keyword
MENU ▼
Read by QxMD icon Read
search

Tissue specific gene network

keyword
https://www.readbyqxmd.com/read/29139535/contribution-of-cranial-neural-crest-cells-to-mouse-skull-development
#1
Taofen Wu, Guiqian Chen, Fei Tian, Hong-Xiang Liu
The mammalian skull vault is a highly regulated structure that evolutionally protects brain growth during vertebrate development. It consists of several membrane bones with different tissue origins (e.g. neural crest-derived frontal bone and mesoderm-derived parietal bone). Although membrane bones are formed through intramembranous ossification, the neural crest-derived frontal bone has superior capabilities for osteoblast activities and bone regeneration via TGF, BMP, Wnt, and FGF signaling pathways. Neural crest (NC) cells are multipotent, and once induced, will follow specific paths to migrate to different locations of the body where they give rise to a diverse array of cell types and tissues...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/29137924/nasal-and-otic-placode-specific-regulation-of-sox2-involves-both-activation-by-sox-sall4-synergism-and-multiple-repression-mechanisms
#2
Satoko Sugahara, Tooru Fujimoto, Hisato Kondoh, Masanori Uchikawa
Transcription factor gene Sox2 is expressed throughout sensory development, but the enhancers that regulate the gene vary depending on the developmental stages and tissues. To gain new insights into the gene regulatory network in sensory placode specification, regulation of the nasal-otic bispecific NOP1 enhancer of Sox2 was investigated in chicken embryos. Deletion and mutational analyses using electroporation showed that transcriptional repression mechanisms in combination with activation mechanisms determine placodal specificity...
November 11, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29126216/pager-2-0-an-update-to-the-pathway-annotated-list-and-gene-signature-electronic-repository-for-human-network-biology
#3
Zongliang Yue, Qi Zheng, Michael T Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y Chen
Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29122012/drug-target-ontology-to-classify-and-integrate-drug-discovery-data
#4
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29118400/differential-transcriptome-regulation-by-3-5-t2-and-3-3-5-t3-in-brain-and-liver-uncovers-novel-roles-for-thyroid-hormones-in-tilapia
#5
A Olvera, C J Martyniuk, N Buisine, V Jiménez-Jacinto, A Sanchez-Flores, L M Sachs, A Orozco
Although 3,5,3'-triiodothyronine (T3) is considered to be the primary bioactive thyroid hormone (TH) due to its high affinity for TH nuclear receptors (TRs), new data suggest that 3,5-diiodothyronine (T2) can also regulate transcriptional networks. To determine the functional relevance of these bioactive THs, RNA-seq analysis was conducted in the cerebellum, thalamus-pituitary and liver of tilapia treated with equimolar doses of T2 or T3. We identified a total of 169, 154 and 2863 genes that were TH-responsive (FDR < 0...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29114054/three-dimensional-visualization-and-a-deep-learning-model-reveal-complex-fungal-parasite-networks-in-behaviorally-manipulated-ants
#6
Maridel A Fredericksen, Yizhe Zhang, Missy L Hazen, Raquel G Loreto, Colleen A Mangold, Danny Z Chen, David P Hughes
Some microbes possess the ability to adaptively manipulate host behavior. To better understand how such microbial parasites control animal behavior, we examine the cell-level interactions between the species-specific fungal parasite Ophiocordyceps unilateralis sensu lato and its carpenter ant host (Camponotus castaneus) at a crucial moment in the parasite's lifecycle: when the manipulated host fixes itself permanently to a substrate by its mandibles. The fungus is known to secrete tissue-specific metabolites and cause changes in host gene expression as well as atrophy in the mandible muscles of its ant host, but it is unknown how the fungus coordinates these effects to manipulate its host's behavior...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29113156/identification-of-potential-therapeutic-targets-for-gliomas-by-bioinformatics-analysis
#7
Ke Ma, Zhihua Cheng, Liqun Sun, Haibo Li
Gliomas are primary tumors that originate in the brain or spinal cord and develop from supportive glial cells. The present study aimed to identify potential candidate molecular markers for the treatment of gliomas, and to explore the underlying mechanisms of this disease. The gene expression profile data GSE50021, which consisted of 10 specimens of normal brain tissues and 35 specimens of glioma tissues, was downloaded from Gene Expression Omnibus (GEO). The methylation microarray data GSE50022, consisting of 28 glioma specimens, was also downloaded from GEO...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29109720/an-organismal-model-for-gene-regulatory-networks-in-the-gut-associated-immune-response
#8
REVIEW
Katherine M Buckley, Jonathan P Rast
The gut epithelium is an ancient site of complex communication between the animal immune system and the microbial world. While elements of self-non-self receptors and effector mechanisms differ greatly among animal phyla, some aspects of recognition, regulation, and response are broadly conserved. A gene regulatory network (GRN) approach provides a means to investigate the nature of this conservation and divergence even as more peripheral functional details remain incompletely understood. The sea urchin embryo is an unparalleled experimental model for detangling the GRNs that govern embryonic development...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29109103/hepatocyte-nuclear-factor-1a-deficiency-causes-hemolytic-anemia-in-mice-by-altering-erythrocyte-sphingolipid-homeostasis
#9
Karin von Wnuck Lipinski, Sarah Weske, Petra Keul, Susann Peters, Hideo A Baba, Gerd Heusch, Markus H Gräler, Bodo Levkau
The Hepatocyte Nuclear Factor (HNF) family regulates complex networks of metabolism and organ development. Human mutations in its prototypical member HNF1A cause maturity-onset of diabetes of the young (MODY) type 3. In this study, we identified an important role for HNF1A in the preservation of erythrocyte membrane integrity, calcium homeostasis and osmotic resistance through a yet unrecognized link of HNF1A to sphingolipid homeostasis. HNF1A(-/-) mice displayed microcytic hypochromic anemia with reticulocytosis that was partially compensated by avid extramedullary erythropoiesis at all erythroid stages in the spleen thereby excluding erythroid differentiation defects...
November 6, 2017: Blood
https://www.readbyqxmd.com/read/29108914/detection-and-analysis-of-apoptosis-and-autophagy-related-mirnas-of-mouse-vascular-endothelial-cells-in-chronic-intermittent-hypoxia-model
#10
Kai-Xiong Liu, Gong-Ping Chen, Ping-Li Lin, Jian-Chai Huang, Xin Lin, Jia-Chao Qi, Qi-Chang Lin
Endothelial dysfunction is the main pathogenic mechanism of cardiovascular complications induced by obstructive sleep apnea/hyponea syndrome (OSAHS). Chronic intermittent hypoxia (CIH) is the primary factor of OSAHS-associated endothelial dysfunction. The hypoxia inducible factor (HIF) pathway regulates the expression of downstream target genes and mediates cell apoptosis caused by CIH-induced endothelial injury. miRNAs play extensive and important negative regulatory roles in this process at the post-transcriptional level...
November 3, 2017: Life Sciences
https://www.readbyqxmd.com/read/29108673/%C3%AE-catenin-acts-in-a-position-independent-regeneration-response-in-the-simple-eumetazoan-hydra
#11
S Gufler, B Artes, H Bielen, I Krainer, M-K Eder, J Falschlunger, A Bollmann, T Ostermann, T Valovka, M Hartl, K Bister, U Technau, B Hobmayer
Wnt/β-Catenin signaling plays crucial roles in regenerative processes in eumetazoans. It also acts in regeneration and axial patterning in the simple freshwater polyp Hydra, whose morphallactic regenerative capacity is unparalleled in the animal kingdom. Previous studies have identified β-catenin as an early response gene activated within the first 30min in Hydra head regeneration. Here, we have studied the role of β-Catenin in more detail. First, we show that nuclear β-Catenin signaling is required for head and foot regeneration...
September 21, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29102647/the-transcriptional-landscape-of-radiation-treated-human-prostate-cancer-analysis-of-a-prospective-tissue-cohort
#12
Simon P Keam, Franco Caramia, Cristina Gamell, Piotr J Paul, Gisela Mir Arnau, Paul J Neeson, Scott G Williams, Ygal Haupt
PURPOSE: The resistance of prostate cancer to radiation therapy (RT) is a significant clinical issue and still largely unable to be guided by patient-specific molecular characteristics. The present study describes the gene expression changes induced in response to RT in human prostate tissue obtained from a prospective tissue acquisition study designed for radiobiology research. METHODS AND MATERIALS: A prospective cohort of 5 men with intermediate-risk and clinically localized tumors were treated with high-dose-rate brachytherapy with 2 × 10-Gy fractions...
September 25, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/29100075/comprehensive-and-integrated-genomic-characterization-of-adult-soft-tissue-sarcomas
#13
(no author information available yet)
Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (TP53, ATRX, RB1) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors...
November 2, 2017: Cell
https://www.readbyqxmd.com/read/29096605/genome-wide-identification-and-expression-analysis-of-calmodulin-like-cml-genes-in-chinese-cabbage-brassica-rapa-l-ssp-pekinensis
#14
Shanshan Nie, Minjuan Zhang, Lugang Zhang
BACKGROUND: Calmodulin-like (CML) proteins are a primary family of plant-specific Ca(2+) sensors that specifically bind to Ca(2+) and deliver a Ca(2+) signal. CML proteins have been identified and characterized in many plant species, such as the model plant Arabidopsis and rice. Based on considerable evidence, the roles of CML proteins are crucial in plant growth and development and in the response to various external stimuli. Nevertheless, the characterization and expression profiling of CML genes in Chinese cabbage (Brassica rapa L...
November 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29094769/differentiation-and-characterization-of-rat-adipose-tissue-mesenchymal-stem-cells-into-endothelial-like-cells
#15
V Cannella, G Piccione, R Altomare, A Marino, P Di Marco, L Russotto, S Di Bella, G Purpari, F Gucciardi, G Cassata, G Damiano, V D Palumbo, A Santoro, C Russo Lacerna, A I Lo Monte, A Guercio
In this study, mesenchymal stem cells were isolated from rat adipose tissue (AD-MSCs) to characterize and differentiate them into endothelial-like cells. AD-MSCs were isolated by mechanical and enzymatic treatments, and their identity was verified by colony-forming units (CFU) test and by differentiation into cells of mesodermal lineages. The endothelial differentiation was induced by plating another aliquot of cells in EGM-2 medium, enriched with specific endothelial growth factors. Five subcultures were performed...
November 2, 2017: Anatomia, Histologia, Embryologia
https://www.readbyqxmd.com/read/29093681/quantitative-and-systems-pharmacology-3-network-based-identification-of-new-targets-for-natural-products-enables-potential-uses-in-aging-associated-disorders
#16
Jiansong Fang, Li Gao, Huili Ma, Qihui Wu, Tian Wu, Jun Wu, Qi Wang, Feixiong Cheng
Aging that refers the accumulation of genetic and physiology changes in cells and tissues over a lifetime has been shown a high risk of developing various complex diseases, such as neurodegenerative disease, cardiovascular disease and cancer. Over the past several decades, natural products have been demonstrated as anti-aging interveners via extending lifespan and preventing aging-associated disorders. In this study, we developed an integrated systems pharmacology infrastructure to uncover new indications for aging-associated disorders by natural products...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29082337/inference-of-cell-type-specific-regulatory-networks-on-mammalian-lineages
#17
Deborah Chasman, Sushmita Roy
Transcriptional regulatory networks are at the core of establishing cell type specific gene expression programs. In mammalian systems, such regulatory networks are determined by multiple levels of regulation, including by transcription factors, chromatin environment, and three-dimensional organization of the genome. Recent efforts to measure diverse regulatory genomic datasets across multiple cell types and tissues offer unprecedented opportunities to examine the context-specificity and dynamics of regulatory networks at a greater resolution and scale than before...
April 2017: Current opinion in systems biology
https://www.readbyqxmd.com/read/29075833/transcriptome-profiling-of-neurosensory-perception-genes-in-wing-tissue-of-two-evolutionary-distant-insect-orders-diptera-drosophila-melanogaster-and-hemiptera-acyrthosiphon-pisum
#18
Sandra Agnel, Martine da Rocha, Alain Robichon
The neurogenesis and neuronal functions in insect wing have been understudied mainly due to technical hindrances that have prevented electrophysiology studies for decades. The reason is that the nano-architecture of the wing chemosensory bristles hampers the receptors accessibility of odorants/tastants to receptors in fixed setup, whereas in nature, the wing flapping mixes these molecules in bristle lymph. In this report, we analyzed the transcriptome of the wing tissue of two species phylogenetically strongly divergent: Drosophila melanogaster a generic model for diptera order (complete metamorphosis) and the aphid acyrthosiphon pisum, representative of hemiptera order (incomplete metamorphosis) for which a conditional winged/wingless polyphenism is under control of population density and resources...
October 26, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29075357/microrna-335-5p-is-a-potential-suppressor-of-metastasis-and-invasion-in-gastric-cancer
#19
Alejandra Sandoval-Bórquez, Iva Polakovicova, Nicolás Carrasco-Véliz, Lorena Lobos-González, Ismael Riquelme, Gonzalo Carrasco-Avino, Carolina Bizama, Enrique Norero, Gareth I Owen, Juan C Roa, Alejandro H Corvalán
BACKGROUND: Multiple aberrant microRNA expression has been reported in gastric cancer. Among them, microRNA-335-5p (miR-335), a microRNA regulated by DNA methylation, has been reported to possess both tumor suppressor and tumor promoter activities. RESULTS: Herein, we show that miR-335 levels are reduced in gastric cancer and significantly associate with lymph node metastasis, depth of tumor invasion, and ultimately poor patient survival in a cohort of Amerindian/Hispanic patients...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29074702/respiratory-consequences-of-targeted-losses-of-hoxa5-gene-function-in-mice
#20
Kim Landry-Truchon, Stéphanie Fournier, Nicolas Houde, Jean-Philippe Rousseau, Lucie Jeannotte, Richard Kinkead
Fetal development of the respiratory tract and diaphragm requires strict coordination between genetically controlled signals and mechanical forces produced by the neural network that generates breathing. Being expressed in the mesenchyme of trachea, lung and diaphragm, and in phrenic motoneurons HOXA5 is a key transcription factor regulating lung development and function. Consequently, most Hoxa5(-/-) mutants die at birth from respiratory failure. However, the extensive effect of the null mutation makes it difficult to identify the origins of respiratory dysfunction in newborns...
October 26, 2017: Journal of Experimental Biology
keyword
keyword
6880
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"