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Gene network inference

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https://www.readbyqxmd.com/read/29782156/combining-high-throughput-sequencing-of-sedadna-and-traditional-palaeolimnological-techniques-to-infer-historical-trends-in-cyanobacterial-communities
#1
Timothy J Tse, Lorne E Doig, Song Tang, Xiaohui Zhang, Weimin Sun, Steve B Wiseman, Cindy Xin Feng, Hongling Liu, John P Giesy, Markus Hecker, Paul D Jones
Freshwaters worldwide are under increasing pressure from anthropogenic activities and changing climate. Unfortunately, many inland waters lack sufficient long-term monitoring to assess environmental trends. Analysis of sedimentary ancient DNA (sedaDNA) is emerging as a means to reconstruct the past occurrence of microbial communities of inland waters. The purpose of this study was to assess a combination of high-throughput sequencing (16S rRNA) of sedaDNA and traditional palaeolimnological analyses to explore multidecadal relationships among cyanobacterial community composition, the potential for cyanotoxin production and palaeoenvironmental proxies...
May 21, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29772079/detection-of-multiple-perturbations-in-multi-omics-biological-networks
#2
Paula J Griffin, Yuqing Zhang, William Evan Johnson, Eric D Kolaczyk
Cellular mechanism-of-action is of fundamental concern in many biological studies. It is of particular interest for identifying the cause of disease and learning the way in which treatments act against disease. However, pinpointing such mechanisms is difficult, due to the fact that small perturbations to the cell can have wide-ranging downstream effects. Given a snapshot of cellular activity, it can be challenging to tell where a disturbance originated. The presence of an ever-greater variety of high-throughput biological data offers an opportunity to examine cellular behavior from multiple angles, but also presents the statistical challenge of how to effectively analyze data from multiple sources...
May 17, 2018: Biometrics
https://www.readbyqxmd.com/read/29769539/integrated-analysis-of-hepatic-mrna-and-mirna-profiles-identified-molecular-networks-and-potential-biomarkers-of-nafld
#3
Mingzhe Zhu, Qianlei Wang, Wenjun Zhou, Tao Liu, Lili Yang, Peiyong Zheng, Li Zhang, Guang Ji
To enhance our understanding of molecular mechanisms and mine novel biomarkers of non-alcoholic fatty liver disease (NAFLD), RNA sequencing was performed to gain hepatic expression profiles of mRNAs and miRNAs in NAFLD and normal rats. Using DESeq with thresholds of a two-fold change and a false discovery rate (FDR) less than 0.05, 336 mRNAs and 21 miRNAs were identified as differentially expressed. Among those, 17 miRNAs (e.g., miR-144-3p, miR-99a-3p, miR-200b-3p, miR-200b-5p, miR-200c-3p, etc.) might serve as novel biomarkers of NAFLD...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769331/temporal-transcriptional-logic-of-dynamic-regulatory-networks-underlying-nitrogen-signaling-and-use-in-plants
#4
Kranthi Varala, Amy Marshall-Colón, Jacopo Cirrone, Matthew D Brooks, Angelo V Pasquino, Sophie Léran, Shipra Mittal, Tara M Rock, Molly B Edwards, Grace J Kim, Sandrine Ruffel, W Richard McCombie, Dennis Shasha, Gloria M Coruzzi
This study exploits time, the relatively unexplored fourth dimension of gene regulatory networks (GRNs), to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. Our "just-in-time" analysis of time-series transcriptome data uncovered a temporal cascade of cis elements underlying dynamic N signaling. To infer transcription factor (TF)-target edges in a GRN, we applied a time-based machine learning method to 2,174 dynamic N-responsive genes. We experimentally determined a network precision cutoff, using TF-regulated genome-wide targets of three TF hubs (CRF4, SNZ, and CDF1), used to "prune" the network to 155 TFs and 608 targets...
May 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29767372/bayesian-network-to-infer-drug-induced-apoptosis-circuits-from-connectivity-map-data
#5
Jiyang Yu, Jose M Silva
The Connectivity Map (CMAP) project profiled human cancer cell lines exposed to a library of anticancer compounds with the goal of connecting cancer with underlying genes and potential treatments. As most targeted anticancer therapeutics aim to induce tumor-selective apoptosis, it is critical to understand the specific cell death pathways triggered by drugs. This can help to better understand the mechanism of how cancer cells respond to chemical stimulations and improve the treatment of human tumors. In this study, using Connectivity MAP microarray-based gene expression data, we applied a Bayesian network modeling approach and identified apoptosis as a major drug-induced cellular pathway...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29762780/an-intersection-network-based-on-combining-snp-co-association-and-rna-co-expression-networks-for-feed-utilization-traits-in-japanese-black-cattle
#6
D Okada, S Endo, H Matsuda, S Ogawa, Y Taniguchi, T Katsuta, T Watanabe, H Iwaisaki
Genome-wide association studies (GWAS) of quantitative traits have detected numerous genetic associations, but they encounter difficulties in pinpointing prominent candidate genes and inferring gene networks. The present study used a systems genetics approach integrating GWAS results with external RNA-expression data to detect candidate gene networks in feed utilization and growth traits of Japanese Black cattle, which are matters of concern. A SNP co-association network was derived from significant correlations between SNPs with effects estimated by GWAS across seven phenotypic traits...
May 12, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29758261/annotating-diseases-using-human-phenotype-ontology-improves-prediction-of-disease-associated-long-non-coding-rnas
#7
Duc-Hau Le, Lan T M Dao
Recently, many long non-coding RNAs (lncRNAs) have been identified and their biological function has been characterized; however, our understanding of their underlying molecular mechanisms related to disease is still limited. To overcome the limitation in experimentally identifying disease-lncRNA associations, computational methods have been proposed as a powerful tool to predict such associations. These methods are usually based on the similarities between diseases or lncRNAs since it was reported that similar diseases are associated with functionally similar lncRNAs...
May 11, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29751546/genome-wide-identification-and-analysis-of-arabidopsis-sodium-proton-antiporter-nhx-and-human-sodium-proton-exchanger-nhe-homologs-in-sorghum-bicolor
#8
P Hima Kumari, S Anil Kumar, Katam Ramesh, Palakolanu Sudhakar Reddy, M Nagaraju, A Bhanu Prakash, Trushar Shah, Ashley Henderson, Rakesh K Srivastava, G Rajasheker, A Chitikineni, Rajeev K Varshney, P Rathnagiri, M Lakshmi Narasu, P B Kavi Kishor
Na⁺ transporters play an important role during salt stress and development. The present study is aimed at genome-wide identification, in silico analysis of sodium-proton antiporter (NHX) and sodium-proton exchanger (NHE)-type transporters in Sorghum bicolor and their expression patterns under varied abiotic stress conditions. In Sorghum , seven NHX and nine NHE homologs were identified. Amiloride (a known inhibitor of Na⁺/H⁺ exchanger activity) binding motif was noticed in both types of the transporters...
May 3, 2018: Genes
https://www.readbyqxmd.com/read/29751086/decanalizing-thinking-on-genetic-canalization
#9
REVIEW
Kerry Geiler-Samerotte, Federica M O Sartori, Mark L Siegal
The concept of genetic canalization has had an abiding influence on views of complex-trait evolution. A genetically canalized system has evolved to become less sensitive to the effects of mutation. When a gene product that supports canalization is compromised, the phenotypic impacts of a mutation should be more pronounced. This expected increase in mutational effects not only has important consequences for evolution, but has also motivated strategies to treat disease. However, recent studies demonstrate that, when putative agents of genetic canalization are impaired, systems do not behave as expected...
May 8, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29746091/a-framework-for-engineering-stress-resilient-plants-using-genetic-feedback-control-and-regulatory-network-rewiring
#10
Mathias Foo, Iulia Gherman, Peijun Zhang, Declan G Bates, Katherine Denby
Crop disease leads to significant waste world-wide, both pre- and post-harvest, with subsequent economic and sustainability consequences. Disease outcome is determined both by the plants' response to the pathogen and by the ability of the pathogen to suppress defense responses and manipulate the plant to enhance colonization. The defense response of a plant is characterized by significant transcriptional reprogramming mediated by underlying gene regulatory networks and components of these networks are often targeted by attacking pathogens...
May 10, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29736721/a-quantitative-systems-pharmacology-approach-to-infer-pathways-involved-in-complex-disease-phenotypes
#11
Mark E Schurdak, Fen Pei, Timothy R Lezon, Diane Carlisle, Robert Friedlander, D Lansing Taylor, Andrew M Stern
Designing effective therapeutic strategies for complex diseases such as cancer and neurodegeneration that involve tissue context-specific interactions among multiple gene products presents a major challenge for precision medicine. Safe and selective pharmacological modulation of individual molecular entities associated with a disease often fails to provide efficacy in the clinic. Thus, development of optimized therapeutic strategies for individual patients with complex diseases requires a more comprehensive, systems-level understanding of disease progression...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29723215/core-signaling-pathways-in-ovarian-cancer-stem-cell-revealed-by-integrative-analysis-of-multi-marker-genomics-data
#12
Tianyu Zhang, Jielin Xu, Siyuan Deng, Fengqi Zhou, Jin Li, Liwei Zhang, Lang Li, Qi-En Wang, Fuhai Li
Tumor recurrence occurs in more than 70% of ovarian cancer patients, and the majority eventually becomes refractory to treatments. Ovarian Cancer Stem Cells (OCSCs) are believed to be responsible for the tumor relapse and drug resistance. Therefore, eliminating ovarian CSCs is important to improve the prognosis of ovarian cancer patients. However, there is a lack of effective drugs to eliminate OCSCs because the core signaling pathways regulating OCSCs remain unclear. Also it is often hard for biologists to identify a few testable targets and infer driver signaling pathways regulating CSCs from a large number of differentially expression genes in an unbiased manner...
2018: PloS One
https://www.readbyqxmd.com/read/29718162/lncfuntk-a-toolkit-for-functional-annotation-of-long-noncoding-rnas
#13
Jiajian Zhou, Yile Huang, Yingzhe Ding, Jie Yuan, Huating Wang, Hao Sun
Motivation: Thousands of long noncoding RNAs (lncRNAs) were newly identified from high throughput RNA-seq data. Functional annotation and prioritization of these lncRNAs for further experimental validation as well as functional investigation is the bottle neck step for many noncoding RNA studies. Results: Here we describe lncFunTK that can run either as standard application or webserver for this purpose. It integrates high throughput sequencing data (i.e., ChIP-seq, CLIP-seq, and RNA-seq) to construct the regulatory network associated with lncRNAs...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29707235/detecting-phenotype-driven-transitions-in-regulatory-network-structure
#14
Megha Padi, John Quackenbush
Complex traits and diseases like human height or cancer are often not caused by a single mutation or genetic variant, but instead arise from functional changes in the underlying molecular network. Biological networks are known to be highly modular and contain dense "communities" of genes that carry out cellular processes, but these structures change between tissues, during development, and in disease. While many methods exist for inferring networks and analyzing their topologies separately, there is a lack of robust methods for quantifying differences in network structure...
2018: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29697365/population-based-statistical-inference-for-temporal-sequence-of-somatic-mutations-in-cancer-genomes
#15
Je-Keun Rhee, Tae-Min Kim
BACKGROUND: It is well recognized that accumulation of somatic mutations in cancer genomes plays a role in carcinogenesis; however, the temporal sequence and evolutionary relationship of somatic mutations remain largely unknown. METHODS: In this study, we built a population-based statistical framework to infer the temporal sequence of acquisition of somatic mutations. Using the model, we analyzed the mutation profiles of 1954 tumor specimens across eight tumor types...
April 20, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29691301/plant-endomembrane-dynamics-studies-of-k-h-antiporters-provide-insights-on-the-effects-of-ph-and-ion-homeostasis
#16
Heven Sze, Salil Chanroj
Plants remodel their cells through the dynamic endomembrane system. Intracellular pH is important for membrane trafficking, but the determinants of pH homeostasis are poorly defined in plants. Electrogenic proton (H+) pumps depend on counter-ion fluxes to establish transmembrane pH gradients at the plasma membrane and endomembranes. Vacuolar-type H+-ATPase-mediated acidification of the trans-Golgi network (TGN) is crucial for secretion and membrane recycling. Pump and counter-ion fluxes are unlikely to fine-tune pH; rather, alkali cation/H+ antiporters, which can alter pH and/or cation homeostasis locally and transiently, are prime candidates...
April 24, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29684207/the-number-of-titrated-microrna-species-dictates-cerna-regulation
#17
Hua-Sheng Chiu, María Rodríguez Martínez, Elena V Komissarova, David Llobet-Navas, Mukesh Bansal, Evan O Paull, José Silva, Xuerui Yang, Pavel Sumazin, Andrea Califano
microRNAs (miRNAs) play key roles in cancer, but their propensity to couple their targets as competing endogenous RNAs (ceRNAs) has only recently emerged. Multiple models have studied ceRNA regulation, but these models did not account for the effects of co-regulation by miRNAs with many targets. We modeled ceRNA and simulated its effects using established parameters for miRNA/mRNA interaction kinetics while accounting for co-regulation by multiple miRNAs with many targets. Our simulations suggested that co-regulation by many miRNA species is more likely to produce physiologically relevant context-independent couplings...
April 19, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29684163/experimental-evolution-of-yeast-for-high-temperature-tolerance
#18
Chih-Jen Huang, Mei-Yeh Lu, Ya-Wen Chang, Wen-Hsiung Li
Thermotolerance is a polygenic trait that contributes to cell survival and growth under unusually high temperatures. Although some genes associated with high temperature growth (Htg+) have been identified, how cells accumulate mutations to achieve prolonged thermotolerance is still mysterious. Here we conducted experimental evolution of a Saccharomyces cerevisiae laboratory strain with stepwise temperature increases for it to grow at 42 °C. Whole genome resequencing of 14 evolved strains and the parental strain revealed a total of 153 mutations in the evolved strains, including single nucleotide variants, small INDELs, and segmental duplication/deletion events...
April 19, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29675796/construction-of-transcriptional-regulatory-network-of-alzheimer-s-disease-based-on-panda-algorithm
#19
Jieyuan Ding, Wei Kong, Xiaoyang Mou, Shuaiqun Wang
The focus of modern biomedical research concentrates on molecular level regulatory mechanisms and how the normal and abnormal phenotypes of tissue functional are affected by regulatory mechanisms. Most of the research on regulatory mechanism starts from the reconstruction of gene regulation network. At present, a large number of reconstruction methods construct the network using a single data set. These methods of inferring and predicting the relationship between the target gene and the transcription factor (TF) can be used to identify individual interactions between genes, while there is not much research on the interaction of many functional-related genes...
April 19, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29671401/comparisons-of-gene-coexpression-network-modules-in-breast-cancer-and-ovarian-cancer
#20
Shuqin Zhang
BACKGROUND: Breast cancer and ovarian cancer are hormone driven and are known to have some predisposition genes in common such as the two well known cancer genes BRCA1 and BRCA2. The objective of this study is to compare the coexpression network modules of both cancers, so as to infer the potential cancer-related modules. METHODS: We applied the eigen-decomposition to the matrix that integrates the gene coexpression networks of both breast cancer and ovarian cancer...
April 11, 2018: BMC Systems Biology
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