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Linking gene expression to phenotypes via pathway information

Irene Papatheodorou, Anika Oellrich, Damian Smedley
2015 Journal of Biomedical Semantics  
Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments.  ...  In recent years there have been many efforts to develop the computational means to traverse from genes to gene expression, model pathways and classify phenotypes.  ...  Figure 1 1 Figure 1 Databases and ontologies for information on genes, pathways and phenotypes. The diagram shows the information flow from genes to phenotypes via pathways.  ... 
doi:10.1186/s13326-015-0013-5 pmid:25901272 pmcid:PMC4404592 fatcat:amhyu67d4jdxviz52xyraw6uky

Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humans

Pascal Gottmann, Meriem Ouni, Lisa Zellner, Markus Jähnert, Kilian Rittig, Dirk Walther, Annette Schürmann
2020 Scientific Reports  
Among these, 38 genes have been associated to metabolic diseases according to the phenotypes of corresponding knockout mice or other results described in the literature. The remaining 13 genes (e.g.  ...  They are expressed at higher levels in metabolically relevant tissues presumably due to altered miRNA-mRNA binding sites.  ...  Besides pathway analysis, network analyses were performed by including information on the phenotype of knockout mice as well as results from other screenings for genes exhibiting a variant in a miRNA binding  ... 
doi:10.1038/s41598-020-64326-4 pmid:32350386 fatcat:nbfwn6pglbayfmjjd3trnlkrfy

CancerGeneNet: linking driver genes to cancer hallmarks

2019 Nucleic Acids Research  
CancerGeneNet (https://signor.uniroma2.it/CancerGeneNet/) is a resource that links genes that are frequently mutated in cancers to cancer phenotypes.  ...  Graph algorithms, in turn, allow to infer likely paths of causal interactions linking cancer associated genes to cancer phenotypes thus offering a rational framework for the design of strategies to revert  ...  RESULTS Retrieving experimental information on causal interactions The CancerGeneNet project aims at linking genes implicated in cancer to cancer phenotypes via causal interactions between proteins (  ... 
doi:10.1093/nar/gkz871 pmid:31598703 pmcid:PMC6943052 fatcat:cjgt7zkou5dh5lucttyv722j6y

MaizeGDB update: new tools, data and interface for the maize model organism database

Carson M. Andorf, Ethalinda K. Cannon, John L. Portwood, Jack M. Gardiner, Lisa C. Harper, Mary L. Schaeffer, Bremen L. Braun, Darwin A. Campbell, Abhinav G. Vinnakota, Venktanaga V. Sribalusu, Miranda Huerta, Kyoung Tak Cho (+7 others)
2015 Nucleic Acids Research  
types (including diversity data, expression data, gene models, and metabolic pathways), and developing and deploying a modern interface.  ...  In addition to coordinating a data resource, the MaizeGDB team co-ordinates activities and provides technical support to the maize research community.  ...  The 'About' menu provides information about the project, outreach efforts, links to social media pages, and helpful links to best utilize the site.  ... 
doi:10.1093/nar/gkv1007 pmid:26432828 pmcid:PMC4702771 fatcat:5ywbtkiv5ncw5nr3ewvlcjqmxu

Predicting phenotypic effects of gene perturbations inC. elegansusing an integrated network model

Karsten Borgwardt
2008 Bioessays  
As genome sequences of species and, recently, individuals (2) continue to be established, an important research question over coming years will be to link variations in individual genes to phenotypic effects  ...  Phenotype prediction Clarifying the link between phenotype and genotype of an orgnanism is at the core of research in genetics.  ...  To conclude, Lee et al. have developed a single genomewide network model for predicting phenotypic effects of gene silencing via RNAi in C. elegans.  ... 
doi:10.1002/bies.20783 pmid:18618771 fatcat:xmmo772k3zh7rk7drg2yre5jpm

Systems Biology Approaches and Applications in Obesity, Diabetes, and Cardiovascular Diseases

Qingying Meng, Ville-Petteri Mäkinen, Helen Luk, Xia Yang
2012 Current Cardiovascular Risk Reports  
These datasets provide us with an opportunity to go beyond conventional reductionist approaches and to pinpoint the specific perturbations in critical biological processes.  ...  The metabolically connected triad of obesity, diabetes, and cardiovascular diseases is a major public health threat, and is expected to worsen due to the global shift toward energy-rich and sedentary living  ...  Causality Inference via Integration of Genetic, Gene Expression, and Disease Phenotypes Based on the central dogma, heritable information flows from DNA to RNA, to proteins, and then to phenotypic traits  ... 
doi:10.1007/s12170-012-0280-y pmid:23326608 pmcid:PMC3543610 fatcat:gjtf52f3ozgznpi4ozzjium6xq

The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research

Ben van Ommen, Ahmed El-Sohemy, John Hesketh, Jim Kaput, Michael Fenech, Chris T. Evelo, Harry J. McArdle, Jildau Bouwman, Georg Lietz, John C. Mathers, Sue Fairweather-Tait, Henk van Kranen (+7 others)
2010 Genes & Nutrition  
The core of the project focuses on access to, and visualization of, genetic/genomic, transcriptomic, proteomic and metabolomic information related to micronutrients.  ...  Micronutrients influence multiple metabolic pathways including oxidative and inflammatory processes.  ...  Fig. 2 The pathways on WikiPathways are linked to relevant information about the entities present.  ... 
doi:10.1007/s12263-010-0192-8 pmid:21189865 pmcid:PMC2989004 fatcat:xgp7bxgqu5hrpi6icreqov7v7m

Bridging the Gap between Genotype and Phenotype via Network Approaches

Yoo-Ah Kim, Teresa M. Przytycka
2013 Frontiers in Genetics  
To address this emerging need, computational approaches increasingly utilize a pathway-centric perspective.  ...  of genotype-phenotype relationships to the level of the molecular mechanisms behind them.  ...  Differently expressed genes are linked to the sink of network flow.  ... 
doi:10.3389/fgene.2012.00227 pmid:23755063 pmcid:PMC3668153 fatcat:hbj7ddx5sjf3hha5gluhywha2a

CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining

A. Pati, Y. Jin, K. Klage, R. F. Helm, L. S. Heath, N. Ramakrishnan
2007 Nucleic Acids Research  
Chains can, for example, relate the knock down of a set of genes during an RNAi experiment to the disruption of a pathway or specific gene expression through another set of genes not directly related to  ...  Besides gene, protein and functional annotations, CMGSDB currently unifies information about 531 RNAi phenotypes obtained from heterogeneous databases using a hierarchical scheme.  ...  Funding to pay  ... 
doi:10.1093/nar/gkm804 pmid:17942411 pmcid:PMC2238953 fatcat:xctnc65jajfkvnk5zdsrr3isoe

GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype

Daeun Ryu, SeongBeom Cho, Hun Kim, Sanghyuk Lee, Wankyu Kim
2014 Bioinformatics  
The GEPdb provides simultaneous interpretation of both genetic risks and potential gene regulatory pathways toward phenotypic outcome by establishing the ternary relationship of genotype-expression-phenotype  ...  GEPdb integrates both genome-wide association studies and expression quantitative trait loci information, the two primary sources of genome-wide mapping for genotype-phenotype and genotype-expression associations  ...  SNPs are entered and linked to the downstream regulated genes via eQTL (G4E).  ... 
doi:10.1093/bioinformatics/btu240 pmid:24812343 fatcat:hutlgf7iufcopoqjt5dxab763e

Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect

Noa Rappaport, Simon Fishilevich, Ron Nudel, Michal Twik, Frida Belinky, Inbar Plaschkes, Tsippi Iny Stein, Dana Cohen, Danit Oz-Levi, Marilyn Safran, Doron Lancet
2017 BioMedical Engineering OnLine  
This necessitates bioinformatics tools linked to comprehensive knowledgebases.  ...  A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient's disease phenotypes  ...  The authors would also like to thank MalaCards users for their feedback and support.  ... 
doi:10.1186/s12938-017-0359-2 pmid:28830434 pmcid:PMC5568599 fatcat:nr5iblpqh5bn5glqnrgelrdehm

The Rice PIPELINE: a unification tool for plant functional genomics

J. Yazaki
2004 Nucleic Acids Research  
A new uni®cation tool for functional genomics, called Rice PIPELINE, has also been developed for the dynamic collection and compilation of genomics data (genome sequences, fulllength cDNAs, gene expression  ...  The mission of Rice PIPELINE is to provide a unique scienti®c resource that pools publicly available rice genomic data for search by clone sequence, clone name, GenBank accession number, or keyword.  ...  They can also obtain information on cis-element motifs, phenotypes with¯anking sequences, and expression pro®les via the KOME report.  ... 
doi:10.1093/nar/gkh001 pmid:14681439 pmcid:PMC308736 fatcat:lftubwobqzgctjwsf3xqny7xci

Predicting molecular mechanisms, pathways, and health outcomes induced by Juul e-cigarette aerosol chemicals using the comparative toxicogenomics database

Cynthia J. Grondin, Allan Peter Davis, Jolene A Wiegers, Thomas C Wiegers, Daniela Sciaky, Robin J Johnson, Carolyn J Mattingly
2021 Current Research in Toxicology  
Curated content in CTD, including chemical-gene, chemical-phenotype, and chemical-disease interactions, as well as associated phenotypes and pathway enrichment, were analyzed to help identify potential  ...  Using the Comparative Toxicogenomics Database (CTD; http://ctdbase.org), a public resource that integrates chemical, gene, phenotype and disease data, we aimed to analyze the potential molecular mechanisms  ...  CGPD-tetramers are novel information blocks that link Chemical-Gene interactions with Phenotype and Disease outcomes.  ... 
doi:10.1016/j.crtox.2021.08.001 pmid:34458863 pmcid:PMC8379377 fatcat:jg7jiurovbbihcvnoaisra4dxu

Probabilistic functional gene societies

Insuk Lee
2011 Progress in Biophysics and Molecular Biology  
Thus each new hypothesis is based on the integration of information from multiple functional links to the query gene.  ...  The GBA approach may work to study complex phenotypes provided with one assumption that genes modulating a complex phenotype are members of the same pathway or closely related pathways.  ... 
doi:10.1016/j.pbiomolbio.2011.01.003 pmid:21281658 fatcat:5p7pg6fzdrfmhhzmcnkg4msjzu

Global Prioritizing Disease Candidate lncRNAs via a Multi-level Composite Network

Qianlan Yao, Leilei Wu, Jia Li, Li guang Yang, Yidi Sun, Zhen Li, Sheng He, Fangyoumin Feng, Hong Li, Yixue Li
2017 Scientific Reports  
When applied to breast cancer, LncPriCNet identified known breast cancer-related lncRNAs, revealed novel lncRNA candidates and inferred their functions via pathway analysis.  ...  It is reasonable to integrate multi-level data regarding genes, phenotypes, lncRNAs and their association information to prioritize disease-related lncRNA candidates.  ...  The first-ranked lncRNA CBR3-AS1 was linked to the TGF-beta signaling pathway.  ... 
doi:10.1038/srep39516 pmid:28051121 pmcid:PMC5209722 fatcat:m4n2bobnzraihcxvz2bzzouvwa
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