in biological pathways or a protein-protein interaction (PPI) network, we can find better biomarkers that lead to more accurate and reproducible prognostic predictions. In fact, recent studies have shown that, "modular markers," that integrate multiple genes with potential interactions can improve disease classification and also provide better understanding of the disease mechanisms...
October 6, 2016: BMC Bioinformatics
Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
BACKGROUND: Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. RESULTS: In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks...
October 6, 2016: BMC Bioinformatics
Delphine Ropers, Aline Métris
Qualitative modeling approaches allow to provide a coarse-grained description of the functioning of cellular networks when experimental data are scarce and heterogeneous. We translate the primary literature data on the response of Escherichia coli to hyperosmotic stress caused by NaCl addition into a piecewise linear (PL) model. We provide a data file of the qualitative model, which can be used for simulation of changes of protein concentrations and of DNA coiling during the physiological response of the bacterium to the stress...
December 2016: Data in Brief
Ji-Yong An, Zhu-Hong You, Xing Chen, De-Shuang Huang, Guiying Yan, Da-Fu Wang
Self-interacting proteins (SIPs) play an essential role in cellular functions and the evolution of protein interaction networks (PINs). Due to the limitations of experimental self-interaction proteins detection technology, it is a very important task to develop a robust and accurate computational approach for SIPs prediction. In this study, we propose a novel computational method for predicting SIPs from protein amino acids sequence. Firstly, a novel feature representation scheme based on Local Binary Pattern (LBP) is developed, in which the evolutionary information, in the form of multiple sequence alignments, is taken into account...
October 19, 2016: Molecular BioSystems
Qiangfeng Wang, Huanxia Yang, Lingjiao Wu, Jian Yao, Xiaohua Meng, Han Jiang, Cheng Xiao, Fusheng Wu
BACKGROUND: In recent years, long non-coding RNAs (lncRNAs) have been shown to play a critical regulatory role in cancer biology. However, the contribution of lncRNAs to papillary thyroid cancer (PTC) remains largely unknown. METHODS: RNA sequencing and quantitative reverse transcription PCR (qRT-PCR) were used to detect and verify, respectively, changes to the transcriptomic profile in 12 PTC tissues compared to paired normal adjacent tissues. The statistical correlation between differentially expressed lncRNAs and clinicopathological characteristics was analysed, and potential lncRNA functions were predicted by examining annotations for the co-expressed mRNAs...
October 19, 2016: Thyroid: Official Journal of the American Thyroid Association
Zhanzhan Xu, Yu Zhou, Yexuan Cao, Thi Lan Anh Dinh, Jing Wan, Min Zhao
Ovarian cancer is the first leading cause of mortality in gynecological malignancies. To identify key genes and microRNAs in ovarian cancer, mRNA microarray dataset GSE36668, GSE18520, GSE14407 and microRNA dataset GSE47841 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and microRNAs (DEMs) were obtained using GEO2R. Functional and pathway enrichment analysis were performed for DEGs using DAVID database. Protein-protein interaction (PPI) network was established by STRING and visualized by Cytoscape...
November 2016: Medical Oncology
Zhi Chen, Hao Wu, Guohua Wang, Ye Feng
BACKGROUND: This study was aimed to explore the molecular mechanisms of hypertensive nephropathy (HTN). METHODS: Gene expression profile of GSE37460, which based on 27 healthy living donor samples (HTN group) and 15 hypertensive nephropathy samples (control group), were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between two groups were identified. STRING database was used to reveal protein-protein interaction (PPI) network of DEGs, followed by the functional enrichment analysis of the PPI network...
October 18, 2016: BMC Nephrology
Salma Jamal, Sukriti Goyal, Asheesh Shanker, Abhinav Grover
BACKGROUND: Alzheimer's disease (AD) is a complex progressive neurodegenerative disorder commonly characterized by short term memory loss. Presently no effective therapeutic treatments exist that can completely cure this disease. The cause of Alzheimer's is still unclear, however one of the other major factors involved in AD pathogenesis are the genetic factors and around 70 % risk of the disease is assumed to be due to the large number of genes involved. Although genetic association studies have revealed a number of potential AD susceptibility genes, there still exists a need for identification of unidentified AD-associated genes and therapeutic targets to have better understanding of the disease-causing mechanisms of Alzheimer's towards development of effective AD therapeutics...
October 18, 2016: BMC Genomics
Shazia Nafis, Kalaiarasan Ponnusamy, Mohammad Husain, R K Brojen Singh, Rameshwar N K Bamezai
An experimentally validated set of apoptosis-regulatory proteins was subjected to network analysis, depicting a scale-free hierarchical fractal network. The power-law distribution of the various topological properties of the network revealed the fractal nature of the network, a signature of self-organization of the network where the network maintained the democratic constitution of nodes at various levels and showed the absence of the centrality-lethality control system. Even though network breakdown under the absence of the centrality-lethality rule of hub removal did not happen, the change in the topological properties of the network could be observed...
October 18, 2016: Molecular BioSystems
Alberto Baggioli, Carlo A Cavallotti, Antonino Famulari
From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other...
October 18, 2016: Physical Chemistry Chemical Physics: PCCP
Karan Kapoor, Michael R Duff, Amit Upadhyay, Joel C Bucci, Arnold M Saxton, Robert J Hinde, Elizabeth E Howell, Jerome Yves Baudry
The dynamics of anion-quadrupole (or anion-) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (PDB: 1EP0), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-anion--) are formed by the protein during the simulated trajectory which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1...
October 18, 2016: Biochemistry
Jing-Yi Li, Li-Li Zheng, Ting-Ting Wang, Min Hu
BACKGROUND: Melanoma is a type of cancer that develops from the pigment-containing cells. Until now, its pathological mechanisms remain largely unknown. The aim of this study was to identify metastasis-related microRNA (miRNAs) and gain an understanding of the biological functions in the metastasis of melanoma. METHODS: We searched the PubMed and Gene Expression Omnibus database to collect miRNA expression profiling datasets about melanoma, with key words of "melanoma", "miRNA", "microarray", and "gene expression profiling"...
2016: Chinese Medical Journal
Maurizio Cirilli, Oxana Bereshchenko, Olga Ermakova, Claus Nerlov
BACKGROUND: C/EBPa and C/EBPb are transcription factors with tissue specific expression regulating several important cellular processes. They work by recruiting protein complexes to a common DNA recognition motif and both are able to compensate each other's absence in many cell types, thus showing functional redundancy. They also play distinct roles in specific cellular pathways and their abnormal functioning gives raise to different human pathologies. METHODS: To investigate the molecular basis of C/EBPa and C/EBPb specificity and redundancy we characterized their in vivo protein-protein interaction networks by Tandem Affinity Purification and Mass Spectrometry...
October 13, 2016: Biochimica et Biophysica Acta
Renu Vyas, Sanket Bapat, Esha Jain, Muthukumarasamy Karthikeyan, Sanjeev Tambe, Bhaskar D Kulkarni
In order to understand the molecular mechanism underlying any disease, knowledge about the interacting proteins in the disease pathway is essential. The number of revealed protein-protein interactions (PPI) is still very limited compared to the available protein sequences of different organisms. Experiment based high-throughput technologies though provide some data about these interactions, those are often fairly noisy. Computational techniques for predicting protein-protein interactions therefore assume significance...
September 30, 2016: Computational Biology and Chemistry
Kamal Taha
This study proposes a new method to determine the functions of an unannotated protein. The proteins and amino acid residues mentioned in biomedical texts associated with an unannotated protein p can be considered as characteristics terms for p, which are highly predictive of the potential functions of p. Similarly, proteins and amino acid residues mentioned in biomedical texts associated with proteins annotated with a functional category f can be considered as characteristics terms of f. We introduce in this paper an information extraction system called IFP_IFC that predicts the functions of an unannotated protein p by representing p and each functional category f by a vector of weights...
October 6, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Catherine E Isom, Smita K Menon, Leonard M Thomas, Ann H West, George B Richter-Addo, Elizabeth A Karr
BACKGROUND: Clostridium difficile is a spore-forming obligate anaerobe that can remain viable for extended periods, even in the presence of antibiotics, which contributes to the persistence of this bacterium as a human pathogen during host-to-host transmission and in hospital environments. We examined the structure and function of a gene product with the locus tag CDR20291_0991 (cdPadR1) as part of our broader goal aimed at elucidating transcription regulatory mechanisms involved in virulence and antibiotic resistance of the recently emergent hypervirulent C...
October 4, 2016: BMC Microbiology
Jennifer S Yokoyama, Gabe Marx, Jesse A Brown, Luke W Bonham, Dan Wang, Giovanni Coppola, William W Seeley, Howard J Rosen, Bruce L Miller, Joel H Kramer, Dena B Dubal
Cognitive decline is a major biomedical challenge as the global population ages. Elevated levels of the longevity factor klotho suppress aging, enhance cognition, and promote synaptic plasticity and neural resilience against aging and Alzheimer's disease (AD)-related pathogenic proteins. Here, we examined the relationship between human genetic variants of KLOTHO and systemic klotho levels - and assessed neuroanatomic correlates of serum klotho in a cohort of healthy older adults. Serum klotho levels were increased with KL-VS heterozygosity, as anticipated...
October 6, 2016: Brain Imaging and Behavior
Anuj Kumar, Drista Sharma, M L Aggarwal, K M Chacko, Tarun Kumar Bhatt
Present chemotherapeutic drugs have limited efficacy and severe side effects. Considering the complexity of cancer, an effective strategy is necessary to discover multiple new drug targets. Cancer/testis antigens are vital for cancer cell progression. We have performed a computational network analysis of cancer/testis antigens and assessed these antigens as drug targets. During this analysis, protein interaction network of 700 human CT antigens was investigated. CT antigen network consisted of eight independent components...
October 5, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
Dongdi Li, Ruth Moorman, Thomas Vanhercke, James Petrie, Surinder Singh, Colin J Jackson
Membrane fatty acid desaturases are a diverse superfamily of enzymes that catalyze the introduction of double bonds into fatty acids. They are essential in a range of metabolic processes, such as the production of omega-3 fatty acids. However, our structure-function understanding of this superfamily is still developing and their range of activities and substrate specificities are broad, and often overlapping, which has made their systematic characterization challenging. A central issue with characterizing these proteins has been the lack of a structural model, which has been overcome with the recent publication of the crystal structures of two mammalian fatty acid desaturases...
2016: Computational and Structural Biotechnology Journal
Junguo Wang, Fang Mei, Xia Gao, Shoulin Wang
Nasopharyngeal carcinoma (NPC) is the most common cancer originating from the nasopharynx, and can be induced by infection with Epstein-Barr virus (EBV). To study the mechanisms of EBV-associated NPC, a microarray of the GSE12452 dataset was analyzed. GSE12452 was downloaded from Gene Expression Omnibus and consisted of 31 NPC samples and 10 normal healthy nasopharyngeal tissue samples. The differentially-expressed genes (DEGs) were screened using the linear models for microarray data package in R. Using Database for Annotation, Visualization and Integrated Discovery software, potential functions of the DEGs were predicted by Gene Ontology and pathway enrichment analyses...
October 2016: Oncology Letters
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