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Sharing and Specificity of Co-expression Networks across 35 Human Tissues
2015
PLoS Computational Biology
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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]
2014
bioRxiv
pre-print
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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]
2022
bioRxiv
pre-print
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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]
2019
bioRxiv
pre-print
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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]
2020
bioRxiv
pre-print
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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
2017
PLoS Genetics
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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]
2016
bioRxiv
pre-print
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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
2015
Nature reviews genetics
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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
2017
Genome Research
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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
2018
PLoS Computational Biology
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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
2020
Biochimica et Biophysica Acta - Molecular Basis of Disease
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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
2019
Computational and Mathematical Methods in Medicine
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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
2021
BMC Ecology and Evolution
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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
2018
Human Molecular Genetics
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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
2020
Neurological Sciences
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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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