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https://www.readbyqxmd.com/read/28097908/common-and-specific-genes-and-peripheral-biomarkers-in-children-and-adults-with-attention-deficit-hyperactivity-disorder
#1
Cristian Bonvicini, Stephen V Faraone, Catia Scassellati
OBJECTIVES: Elucidating the biological mechanisms involved in Attention-deficit/hyperactivity disorder (ADHD) has been challenging. Relatively unexplored is the fact that these mechanisms can differ with age. METHODS: We present an overview on the major differences between children and adults with ADHD, describing several studies from genomics to metabolomics performed in ADHD children and in adults. A systematic search (up until February, 2016) was conducted. RESULTS: From a PRISMA flow-chart, a total of eligibility 350 studies from genomics and metabolomics were found for cADHD and 91 for aADHD...
January 18, 2017: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/28094815/drd2-co-expression-network-and-a-related-polygenic-index-predict-imaging-behavioral-and-clinical-phenotypes-linked-to-schizophrenia
#2
G Pergola, P Di Carlo, E D'Ambrosio, B Gelao, L Fazio, M Papalino, A Monda, G Scozia, B Pietrangelo, M Attrotto, J A Apud, Q Chen, V S Mattay, A Rampino, G Caforio, D R Weinberger, G Blasi, A Bertolino
Genetic risk for schizophrenia (SCZ) is determined by many genetic loci whose compound biological effects are difficult to determine. We hypothesized that co-expression pathways of SCZ risk genes are associated with system-level brain function and clinical phenotypes of SCZ. We examined genetic variants related to the dopamine D2 receptor gene DRD2 co-expression pathway and associated them with working memory (WM) behavior, the related brain activity and treatment response. Using two independent post-mortem prefrontal messenger RNA (mRNA) data sets (total N=249), we identified a DRD2 co-expression pathway enriched for SCZ risk genes...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28093455/genomewide-landscape-of-gene-metabolome-associations-in-escherichia-coli
#3
Tobias Fuhrer, Mattia Zampieri, Daniel C Sévin, Uwe Sauer, Nicola Zamboni
Metabolism is one of the best-understood cellular processes whose network topology of enzymatic reactions is determined by an organism's genome. The influence of genes on metabolite levels, however, remains largely unknown, particularly for the many genes encoding non-enzymatic proteins. Serendipitously, genomewide association studies explore the relationship between genetic variants and metabolite levels, but a comprehensive interaction network has remained elusive even for the simplest single-celled organisms...
January 16, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28087642/stxbp4-drives-tumor-growth-and-is-associated-with-poor-prognosis-through-pdgf-receptor-signaling-in-lung-squamous-cell-carcinoma
#4
Yukihiro Otaka, Susumu Rokudai, Kyoichi Kaira, Michiru Fujieda, Ikuko Horikoshi, Reika Kawabata, Shinji Yoshiyama, Takehiko Yokobori, Yoichi Ohtaki, Kimihiro Shimizu, Tetsunari Oyama, Jun'ichi Tamura, Carol Prives, Masahiko Nishiyama
PURPOSE: Expression of the ΔN isoform of p63 (ΔNp63) is a diagnostic marker highly specific for lung squamous cell carcinoma (SCC). We previously found that Syntaxin Binding Protein 4 (STXBP4) regulates ΔNp63 ubiquitination, suggesting that STXBP4 may also be a SCC biomarker. To address this issue, we investigated the role of STXBP4 expression in SCC biology and the impact of STXBP4 expression on SCC prognosis. EXPERIMENTAL DESIGN: We carried out a clinicopathological analysis of STXBP4 expression in 87 lung SCC patients...
January 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#5
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086790/rna-sequencing-for-global-gene-expression-associated-with-muscle-growth-in-a-single-male-modern-broiler-line-compared-to-a-foundational-barred-plymouth-rock-chicken-line
#6
Byung-Whi Kong, Nicholas Hudson, Dongwon Seo, Seok Lee, Bhuwan Khatri, Kentu Lassiter, Devin Cook, Alissa Piekarski, Sami Dridi, Nicholas Anthony, Walter Bottje
BACKGROUND: Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations accumulated in modern broiler breeder lines during selective breeding conducted over several decades. METHODS: To identify genes important in determining muscle growth and feed efficiency in broilers, RNA sequencing (RNAseq) was conducted with breast muscle in modern pedigree male (PeM) broilers (n = 6 per group), and with an unselected foundation broiler line (Barred Plymouth Rock; BPR)...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086788/comprehensive-circrna-expression-profile-and-selection-of-key-circrnas-during-priming-phase-of-rat-liver-regeneration
#7
Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang, Cunshuan Xu
BACKGROUND: Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28077403/gene-co-expression-analysis-for-functional-classification-and-gene-disease-predictions
#8
Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28074855/mir-218-targets-mecp2-and-inhibits-heroin-seeking-behavior
#9
Biao Yan, Zhaoyang Hu, Wenqing Yao, Qiumin Le, Bo Xu, Xing Liu, Lan Ma
MicroRNAs (miRNAs) are a class of evolutionarily conserved, 18-25 nucleotide non-coding sequences that post-transcriptionally regulate gene expression. Recent studies implicated their roles in the regulation of neuronal functions, such as learning, cognition and memory formation. Here we report that miR-218 inhibits heroin-induced behavioral plasticity. First, network propagation-based method was used to predict candidate miRNAs that played potential key roles in regulating drug addiction-related genes. Microarray screening was also carried out to identify miRNAs responding to chronic heroin administration in the nucleus accumbens (NAc)...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074633/a-computational-interactome-for-prioritizing-genes-associated-with-complex-agronomic-traits-in-rice
#10
Shiwei Liu, Yihui Liu, Jiawei Zhao, Shitao Cai, Hongmei Qian, Kaijing Zuo, Lingxia Zhao, Lida Zhang
Rice is one of the most important staple foods for more than half of the world's population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet/) using machine-learning with structural relationship and functional information...
January 11, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28074002/metabolic-profiling-in-formalin-fixed-and-paraffin-embedded-prostate-cancer-tissues
#11
Stefano Cacciatore, Giorgia Zadra, Clyde Bango, Kathryn L Penney, Svitlana Tyekucheva, Oscar Yanes, Massimo Loda
: Metabolite profiling has significantly contributed to a deeper understanding of the biochemical metabolic networks and pathways in cancer cells. Metabolomics-based biomarker discovery would greatly benefit from the ability to interrogate retrospective annotated clinical specimens archived as formalin-fixed paraffin-embedded (FFPE) material. Mass spectrometry-based metabolomic analysis was performed in matched frozen and FFPE human prostate cancers as well as isogenic prostate cancer cell lines...
January 10, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28073787/col6a5-variants-in-familial-neuropathic-chronic-itch
#12
Filippo Martinelli-Boneschi, Marina Colombi, Marco Castori, Grazia Devigili, Roberto Eleopra, Rayaz A Malik, Marco Ritelli, Nicoletta Zoppi, Chiara Dordoni, Melissa Sorosina, Paola Grammatico, Hassan Fadavi, Monique M Gerrits, Rowida Almomani, Catharina G Faber, Ingemar S J Merkies, Daniela Toniolo, Massimiliano Cocca, Claudio Doglioni, Stephen G Waxman, Sulayman D Dib-Hajj, Michela M Taiana, Jenny Sassone, Raffaella Lombardi, Daniele Cazzato, Andrea Zauli, Silvia Santoro, Margherita Marchi, Giuseppe Lauria
Itch is thought to represent the peculiar response to stimuli conveyed by somatosensory pathways shared with pain through the activation of specific neurons and receptors. It can occur in association with dermatological, systemic and neurological diseases, or be the side effect of certain drugs. However, some patients suffer from chronic idiopathic itch that is frequently ascribed to psychological distress and for which no biomarker is available to date. We investigated three multigenerational families, one of which diagnosed with joint hypermobility syndrome/Ehlers-Danlos syndrome hypermobility type (JHS/EDS-HT), characterized by idiopathic chronic itch with predominantly proximal distribution...
January 9, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28062449/context-sensitive-network-based-disease-genetics-prediction-and-its-implications-in-drug-discovery
#13
Yang Chen, Rong Xu
MOTIVATION: Disease phenotype networks play an important role in computational approaches to identifying new disease-gene associations. Current disease phenotype networks often model disease relationships based on pairwise similarities, therefore ignore the specific context on how two diseases are connected. In this study, we propose a new strategy to model disease associations using context-sensitive networks (CSNs). We developed a CSN-based phenome-driven approach for disease genetics prediction, and investigated the translational potential of the predicted genes in drug discovery...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28053519/network-pharmacology-based-identification-of-key-pharmacological-pathways-of-yin-huang-qing-fei-capsule-acting-on-chronic-bronchitis
#14
Guohua Yu, Yanqiong Zhang, Weiqiong Ren, Ling Dong, Junfang Li, Ya Geng, Yi Zhang, Defeng Li, Haiyu Xu, Hongjun Yang
For decades in China, the Yin-Huang-Qing-Fei capsule (YHQFC) has been widely used in the treatment of chronic bronchitis, with good curative effects. Owing to the complexity of traditional Chinese herbal formulas, the pharmacological mechanism of YHQFC remains unclear. To address this problem, a network pharmacology-based strategy was proposed in this study. At first, the putative target profile of YHQFC was predicted using MedChem Studio, based on structural and functional similarities of all available YHQFC components to the known drugs obtained from the DrugBank database...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28053168/ccnet-database-of-co-expression-networks-with-functional-modules-for-diploid-and-polyploid-gossypium
#15
Qi You, Wenying Xu, Kang Zhang, Liwei Zhang, Xin Yi, Dongxia Yao, Chunchao Wang, Xueyan Zhang, Xinhua Zhao, Nicholas J Provart, Fuguang Li, Zhen Su
Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28049415/improving-protein-complex-prediction-by-reconstructing-a-high-confidence-protein-protein-interaction-network-of-escherichia-coli-from-different-physical-interaction-data-sources
#16
Shirin Taghipour, Peyman Zarrineh, Mohammad Ganjtabesh, Abbas Nowzari-Dalini
BACKGROUND: Although different protein-protein physical interaction (PPI) datasets exist for Escherichia coli, no common methodology exists to integrate these datasets and extract reliable modules reflecting the existing biological process and protein complexes. Naïve Bayesian formula is the highly accepted method to integrate different PPI datasets into a single weighted PPI network, but detecting proper weights in such network is still a major problem. RESULTS: In this paper, we proposed a new methodology to integrate various physical PPI datasets into a single weighted PPI network in a way that the detected modules in PPI network exhibit the highest similarity to available functional modules...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28047421/mo-de-207b-03-improved-cancer-classification-using-patient-specific-biological-pathway-information-via-gene-expression-data
#17
M Young, D Craft
PURPOSE: To develop an efficient, pathway-based classification system using network biology statistics to assist in patient-specific response predictions to radiation and drug therapies across multiple cancer types. METHODS: We developed PICS (Pathway Informed Classification System), a novel two-step cancer classification algorithm. In PICS, a matrix m of mRNA expression values for a patient cohort is collapsed into a matrix p of biological pathways. The entries of p, which we term pathway scores, are obtained from either principal component analysis (PCA), normal tissue centroid (NTC), or gene expression deviation (GED)...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28041882/lncrna-functional-networks-in-oligodendrocytes-reveal-stage-specific-myelination-control-by-an-lncol1-suz12-complex-in-the-cns
#18
Danyang He, Jincheng Wang, Yulan Lu, Yaqi Deng, Chuntao Zhao, Lingli Xu, Yinhuai Chen, Yueh-Chiang Hu, Wenhao Zhou, Q Richard Lu
Long noncoding RNAs (lncRNAs) are emerging as important regulators of cellular functions, but their roles in oligodendrocyte myelination remain undefined. Through de novo transcriptome reconstruction, we establish dynamic expression profiles of lncRNAs at different stages of oligodendrocyte development and uncover a cohort of stage-specific oligodendrocyte-restricted lncRNAs, including a conserved chromatin-associated lncOL1. Co-expression network analyses further define the association of distinct oligodendrocyte-expressing lncRNA clusters with protein-coding genes and predict lncRNA functions in oligodendrocyte myelination...
December 28, 2016: Neuron
https://www.readbyqxmd.com/read/28028756/expression-of-mirna-155-mirna-223-mirna-31-mirna-21-mirna-125b-and-mirna-146a-in-the-inflammatory-pathway-of-hidradenitis-suppurativa
#19
S Hessam, M Sand, M Skrygan, T Gambichler, F G Bechara
Hidradenitis suppurativa (HS) has been associated with marked inflammatory perturbation. The mechanisms regulating the inflammatory network remain elusive. microRNAs (miRNAs) have been described as gene regulators of inflammation. We evaluated the messenger RNA (mRNA) expression levels of six selected inflammation-related miRNAs in lesional and perilesional skin samples of HS patients and in healthy controls. Samples of 15 HS patients and 10 healthy controls were included in this prospective study. Expression levels of the miRNAs miRNA-155-5p, miRNA-223-5p, miRNA-31-5p, miRNA-21-5p, miRNA-125b-5p, and miRNA-146a-5p were studied by quantitative real-time reverse transcription polymerase chain reaction...
December 28, 2016: Inflammation
https://www.readbyqxmd.com/read/28027310/m6a-driver-identifying-context-specific-mrna-m6a-methylation-driven-gene-interaction-networks
#20
Song-Yao Zhang, Shao-Wu Zhang, Lian Liu, Jia Meng, Yufei Huang
As the most prevalent mammalian mRNA epigenetic modification, N6-methyladenosine (m6A) has been shown to possess important post-transcriptional regulatory functions. However, the regulatory mechanisms and functional circuits of m6A are still largely elusive. To help unveil the regulatory circuitry mediated by mRNA m6A methylation, we develop here m6A-Driver, an algorithm for predicting m6A-driven genes and associated networks, whose functional interactions are likely to be actively modulated by m6A methylation under a specific condition...
December 2016: PLoS Computational Biology
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