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Network protein function prediction

Li Gao, Li-Jie Zhang, Sheng-Hua Li, Li-Li Wei, Bin Luo, Rong-Quan He, Shuang Xia
BACKGROUND: MiR-452-5p has been reported to be down-regulated in prostate cancer, affecting the development of this type of cancer. However, the molecular mechanism of miR-452-5p in prostate cancer remains unclear. Therefore, we investigated the network of target genes of miR-452-5p in prostate cancer using bioinformatics analyses. MATERIALS AND METHODS: We first analyzed the expression profiles and prognostic value of miR-452-5p in prostate cancer tissues from a public database...
March 6, 2018: Pathology, Research and Practice
Longcan Mei, Yanping Zhou, Lizhe Zhu, Changlin Liu, Zhuo Wu, Fangkui Wang, Gefei Hao, Di Yu, Hong Yuan, Yanfang Cui
A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm...
March 20, 2018: International Journal of Molecular Sciences
Zacharenia Nikitaki, Marcela Holá, Mattia Donà, Athanasia Pavlopoulou, Ioannis Michalopoulos, Karel J Angelis, Alexandros G Georgakilas, Anca Macovei, Alma Balestrazzi
Eukaryotic genome surveillance is dependent on the multiple, highly coordinated network functions of the DNA damage response (DDR). Highlighted conserved features of DDR in plants and animals represent a challenging opportunity to develop novel interdisciplinary investigations aimed at expanding the sets of DNA damage biomarkers currently available for radiation exposure monitoring (REM) in environmental and biomedical applications. In this review, common and divergent features of the most relevant DDR players in animals and plants are described, including the intriguing example of the plant and animal kingdom-specific master regulators SOG1 (suppressor of gamma response) and p53...
January 2018: Mutation Research
Sameer Khurana, Reda Rawi, Khalid Kunji, Gwo-Yu Chuang, Halima Bensmail, Raghvendra Mall
Motivation: Protein solubility plays a vital role in pharmaceutical research and production yield. For a given protein, the extent of its solubility can represent the quality of its function, and is ultimately defined by its sequence. Thus, it is imperative to develop novel, highly accurate in silico sequence-based protein solubility predictors. Methods: In this work we propose, DeepSol, a novel Deep Learning based protein solubility predictor. The backbone of our framework is a Convolutional Neural Network (CNN) that exploits k-mer structure and additional sequence and structural features extracted from the protein sequence...
March 15, 2018: Bioinformatics
Yadong Dong, Yongqi Sun, Chao Qin
The existing protein complex detection methods can be broadly divided into two categories: unsupervised and supervised learning methods. Most of the unsupervised learning methods assume that protein complexes are in dense regions of protein-protein interaction (PPI) networks even though many true complexes are not dense subgraphs. Supervised learning methods utilize the informative properties of known complexes; they often extract features from existing complexes and then use the features to train a classification model...
2018: PloS One
Rong-Quan He, Xia Yang, Liang Liang, Gang Chen, Jie Ma
The present study aimed to explore the potential clinical significance of microRNA (miR)-124-3p expression in the hepatocarcinogenesis and development of hepatocellular carcinoma (HCC), as well as the potential target genes of functional HCC pathways. Reverse transcription-quantitative polymerase chain reaction was performed to evaluate the expression of miR-124-3p in 101 HCC and adjacent non-cancerous tissue samples. Additionally, the association between miR-124-3p expression and clinical parameters was also analyzed...
April 2018: Oncology Letters
Li-Qiang Zheng, Shan-Yi Li, Cheng-Xin Li
The aim of the present study was to identify the potential autophagy-related genes and to explore the underlying molecular mechanisms involved in cutaneous squamous cell carcinoma of head and neck (cSCCHN) by bioinformatics analysis. The Gene Expression Omnibus (GEO) series GSE86544 was downloaded from the GEO database. The primary data was generated from cSCCHN with clinical perineural invasion (PNI) and cSCCHN without PNI, and was further analyzed in order to identify differentially expressed genes (DEGs)...
April 2018: Oncology Letters
Yibin Hao, Jianhua Zhang, Guoyong Shan, Ning Zhang, Wenwen Jin, Kejun Nan
Objective: to establish regulatory network of colorectal cancer involving p42.3 protein and to provide theoretical evidence for deep functional exploration of p42.3 protein in the onset and development of colorectal cancer. Methods: with protein similarity algorithm, reference protein set of p42.3 cell apoptosis was built according to structural features of p42.3. GO and KEGG databases were used to establish regulatory network of tumor cell apoptosis involving p42.3; meanwhile, the largest possible working pathway that involves p42...
December 2017: Saudi Journal of Biological Sciences
Atefeh Rabiee, Marcus Krüger, Jacob Ardenkjær-Larsen, C Ronald Kahn, Brice Emanuelli
Insulin/IGF-1 action is driven by a complex and highly integrated signalling network. Loss-of-function studies indicate that the major insulin/IGF-1 receptor substrate (IRS) proteins, IRS-1 and IRS-2, mediate different biological functions in vitro and in vivo, suggesting specific signalling properties despite their high degree of homology. To identify mechanisms contributing to the differential signalling properties of IRS-1 and IRS-2 in the mediation of insulin/IGF-1 action, we performed comprehensive mass spectrometry (MS)-based phosphoproteomic profiling of brown preadipocytes from wild type, IRS-1-/- and IRS-2-/- mice in the basal and IGF-1-stimulated states...
March 14, 2018: Cellular Signalling
Afsar R Naqvi, Alexandra Seal, Jennifer Shango, Maria Brambila Navarette, Gloria Martinez, Gabriela Chapa, Shirin Hasan, Tejabhiram Yadavalli, Dinesh Jaishankar, Deepak Shukla, Salvador Nares
MicroRNAs (miRNAs) are small, non-coding RNAs of ~18-25 nucleotides that have gained extensive attention as critical regulators in complex gene networks including immune cell lineage commitment, differentiation, maturation, and maintenance of immune homeostasis and function. Many viruses encode miRNAs that directly downregulate the expression of factors of the innate immune system, which includes proteins involved in promoting apoptosis and recruitment. In this study, we examined the expression profiles of three previously identified viral miRNAs (v-miRs) from the human herpesvirus (HHV) family, HSV-1 (miR-H1), KSHV (miR-K12-3-3p), and HCMV (miR-US4) in healthy and diseased periodontal tissues and observed increased levels of v-miRs in diseased tissues...
March 14, 2018: Biochimica et Biophysica Acta
Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Luca Häfliger, Jonas Behr, Hesam Montazeri, Michael N Hall, Niko Beerenwinkel
Motivation: Several molecular events are known to be cancer-related, including genomic aberrations, hypermethylation of gene promoter regions, and differential expression of microRNAs. These aberration events are very heterogeneous across tumors and it is poorly understood how they affect the molecular makeup of the cell, including the transcriptome and proteome. Protein interaction networks can help decode the functional relationship between aberration events and changes in gene and protein expression...
March 14, 2018: Bioinformatics
Yimin Wang, Fang Ye, Chanyan Huang, Faling Xue, Yingyuan Li, Shaowei Gao, Zeting Qiu, Si Li, Qinchang Chen, Huaqiang Zhou, Yiyan Song, Wenqi Huang, Wulin Tan, Zhongxing Wang
BACKGROUND: Neuropathic pain is one of the common complications after spinal cord injury (SCI), affecting patients' life quality. The molecular mechanism for neuropathic pain after SCI is still unclear. We aimed to discover potential genes and MicroRNAs(miRNAs) related to neuropathic pain by bioinformatics method. METHODS: Microarray data of GSE69901 were obtained from Gene Expression Omnibus (GEO) database. Peripheral blood samples from patients with or without neuropathic pain after spinal cord injury (SCI) were collected...
March 15, 2018: Clinical Journal of Pain
Soumya Luthra, Uma Chandran, Brenda Diergaarde, Michael Becich, Adrian V Lee, Carola A Neumann
Increased reactive species (RS; reactive oxygen and nitrogen species) are a byproduct of both enzymatic and non-enzymatic systems, and critical in cancer development, including breast tumorigenesis. To investigate the role of RS-related genes in breast cancer, expression levels of the most common annotated genes involved in regulating cellular RS levels and proteins that are substrates of RS in specific subtypes of breast cancer 9 were evaluated using public data bases. Based on the premise that increased RS promote tumor formation, and breast cancer subtypes vary in aggressiveness, we hypothesized that specific RS gene expression signatures are associated with breast cancer aggressiveness and patient survival...
March 12, 2018: Free Radical Biology & Medicine
Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
François Ancien, Fabrizio Pucci, Maxime Godfroid, Marianne Rooman
The classification of human genetic variants into deleterious and neutral is a challenging issue, whose complexity is rooted in the large variety of biophysical mechanisms that can be responsible for disease conditions. For non-synonymous mutations in structured proteins, one of these is the protein stability change, which can lead to loss of protein structure or function. We developed a stability-driven knowledge-based classifier that uses protein structure, artificial neural networks and solvent accessibility-dependent combinations of statistical potentials to predict whether destabilizing or stabilizing mutations are disease-causing...
March 14, 2018: Scientific Reports
Matthew Tien, Aretha Fiebig, Sean Crosson
Cells adapt to shifts in their environment by remodeling transcription. Measuring changes in transcription at the genome scale is now routine, but defining the functional significance of individual genes within large gene expression datasets remains a major challenge. We applied a network-based algorithm to interrogate publicly available gene expression data to predict genes that serve major functional roles in Caulobacter crescentus stress survival. This approach identified GsrN, a conserved small RNA that is directly activated by the general stress sigma factor, σT , and functions as a potent post-transcriptional regulator of survival across distinct conditions including osmotic and oxidative stress...
March 14, 2018: ELife
Chengxin Zhang, Wei Zheng, Peter L Freddolino, Yang Zhang
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO, to deduce Gene Ontology attributes of proteins by combining sequence homology-based annotation with low-resolution structure prediction and comparison, and partner's-homology based protein-protein network mapping. The pipeline was tested on a large-scale set of 1000 non-redundant proteins from the CAFA3 experiment...
March 10, 2018: Journal of Molecular Biology
Hailing Yang, Xiaofei Zhang, Guangda Xin
BACKGROUND: Recent studies have reported that mesenchymal stem cells (MSCs) exert therapeutic effects on the treatment of diabetic nephropathy (DN), but the underlying mechanisms remain unclear. METHODS: A dataset GSE65561 was obtained from Gene Expression Omnibus (GEO) database, which contained four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs (group 2), five DN samples (group 3) and five DN samples co-cultured with MSCs (group 4)...
March 13, 2018: Renal Failure
Serina L Robinson, Jonathan P Badalamenti, Anthony G Dodge, Lambros J Tassoulas, Lawrence P Wackett
Biuret is a minor component of urea fertilizer and an intermediate in s-triazine herbicide biodegradation. The microbial metabolism of biuret has never been comprehensively studied. Here we enriched and isolated bacteria from a potato field that grew on biuret as a sole nitrogen source. We sequenced the genome of the fastest-growing isolate, Herbaspirillum sp. BH-1 and identified genes encoding putative biuret hydrolases (BHs). We purified and characterized a functional BH enzyme from Herbaspirillum sp. BH-1 and two other bacteria from divergent phyla...
March 12, 2018: Environmental Microbiology
Yanxiong Gan, Shichao Zheng, Jiaqi Zhao, Chen Zhang, Tianhui Gao, Wan Liao, Qiang Fu, Chaomei Fu
ETHNOPHARMACOLOGICAL RELEVANCE: Curcuma phaeocaulis Val. (CP), as the vital medicines for blood-breaking and disorder-eliminating, has been widely used for hepatitis with good curative effects. Owing to the complexity of traditional Chinese medicine, the pharmacological mechanism of CP remains unclear. To solve this problem, a protein network module-based approach was proposed in this study. MATERIALS AND METHODS: Firstly, the content of active components of CP was detected based on HPLC-DAD...
March 8, 2018: Journal of Ethnopharmacology
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