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Gene regulatory network

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https://www.readbyqxmd.com/read/28108733/systematic-analysis-of-molecular-mechanisms-for-hcc-metastasis-via-text-mining-approach
#1
Cheng Zhen, Caizhong Zhu, Haoyang Chen, Yiru Xiong, Junyuan Tan, Dong Chen, Jin Li
OBJECTIVE: To systematically explore the molecular mechanism for hepatocellular carcinoma (HCC) metastasis and identify regulatory genes with text mining methods. RESULTS: Genes with highest frequencies and significant pathways related to HCC metastasis were listed. A handful of proteins such as EGFR, MDM2, TP53 and APP, were identified as hub nodes in PPI (protein-protein interaction) network. Compared with unique genes for HBV-HCCs, genes particular to HCV-HCCs were less, but may participate in more extensive signaling processes...
January 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28108556/confirmation-of-five-novel-susceptibility-loci-for-systemic-lupus-erythematosus-sle-and-integrated-network-analysis-of-82-sle-susceptibility-loci
#2
Julio E Molineros, Wanling Yang, Xu-Jie Zhou, Celi Sun, Yukinori Okada, Huoru Zhang, Kek Heng Chua, Yu-Lung Lau, Yuta Kochi, Akari Suzuki, Kazuhiko Yamamoto, Jianyang Ma, So-Young Bang, Hye-Soon Lee, Kwangwoo Kim, Sang-Cheol Bae, Hong Zhang, Nan Shen, Loren L Looger, Swapan K Nath
We recently identified ten novel SLE susceptibility loci in Asians and uncovered several additional suggestive loci requiring further validation. This study aimed to replicate five of these suggestive loci in a Han Chinese cohort from Hong Kong, followed by meta-analysis (11,656 cases and 23,968 controls) on previously reported Asian and European populations, and perform bioinformatic analyses on all 82 reported SLE loci to identify shared regulatory signatures. We performed a battery of analyses for these five loci, as well as joint analyses on all 82 SLE loci...
January 20, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28108491/transcriptome-analysis-identifies-multifaceted-regulatory-mechanisms-dictating-a-genetic-switch-from-neuronal-network-establishment-to-maintenance-during-postnatal-prefrontal-cortex-development
#3
Yvet Kroeze, Martin Oti, Ellen van Beusekom, Roel H M Cooijmans, Hans van Bokhoven, Sharon M Kolk, Judith R Homberg, Huiqing Zhou
The prefrontal cortex (PFC) is one of the latest brain regions to mature, which allows the acquisition of complex cognitive abilities through experience. To unravel the underlying gene expression changes during postnatal development, we performed RNA-sequencing (RNA-seq) in the rat medial PFC (mPFC) at five developmental time points from infancy to adulthood, and analyzed the differential expression of protein-coding genes, long intergenic noncoding RNAs (lincRNAs), and alternative exons. We showed that most expression changes occur in infancy, and that the number of differentially expressed genes reduces toward adulthood...
January 19, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28108450/netland-quantitative-modeling-and-visualization-of-waddington-s-epigenetic-landscape-using-probabilistic-potential
#4
Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng
: Waddington's epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks. Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington's landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of gene regulatory networks (GRNs), and visualizing the corresponding Waddington's epigenetic landscape in three dimensions without restriction on the number of genes in a GRN...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108192/epidemiology-and-pathophysiology-of-childhood-narcolepsy
#5
REVIEW
Thomas J Dye, Neepa Gurbani, Narong Simakajornboon
It is now recognized that there are two types of narcolepsy. Narcolepsy type I or Narcolepsy with cataplexy is caused by the loss of hypocretin or orexin neurons. Narcolepsy type II or narcolepsy without cataplexy has normal hypocretin and the etiology is unknown. Hypocretin is a neuropeptide produced by neurons in the lateral hypothalamus. Both genetic and environmental factors play a crucial role in the pathogenesis of narcolepsy. Most patients with narcolepsy type I and half of patients with narcolepsy type II carry HLA-DQB1*0602...
December 21, 2016: Paediatric Respiratory Reviews
https://www.readbyqxmd.com/read/28107180/identification-of-micrornas-implicated-in-the-late-differentiation-stages-of-normal-b-cells-suggests-a-central-role-for-mirna-targets-zeb1-and-tp53
#6
Giorgio Malpeli, Stefano Barbi, Simonetta Zupo, Gabriele Tosadori, Giovanni Scardoni, Anna Bertolaso, Silvia Sartoris, Stefano Ugel, Caterina Vicentini, Matteo Fassan, Annalisa Adamo, Mauro Krampera, Maria Teresa Scupoli, Carlo Maria Croce, Aldo Scarpa
In the late B cell differentiation stages, miRNAs expression modifications promoting or inhibiting key pathways are only partially defined. We isolated 29 CD19+ human B cell samples at different stages of differentiation: B cells from peripheral blood; naïve, germinal center (GC) and subepithelial (SE) B cells from tonsils. SE cells were further split in activated and resting B cell. The miRNA expression profile of these B cells was assessed by microarray analysis and selected miRNAs were validated by quantitative RT-PCR and in situ hybridization on normal tonsils...
January 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28106109/center-of-mass-in-complex-networks
#7
Chuanji Fu, Yachun Gao, Shimin Cai, Hongchun Yang, Chun Yang
Network dynamics is always a big challenge in nonlinear dynamics. Although great advancements have been made in various types of complex systems, an universal theoretical framework is required. In this paper, we introduce the concept of center of 'mass' of complex networks, where 'mass' stands for node importance or centrality in contrast to that of particle systems, and further prove that the phase transition and evolutionary state of the system can be characterized by the activity of center of 'mass'. The steady states of several complex networks (gene regulatory networks and epidemic spreading systems) are then studied by analytically calculating the decoupled equation of the dynamic activity of center of 'mass', which is derived from the dynamic equation of the complex networks...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28106108/isl2b-regulates-anterior-second-heart-field-development-in-zebrafish
#8
Hagen R Witzel, Sirisha Cheedipudi, Rui Gao, Didier Y R Stainier, Gergana D Dobreva
After initial formation, the heart tube grows by addition of second heart field progenitor cells to its poles. The transcription factor Isl1 is expressed in the entire second heart field in mouse, and Isl1-deficient mouse embryos show defects in arterial and venous pole development. The expression of Isl1 is conserved in zebrafish cardiac progenitors; however, Isl1 is required for cardiomyocyte differentiation only at the venous pole. Here we show that Isl1 homologues are expressed in specific patterns in the developing zebrafish heart and play distinct roles during cardiac morphogenesis...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28106101/the-systematic-analysis-of-coding-and-long-non-coding-rnas-in-the-sub-chronic-and-chronic-stages-of-spinal-cord-injury
#9
Raquel Cuevas-Diaz Duran, Han Yan, Yiyan Zheng, Xingfan Huang, Raymond Grill, Dong H Kim, Qilin Cao, Jia Qian Wu
Spinal cord injury (SCI) remains one of the most debilitating neurological disorders and the majority of SCI patients are in the chronic phase. Previous studies of SCI have usually focused on few genes and pathways at a time. In particular, the biological roles of long non-coding RNAs (lncRNAs) have never been characterized in SCI. Our study is the first to comprehensively investigate alterations in the expression of both coding and long non-coding genes in the sub-chronic and chronic stages of SCI using RNA-Sequencing...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105929/a-compendium-of-human-genes-regulating-feeding-behavior-and-body-weight-its-functional-characterization-and-identification-of-gwas-genes-involved-in-brain-specific-ppi-network
#10
Elena V Ignatieva, Dmitry A Afonnikov, Olga V Saik, Evgeny I Rogaev, Nikolay A Kolchanov
BACKGROUND: Obesity is heritable. It predisposes to many diseases. The objectives of this study were to create a compendium of genes relevant to feeding behavior (FB) and/or body weight (BW) regulation; to construct and to analyze networks formed by associations between genes/proteins; and to identify the most significant genes, biological processes/pathways, and tissues/organs involved in BW regulation. RESULTS: The compendium of genes controlling FB or BW includes 578 human genes...
December 22, 2016: BMC Genetics
https://www.readbyqxmd.com/read/28105909/on-the-inconsistency-of-%C3%A2-1-penalised-sparse-precision-matrix-estimation
#11
Otte Heinävaara, Janne Leppä-Aho, Jukka Corander, Antti Honkela
BACKGROUND: Various ℓ 1-penalised estimation methods such as graphical lasso and CLIME are widely used for sparse precision matrix estimation and learning of undirected network structure from data. Many of these methods have been shown to be consistent under various quantitative assumptions about the underlying true covariance matrix. Intuitively, these conditions are related to situations where the penalty term will dominate the optimisation. RESULTS: We explore the consistency of ℓ 1-based methods for a class of bipartite graphs motivated by the structure of models commonly used for gene regulatory networks...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28104719/molecular-regulation-of-temperature-dependent-floral-induction-in-tulipa-gesneriana
#12
Hendrika Leeggangers, Harm Nijveen, Judit Nadal Bigas, Henk W M Hilhorst, Richard G H Immink
The vegetative to reproductive phase change in tulip is promoted by increasing temperatures during spring. The warm winters of recent years interfere with this process and are calling for new adapted cultivars. A better understanding of the underlying molecular mechanisms would be of help, but unlike the model plant Arabidopsis, very little is known about floral induction in tulip. To shed light on the gene regulatory network controlling flowering in tulip, RNA-sequencing was performed on meristem-enriched tissue collected under two contrasting temperature conditions, low and high...
January 19, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28104410/the-drd2-rs1076560-polymorphism-and-schizophrenia-related-intermediate-phenotypes-a-systematic-review-and-meta-analysis
#13
REVIEW
Jurjen J Luykx, Juliette L Broersen, Max de Leeuw
Intermediate phenotypes may contribute to elucidate the genetic determinants of schizophrenia. A regulatory dopamine 2-receptor gene (DRD2) polymorphism (rs1076560; G > T) has been identified as a genetic risk factor for schizophrenia. Studies report conflicting results on its involvement in schizophrenia intermediate phenotypes and no systematic review on this topic has been published. Therefore, we aimed to assess whether this polymorphism is implicated in schizophrenia intermediate phenotypes by performing a systematic review and meta-analysis...
January 16, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28103887/microrna-expression-patterns-and-signalling-pathways-in-the-development-and-progression-of-childhood-solid-tumours
#14
REVIEW
Anna L Leichter, Michael J Sullivan, Michael R Eccles, Aniruddha Chatterjee
The development of childhood solid tumours is tied to early developmental processes. These tumours may be complex and heterogeneous, and elucidating the aberrant mechanisms that alter the early embryonic environment and lead to disease is essential to our understanding of how these tumours function. MicroRNAs (miRNAs) are vital regulators of gene expression at all stages of development, and their crosstalk via developmental signalling pathways is essential for orchestrating regulatory control in processes such as proliferation, differentiation and apoptosis of cells...
January 19, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28102867/a-systems-approach-for-the-elucidation-of-crucial-genes-and-network-constituents-of-cervical-intraepithelial-neoplasia-1-cin1
#15
Shikha Suman, Ashutosh Mishra, Anurag Kulshrestha
Cervical intra-epithelial neoplasia 1 (CIN1) is a pre-cancerous cervical cancer condition characterized by changes in the squamous cells of the cervix. Early detection may facilitate treatment as CIN1 may increase the risk of developing cervical cancer. An extensive system level analysis has been carried out to detect crucial network components of CIN1. Differential expression analysis was performed to identify genes that are differentially expressed in CIN1 in comparison to normal cells. Gene Ontology (GO) and pathway enrichment analyses of DEGs were followed by the construction of a protein-protein interaction (PPI) network...
January 19, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28101583/integrated-analysis-of-microrna-and-transcription-factor-reveals-important-regulators-and-regulatory-motifs-in-adult-b-cell-acute-lymphoblastic-leukemia
#16
Xiao-Cong Lin, Xin-Guang Liu, Yu-Ming Zhang, Ning Li, Zhi-Gang Yang, Wei-Yu Fu, Liu-Bo Lan, Hai-Tao Zhang, Yong Dai
B-cell acute lymphoblastic leukemia (B‑ALL) is an aggressive hematological malignancy and a leading cause of cancer-related mortality in children and young adults. The molecular mechanisms involved in the regulation of its gene expression has yet to be fully elucidated. In the present study, we performed large scale expression profiling of microRNA (miRNA) and transcription factor (TF) by Illumina deep‑sequencing and TF array technology, respectively, and identified 291 differentially expressed miRNAs and 201 differentially expressed TFs in adult B‑ALL samples relative to their controls...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28100450/a-2-oxoglutarate-dependent-dioxygenase-mediates-the-biosynthesis-of-glucoraphasatin-in-radish
#17
Tomohiro Kakizaki, Hiroyasu Kitashiba, Zhongwei Zou, Feng Li, Nobuko Fukino, Takayoshi Ohara, Takeshi Nishio, Masahiko Ishida
Glucosinolates (GSLs) are secondary metabolites whose degradation products confer intrinsic flavors and aromas to Brassicaceae vegetables. Several structures of GSLs are known in the Brassicaceae, and the biosynthetic pathway and regulatory networks have been elucidated in Arabidopsis thaliana. GSLs are precursors of chemical defense substances against herbivorous pests. Specific GSLs can act as feeding blockers or stimulants, depending on the pest species. Natural selection has led to diversity in the GSL compositions even within individual species...
January 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28100172/integrated-genomics-based-mapping-reveals-the-genetics-underlying-maize-flavonoid-biosynthesis
#18
Min Jin, Xuehai Zhang, Mingchao Zhao, Min Deng, Yuanhao Du, Yang Zhou, Shouchuang Wang, Takayuki Tohge, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman, Jianbing Yan, Weiwei Wen
BACKGROUND: Flavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway...
January 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28100166/smite-an-r-bioconductor-package-that-identifies-network-modules-by-integrating-genomic-and-epigenomic-information
#19
N Ari Wijetunga, Andrew D Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim, John M Greally
BACKGROUND: The molecular assays that test gene expression, transcriptional, and epigenetic regulation are increasingly diverse and numerous. The information generated by each type of assay individually gives an insight into the state of the cells tested. What should be possible is to add the information derived from separate, complementary assays to gain higher-confidence insights into cellular states. At present, the analysis of multi-dimensional, massive genome-wide data requires an initial pruning step to create manageable subsets of observations that are then used for integration, which decreases the sizes of the intersecting data sets and the potential for biological insights...
January 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28099866/effector-regulatory-t-cell-differentiation-and-immune-homeostasis-depend-on-the-transcription-factor-myb
#20
Sheila Dias, Angela D'Amico, Erika Cretney, Yang Liao, Julie Tellier, Christine Bruggeman, Francisca F Almeida, Jamie Leahy, Gabrielle T Belz, Gordon K Smyth, Wei Shi, Stephen L Nutt
FoxP3-expressing regulatory T (Treg) cells are essential for maintaining immune homeostasis. Activated Treg cells undergo further differentiation into an effector state that highly expresses genes critical for Treg cell function, although how this process is coordinated on a transcriptional level is poorly understood. Here, we demonstrate that mice lacking the transcription factor Myb in Treg cells succumbed to a multi-organ inflammatory disease. Myb was specifically expressed in, and required for the differentiation of, thymus-derived effector Treg cells...
January 17, 2017: Immunity
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