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WeGET: predicting new genes for molecular systems by weighted co-expression

Radek Szklarczyk, Wout Megchelenbrink, Pavel Cizek, Marie Ledent, Gonny Velemans, Damian Szklarczyk, Martijn A. Huynen
<span title="2015-11-17">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
We have developed the Weighted Gene Expression Tool and database (WeGET, http://weget.cmbi.umcn. nl) for the prediction of new genes of a molecular system by correlated gene expression.  ...  WeGET ranks new candidate genes by calculating their weighted coexpression with that system. A weighted rank is calculated for human genes and their mouse orthologs.  ...  Table 2 shows genes co-expressing with the neuropathic pain molecular system as calculated by WeGET.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1228">doi:10.1093/nar/gkv1228</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26582928">pmid:26582928</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702868/">pmcid:PMC4702868</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gqmmdjvusvc5hl4pxlx4bnhfj4">fatcat:gqmmdjvusvc5hl4pxlx4bnhfj4</a> </span>
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Identifying gene function and module connections by the integration of multi-species expression compendia [article]

Hao Li, Daria Rukina, Fabrice P. A. David, Terytty Yang Li, Chang-Myung Oh, Arwen W. Gao, Elena Katsyuba, Maroun Bou Sleiman, Andrea Komljenovic, Qingyao Huang, Robert W. Williams, Marc W. Robinson-Rechavi (+3 others)
<span title="2019-05-24">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The GeneBridge tools together with the expression compendia are available at systems-genetics.org, to facilitate the identification of connections linking genes, modules, phenotypes, and diseases.  ...  We developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes.  ...  We then compared the area under the receiver operating characteristic (ROC) curve (AUC) with the ones obtained from WeGET, a method predicting novel genes for various modules based on weighted co-expression  ... 
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The 2016 database issue ofNucleic Acids Researchand an updated molecular biology database collection

Daniel J. Rigden, Xosé M. Fernández-Suárez, Michael Y. Galperin
<span title="2016-01-03">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The NAR online Molecular Biology Database Collection, http: //www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought  ...  A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their  ...  ACKNOWLEDGEMENTS We thank NAR Editorial Administrator Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their great efforts in compiling this  ... 
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A prioritized and validated resource of mitochondrial proteins in Plasmodium identifies leads to unique biology [article]

Selma L van Esveld, Lisette Meerstein-Kessel, Cas Boshoven, Jochem Baaij, Konstantin Barylyuk, Jordy Coolen, Ronald A J Duim, Bas E. Dutilh, Daniel Rios Garza, Marijn Letterie, Nicholas I Proellochs, Michelle N de Ridder (+5 others)
<span title="2021-01-23">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Many data sources contain information about mitochondrial localization, including proteome and gene expression profiles, orthology to mitochondrial proteins from other species, co-evolutionary relationships  ...  Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by anti-malarial drugs.  ...  Szklarczyk R, Megchelenbrink W, Cizek P, Ledent M, Velemans G, Szklarczyk D, et al. 833 WeGET: predicting new genes for molecular systems by weighted co-expression.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.01.22.427784">doi:10.1101/2021.01.22.427784</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jzuq3ux7dvhxnavt7p3lybxgx4">fatcat:jzuq3ux7dvhxnavt7p3lybxgx4</a> </span>
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A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome

Selma L. van Esveld, Şirin Cansız-Arda, Fenna Hensen, Robin van der Lee, Martijn A. Huynen, Johannes N. Spelbrink
<span title="2019-11-15">2019</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4dl6zyzmsrhczjurbzfc3hrzn4" style="color: black;">Frontiers in Cell and Developmental Biology</a> </i> &nbsp;
combine these two mitochondrial-enriched datasets as well as published whole-cell datasets of RNA-binding proteins with various online resources, such as mitochondrial localization from MitoCarta 2.0 and co-expression  ...  the prediction instead of the published whole-cell datasets.  ...  Gerstberger et al., 2014; Finn et al., 2016 1520 1.33 Co-expression with mtRNA interactors Weighted co-expression with known mtRNA interacting proteins c calculated using WeGET.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fcell.2019.00283">doi:10.3389/fcell.2019.00283</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31803741">pmid:31803741</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6873792/">pmcid:PMC6873792</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kcrrnqcurvadnbzi6vdtewy2vi">fatcat:kcrrnqcurvadnbzi6vdtewy2vi</a> </span>
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CiliaCarta: An integrated and validated compendium of ciliary genes

Teunis J. P. van Dam, Julie Kennedy, Robin van der Lee, Erik de Vrieze, Kirsten A. Wunderlich, Suzanne Rix, Gerard W. Dougherty, Nils J. Lambacher, Chunmei Li, Victor L. Jensen, Michel R. Leroux, Rim Hjeij (+37 others)
<span title="2019-05-16">2019</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered.  ...  We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function.  ...  Mutation Project for nematode reagents.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0216705">doi:10.1371/journal.pone.0216705</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31095607">pmid:31095607</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6522010/">pmcid:PMC6522010</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fvlffokpfjfz5a6n7pawgsrxjm">fatcat:fvlffokpfjfz5a6n7pawgsrxjm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191214053851/https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0216705&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d2/f6/d2f6bb5fb2a3b895a976d5d32a05afe265db8ea2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0216705"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522010" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification of Signaling Pathways Targeted by the Food Contaminant FB1: Transcriptome and Kinome Analysis of Samples from Pig Liver and Intestine

Marion Régnier, Pascal Gourbeyre, Philippe Pinton, Scott Napper, Joëlle Laffite, Anne-Marie Cossalter, Jean-Denis Bailly, Yannick Lippi, Justine Bertrand-Michel, Ana Paula F.R.L. Bracarense, Hervé Guillou, Nicolas Loiseau (+1 others)
<span title="2017-10-17">2017</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/w3sptsgqmnhahblgcwsb2to3zq" style="color: black;">Molecular Nutrition &amp; Food Research</a> </i> &nbsp;
Immun. 2013, 81, 226-237. [31] Szklarczyk, R., Megchelenbrink, W., Cizek, P., Ledent, M., et al., WeGET: predicting new genes for molecular systems by weighted co-expression.  ...  Gene expression analysis For the gene expression analysis, total RNA was extracted in lysing matrix D tubes (MP Biomedicals, Illkirch, France) containing guanidine thiocyanate-acid phenol (Eurobio).  ...  This article is protected by copyright.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/mnfr.201700433">doi:10.1002/mnfr.201700433</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28875582">pmid:28875582</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t3ycgidxjzcc3jci52tlli6joy">fatcat:t3ycgidxjzcc3jci52tlli6joy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201107171907/https://hal.archives-ouvertes.fr/hal-01606651/file/2017_Regnier-Molecular_Nutrition_Food_Research_1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/53/07/5307a0b3049e55d64321a7f00fd093425edae575.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/mnfr.201700433"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

CiliaCarta: An Integrated And Validated Compendium Of Ciliary Genes [article]

Teunis J. P. van Dam, Julie Kennedy, Robin van der Lee, Erik de Vrieze, Kirsten A. Wunderlich, Suzanne Rix, Gerard W. Dougherty, Nils J. Lambacher, Chunmei Li, Victor L. Jensen, Michael R. Leroux, Rim Hjeij (+36 others)
<span title="2017-04-03">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered.  ...  We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function.  ...  screen data set 9 In expression screening 63 separate gene--expression data sets are weighted for their potential to 10 predict new genes for a system by measuring, per data set, the level of co--expression  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/123455">doi:10.1101/123455</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cg5laholendyfaynsuiljbjr74">fatcat:cg5laholendyfaynsuiljbjr74</a> </span>
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4th Conference of Cereal Biotechnology and Breeding (CBB4), November 6–9, 2017, Budapest, Hungary – Book of Abstracts

<span title="">2017</span> <i title="Akademiai Kiado Zrt."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5adsrlegajfttltfa2wp55vayq" style="color: black;">Cereal research communications</a> </i> &nbsp;
Editing net blotch susceptibility genes for disease resistance in barley using CRISPR/Cas9 through gene gun bombardment Acknowledgments This work was supported by the Hungarian Research Fund K101794.  ...  Acknowledgments The research was funded by the National Centre for Research and Development, PBS3/ B8/17/2015.  ...  Wax was weighted and analysed by GC-FID. Tested lines differ in yield, expressed as thousand grain weight. In optimal conditions wax-less lines were characterized by lower yield.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1556/0806.45.2017.100">doi:10.1556/0806.45.2017.100</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3rrvrijpwzh6ddwlbxuu4afanm">fatcat:3rrvrijpwzh6ddwlbxuu4afanm</a> </span>
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