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Sharing and Specificity of Co-expression Networks across 35 Human Tissues

Emma Pierson, Daphne Koller, Alexis Battle, Sara Mostafavi, Isidore Rigoutsos
2015 PLoS Computational Biology  
This data provides an opportunity for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes.  ...  To address this problem, we infer tissue-specific gene co-expression networks for 35 tissues in the GTEx dataset using a novel algorithm, GNAT, that uses a hierarchy of tissues to share data between related  ...  The Brain Bank was supported by a supplements to University of Miami grants DA006227 and DA033684 and to contract N01MH000028.  ... 
doi:10.1371/journal.pcbi.1004220 pmid:25970446 pmcid:PMC4430528 fatcat:wtk32eyf2fdbhbe6ownuvwk2hu

Sharing and specificity of co-expression networks across 35 human tissues [article]

Emma Pierson, GTEx Consortium, Daphne Koller, Alexis Battle, Sara Mostafavi
2014 bioRxiv   pre-print
This data provides an opportunity for deriving shared and tissue-specific gene regulatory networks on the basis of co-expression between genes.  ...  To address this problem, we infer tissue-specific gene co-expression networks for 35 tissues in the GTEx dataset using a novel algorithm, GNAT, that uses a hierarchy of tissues to share data between related  ...  The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health.  ... 
doi:10.1101/010843 fatcat:vnxey4gynbfmrbofr7enxisu7a

Deciphering the tissue-specific regulatory role of intronless genes across cancers [article]

Katia Aviña-Padilla, José Antonio Ramírez-Rafael, Gabriel Emilio Herrera-Oropeza, Guillermo Romero, Octavio Zambada-Moreno, Ishaan Gupta, Maribel Hernández-Rosales
2022 bioRxiv   pre-print
This study highlights that differentially expressed human intronless genes across cancer types are prevalent in epigenetic regulatory roles participating in specific PPI networks for ESCA, GBM, and LUAD  ...  We identified 940 protein-coding IGs in the human genome, of which about 35% were differentially expressed across the analyzed cancer datasets.  ...  Special thanks to Fernando Flores for helping with designing and constructing the co-expression network. We are also thankful to Carlos González for visualization and technical support.  ... 
doi:10.1101/2022.02.21.481319 fatcat:6znbtjgxxzf5dgk7lllbcgrfym

Long non-coding RNA gene regulation and trait associations across human tissues [article]

Olivia M. de Goede, Nicole M. Ferraro, Daniel C. Nachun, Abhiram Rao, François Aguet, Alvaro N. Barbeira, Stephane E Castel, Sarah Kim-Hellmuth, YoSon Park, Alexandra J. Scott, Benjamin J. Strober, Christopher D. Brown (+10 others)
2019 bioRxiv   pre-print
To systematically identify hallmarks of biological function, we used the GTEx v8 data to profile the expression, regulation, network relationships and trait associations of lncRNA genes across 49 tissues  ...  This work provides a comprehensive resource to interrogate lncRNA genes of interest and annotate cell type and human trait relevance.  ...  Acknowledgments: We thank the Montgomery and Kirkegaard labs for their feedback on this work.  ... 
doi:10.1101/793091 fatcat:diepdlfutne2hco7awzhywufvq

The landscape of molecular chaperones across human tissues reveals a layered architecture of core and variable chaperones [article]

Netta Shemesh, Juman Jubran, Mehtap Abu-Qarn, Eyal Simonovky, Omer Basha, Idan Hekselman, Shiran Dror, Ekaterina Vinogradov, Serena Carra, Anat Ben-Zvi, Esti Yeger-Lotem
2020 bioRxiv   pre-print
Here, we used human tissue RNA-sequencing profiles to analyze the expression and organization of chaperones across 29 main tissues.  ...  Altogether, this suggests a layered architecture of chaperones across tissues that is composed of shared core elements that are complemented by variable elements which give rise to tissue-specific functions  ...  Acknowledgements: This study was funded by Israel Ministry of Science and  ... 
doi:10.1101/2020.03.04.976720 fatcat:kf5prvmklzcbrig4x74s2je34u

Shared genetic regulatory networks for cardiovascular disease and type 2 diabetes in multiple populations of diverse ethnicities in the United States

Le Shu, Kei Hang K. Chan, Guanglin Zhang, Tianxiao Huan, Zeyneb Kurt, Yuqi Zhao, Veronica Codoni, David-Alexandre Trégouët, Jun Yang, James G. Wilson, Xi Luo, Daniel Levy (+4 others)
2017 PLoS Genetics  
studies (GWAS) for CVD and T2D, expression quantitative trait loci (eQTLs), ENCODE, and tissue-specific gene network models (both coexpression and graphical models) from CVD and T2D relevant tissues.  ...  Findings from this in-depth assessment of genetic and functional data from multiple human cohorts provide strong support that common sets of tissue-specific molecular networks drive the pathogenesis of  ...  Acknowledgments We thank investigators from the National Women's Health Initiative (WHI), the Framingham Heart Study, the Jackson Hearth Study, the DIAGRAM Consortium, and the CARDIoGRAM-plusC4D for sharing  ... 
doi:10.1371/journal.pgen.1007040 pmid:28957322 pmcid:PMC5634657 fatcat:53immh7tbnhmppghtgf45zyuee

Co-expression networks reveal the tissue-specific regulation of transcription and splicing [article]

Ashis Saha, Yungil Kim, Ariel D. H. Gewirtz, Brian Jo, Chuan Gao, Ian C McDowell, Barbara E Engelhardt, Alexis Battle
2016 bioRxiv   pre-print
Using both TWNs and TSNs, we characterized gene co-expression patterns shared across tissues.  ...  Using the Genotype-Tissue Expression (GTEx) project v6 RNA-sequencing data across 44 tissues in 449 individuals, we evaluated shared and tissue-specific network relationships.  ...  Tissue-specific networks (TSNs) We built tissue-specific gene co-expression networks (TSNs) using an unsupervised Bayesian biclustering model, BicMix, on the gene level quantification from all of the GTEx  ... 
doi:10.1101/078741 fatcat:b6x3silvebbmtanvgaeracmidm

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

Neelroop N. Parikshak, Michael J. Gandal, Daniel H. Geschwind
2015 Nature reviews genetics  
Acknowledgements The authors thank L. de la Torre-Ubieta and H. Won for assistance with Figure 1 , as well as members of the Geschwind laboratory and K. Lage for critical reading of the manuscript.  ...  To reduce bias and improve tissue specificity for genome-wide networks in the absence of tissue-specific PPIs, one approach is to intersect tissue-specific RNA expression or co-expression with literature-curated  ...  Both involved extensive bioinformatic analyses of expression data from in vitro neural progenitor models and identified transcriptomic changes shared across the post-mortem human brain, human neural cell  ... 
doi:10.1038/nrg3934 pmid:26149713 pmcid:PMC4699316 fatcat:nbpdeq7rgzdszmlyrnmunduexy

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Ashis Saha, Yungil Kim, Ariel D.H. Gewirtz, Brian Jo, Chuan Gao, Ian C. McDowell, Barbara E. Engelhardt, Alexis Battle
2017 Genome Research  
Our networks provide an improved understanding of the complex relationships of the human transcriptome across tissues.  ...  Gene co-expression networks capture biologically important patterns in gene expression data, enabling functional analyses of genes, discovery of biomarkers, and interpretation of genetic variants.  ...  Acknowledgments The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health.  ... 
doi:10.1101/gr.216721.116 pmid:29021288 pmcid:PMC5668942 fatcat:zcgy33cnvndpbgidoengvcqosu

Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network

Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura Saba, Katerina Kechris, Qunhua Li
2018 PLoS Computational Biology  
Additionally, we observed that the tumor-specific hub genes tend to have few shared edges with normal tissue, revealing tumor-specific regulatory mechanism.  ...  Here we develop the condition-adaptive fused graphical lasso (CFGL), a data-driven approach to incorporate condition specificity in the estimation of co-expression networks.  ...  This agrees with the observation in the previous analysis [5] of the co-expression network for 35 human tissues in the GTEx project, in which genes with tissue-specific functions were observed to have  ... 
doi:10.1371/journal.pcbi.1006436 pmid:30240439 pmcid:PMC6173447 fatcat:rjxmlwuufbcxlidlpyuoiuff2m

Cross-disease analysis of depression, ataxia and dystonia highlights a role for synaptic plasticity and the cerebellum in the pathophysiology of these comorbid diseases

Miaozhen Huang, Tom J. de Koning, Marina A.J. Tijssen, Dineke S. Verbeek
2020 Biochimica et Biophysica Acta - Molecular Basis of Disease  
We then assessed shared genes in terms of functional enrichment, pathway analysis, molecular connectivity, expression profiles and brain-tissue-specific gene co-expression networks.  ...  We therefore aimed to increase our understanding of their shared pathophysiology by investigating their shared biological pathways and molecular networks.  ...  and methodology of the study and revised it critically; DSV concepted the study, designed the methodology of study, supervised the study, wrote and revised the paper.  ... 
doi:10.1016/j.bbadis.2020.165976 pmid:33011198 fatcat:t36a2dxcq5fzjdpzgiaw5h5n64

Portrait of Tissue-Specific Coexpression Networks of Noncoding RNAs (miRNA and lncRNA) and mRNAs in Normal Tissues

Claudia Cava, Gloria Bertoli, Isabella Castiglioni
2019 Computational and Mathematical Methods in Medicine  
In this work, we performed a computational approach that identifies tissue-specific co-expression networks by integrating miRNAs, long-non-coding RNAs, and mRNAs in more than eight thousands of human samples  ...  Our analysis (1) shows that long-non coding RNAs and miRNAs have a high specificity, (2) confirms several known tissue-specific RNAs, and (3) identifies new tissue-specific co-expressed RNAs that are currently  ...  disease-related miRNAs/lncRNAs based on the tissue-specific co-expression networks.  ... 
doi:10.1155/2019/9029351 pmid:31565069 pmcid:PMC6745163 fatcat:fyuqzkjcgvgadcyyby4h5o5che

Region-specific expression of young small-scale duplications in the human central nervous system

Solène Brohard-Julien, Vincent Frouin, Vincent Meyer, Smahane Chalabi, Jean-François Deleuze, Edith Le Floch, Christophe Battail
2021 BMC Ecology and Evolution  
Beside the influence of gene expression level on region-specificity, we observed the contribution of both duplication age and duplication type to the CNS region-specificity of paralogs.  ...  Results Our work explored intra-organ expression properties of paralogs through multiple territories of the human central nervous system (CNS) using transcriptome data generated by the Genotype-Tissue  ...  We thank Steven McGinn and Elizabeth May for English language editing.  ... 
doi:10.1186/s12862-021-01794-w pmid:33882820 fatcat:ne4wrrs4qjcqhjtw7hyqf4iqca

Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks

John M Bryan, Temesgen D Fufa, Kapil Bharti, Brian P Brooks, Robert B Hufnagel, David M McGaughey
2018 Human Molecular Genetics  
RNA-seq gene expression analyses have been used extensively, for example, to profile specific eye tissues and in large consortium studies, like the GTEx project, to study tissue-specific gene expression  ...  We also leverage our large collection of retina and RPE-choroid tissues to build the first human weighted gene correlation networks and use them to highlight known biological pathways and eye gene disease  ...  We would like to thank the 21 eye research projects whose public sharing of their raw sequencing data and metadata made this project possible.  ... 
doi:10.1093/hmg/ddy239 pmid:30239781 pmcid:PMC6140774 fatcat:fsqexx2xujaxziy42ageg4euaa

Proposed minimal essential co-expression and physical interaction networks involved in the development of cognition impairment in human mid and late life

Zahra Salehi, Masoud Arabfard, Omid Sadatpour, Mina Ohadi
2020 Neurological Sciences  
APP was the major hub in the integrated and tissue-specific co-expression networks, whereas insulin was the major hub in the physical interaction network.  ...  The aim of this study was to identify the minimal essential co-expression and physical interaction networks involved in the development of cognition impairment in human mid and late life.  ...  NOTCH1 was another hub shared across the co-expression and physical interaction networks.  ... 
doi:10.1007/s10072-020-04594-0 pmid:32676761 fatcat:loxyhe2fwzbapj776656mw2w6i
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