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OmicsMapNet: Transforming omics data to take advantage of Deep Convolutional Neural Network for discovery [article]

Shiyong Ma, Zhen Zhang
<span title="2019-05-23">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
As an example, we used the KEGG BRITE database to rearrange RNA-Seq expression data of TCGA diffuse glioma samples as treemaps to capture the functional hierarchical structure of genes in 2D images.  ...  Deep Convolutional Neural Networks (CNN) were derived using tools from TensorFlow to learn the grade of TCGA LGG and GBM samples with relatively high accuracy.  ...  quantitative proteomics data using simplified version of GO annotation -Generic GO slim (Halligan et al. 2007) , and Bernhardt (Bernhardt et al. 2009 ) visualized gene expression data via Voronoi treemaps  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1804.05283v2">arXiv:1804.05283v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6hsyfjumzrgf3opv7ltnef45v4">fatcat:6hsyfjumzrgf3opv7ltnef45v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200929155656/https://arxiv.org/vc/arxiv/papers/1804/1804.05283v1.pdf" title="fulltext PDF download [not primary version]" 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] <span style="color: #f43e3e;">&#10033;</span> <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fb/38/fb387136e2772e987e3d5744eb84421505c716f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1804.05283v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Visual account of protein investment in cellular functions

W. Liebermeister, E. Noor, A. Flamholz, D. Davidi, J. Bernhardt, R. Milo
<span title="2014-06-02">2014</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
We make interactive visualizations of published proteome datasets accessible at www.proteomaps.net.  ...  This article aims to give a broad perspective on the composition of proteomes as gleaned from recent quantitative proteomics studies.  ...  Here, we visualize quantitative proteome data using a graphical tool we call proteomaps, where proteins are shown as polygons whose sizes indicate the abundances.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1314810111">doi:10.1073/pnas.1314810111</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24889604">pmid:24889604</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4060655/">pmcid:PMC4060655</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7ubryivd6jabna5cverieizpmy">fatcat:7ubryivd6jabna5cverieizpmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724135159/http://www.pnas.org/content/pnas/111/23/8488.full.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/99/ba/99ba367c571b72c7bb2039c35b0534dab0069ebd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1314810111"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060655" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress

Melanie Hillion, Jörg Bernhardt, Tobias Busche, Martina Rossius, Sandra Maaß, Dörte Becher, Mamta Rawat, Markus Wirtz, Rüdiger Hell, Christian Rückert, Jörn Kalinowski, Haike Antelmann
<span title="2017-04-26">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
In total, 58 proteins with S-mycothiolated Cys-peptides were identified (Table 1, Table S1A -C) which are visualized in Voronoi treemaps in relation to the total protein abundance of all proteins present  ...  in the proteome (Fig. 2) .  ...  Quantification of the redox status of 1098 Cys residues by OxICAT and visualization of the thiol-oxidation levels using "Voronoi redox treemaps".  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-01179-4">doi:10.1038/s41598-017-01179-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28446771">pmid:28446771</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5430705/">pmcid:PMC5430705</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gifotoyolnantk6564is5uphnq">fatcat:gifotoyolnantk6564is5uphnq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719044547/http://dspace.mit.edu/bitstream/handle/1721.1/110027/Hillion-2017-Monitoring%20global%20protein%20thiol-o.pdf;jsessionid=944FE7C18586FFFB4810084973011033?sequence=1" 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/40/b3/40b3b87b1b824cf3bc462800acb199ac5533d3b9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-01179-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430705" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Visualizing Multivariate Hierarchic Data Using Enhanced Radial Space-Filling Layout [chapter]

Ming Jia, Ling Li, Erin Boggess, Eve Syrkin Wurtele, Julie A. Dickerson
<span title="">2010</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
This paper illustrates the use of the ERSF layout to explore pathway and gene ontologies using a gene expression dataset from E. coli.  ...  This paper illustrates the use of the ERSF layout to explore pathway and gene ontologies using a gene expression dataset from E. coli.  ...  Node-link graph and treemaps [10] are also widely used to visualize ontology.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-17289-2_34">doi:10.1007/978-3-642-17289-2_34</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ffe6gilmrfarpjwigoi5bc2gwy">fatcat:ffe6gilmrfarpjwigoi5bc2gwy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200307155112/https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1017&amp;context=gdcb_las_conf" 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/eb/b7/ebb7274933e9e47fe17d05d9cf5f5fb667ce00a2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-17289-2_34"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Comparative secretome analyses of human and zoonotic Staphylococcus aureus isolates of CC8, CC22 and CC398

Tobias Busche, Mélanie Hillion, Vu Van Loi, David Berg, Birgit Walther, Torsten Semmler, Birgit Strommenger, Wolfgang Witte, Christiane Cuny, Alexander Mellmann, Mark A. Holmes, Jörn Kalinowski (+3 others)
<span title="2018-09-10">2018</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63atlvwyorhorfip35rcvk6bey" style="color: black;">Molecular &amp; Cellular Proteomics</a> </i> &nbsp;
Using secretome analysis, we identified 869 secreted proteins with 538 commons in eight isolates of CC8, CC22, and CC398.  ...  label-free quantitative proteomics.  ...  Quantification of LFQ intensities of the peptides in the 24 exoproteome samples was performed using label-free quantitative proteomics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.ra118.001036">doi:10.1074/mcp.ra118.001036</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30201737">pmid:30201737</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6283302/">pmcid:PMC6283302</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ibq5lybmaffppkq7nqlo3ybxey">fatcat:ibq5lybmaffppkq7nqlo3ybxey</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190217205845/http://pdfs.semanticscholar.org/0754/40bad0bfb25847b402efa02dc4aa627ee766.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/07/54/075440bad0bfb25847b402efa02dc4aa627ee766.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.ra118.001036"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283302" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions

Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C. Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina (+12 others)
<span title="2017-09-08">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Using an in vivo murine pneumonia model, our data-independent acquisition quantification analysis revealed for the first time the in vivo proteome adaptation of S. aureus.  ...  Visualization of proteomics results in Voronoi-like treemaps. Voronoi-like treemaps 57 were generated using the Paver 2.0 software (Decodon GmbH, Greifswald, Germany).  ...  Although proteomic studies using mass spectrometry MS have partially met these requirements, there is the need to extend proteomics to provide highly reproducible, quantitative, sensitive, and comprehensive  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-10059-w">doi:10.1038/s41598-017-10059-w</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28887440">pmid:28887440</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5591248/">pmcid:PMC5591248</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5qeo5bjo2zd3tbrs6awtkiuts4">fatcat:5qeo5bjo2zd3tbrs6awtkiuts4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208161919/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5591248&amp;blobtype=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/d2/01/d2011fa1123c7b91b224b239666c22f3ffce9dbe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-10059-w"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5591248" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection

Marie-Laurence Lemay, Sandra Maaß, Andreas Otto, Jérémie Hamel, Pier-Luc Plante, Geneviève M. Rousseau, Denise M. Tremblay, Rong Shi, Jacques Corbeil, Stéphane M. Gagné, Dörte Becher, Sylvain Moineau
<span title="2020-07-24">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ockrmqzwdnfq3b4pukv44pnfgu" style="color: black;">Viruses</a> </i> &nbsp;
Here, we developed an integrative approach, making use of structural biology, genomics, physiology, and proteomics to provide insights into the function of ORF47, the most conserved non-structural protein  ...  This siphophage infects Lactococcus lactis MG1363, a model strain used to study Gram-positive lactic acid bacteria.  ...  Furthermore, we used label-free quantitative proteomics to compare the proteotypes of L. lactis MG1363 infected by either phage p2∆47 or p2 [10] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/v12080797">doi:10.3390/v12080797</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32722163">pmid:32722163</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7472136/">pmcid:PMC7472136</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zftzpdsnordebg6got3owvworm">fatcat:zftzpdsnordebg6got3owvworm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200725062024/https://res.mdpi.com/d_attachment/viruses/viruses-12-00797/article_deploy/viruses-12-00797.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/00/de/00dea7f336cf3a71859e8586b92f30650db83b1e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/v12080797"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7472136" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

Martin Grube, Tomislav Cernava, Jung Soh, Stephan Fuchs, Ines Aschenbrenner, Christian Lassek, Uwe Wegner, Dörte Becher, Katharina Riedel, Christoph W Sensen, Gabriele Berg
<span title="2014-07-29">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ii4mp46mlndibnz4acpdnnmvou" style="color: black;">The ISME Journal</a> </i> &nbsp;
Metagenomic and proteomic data were comparatively assessed and visualized by Voronoi treemaps. The study was complemented with molecular, microscopic and physiological assays.  ...  We have explored the metabolic potentials of the microbiome using the lung lichen Lobaria pulmonaria as the model.  ...  Voronoi treemaps Voronoi treemaps were generated using Paver (Decodon, Greifswald, Germany, http://www. decodon.com/).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ismej.2014.138">doi:10.1038/ismej.2014.138</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25072413">pmid:25072413</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4303634/">pmcid:PMC4303634</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/on64cyfj6nhlzkdjg6y7gphry4">fatcat:on64cyfj6nhlzkdjg6y7gphry4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200314010722/https://www.nature.com/articles/ismej2014138.pdf?error=cookies_not_supported&amp;code=48bdb44c-5f4f-4f40-a662-8d9f81a1c6a6" 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/8d/b4/8db4164a294cf4b00d9b1b7d7d85dcc07088d85c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ismej.2014.138"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303634" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detailed Soluble Proteome Analyses of a Dairy-Isolated Enterococcus faecalis: A Possible Approach to Assess Food Safety and Potential Probiotic Value

Simona Cirrincione, Bernd Neumann, Daniela Zühlke, Katharina Riedel, Enrica Pessione
<span title="2019-05-17">2019</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p7xhj7bi55c75nlff72jgml6mm" style="color: black;">Frontiers in Nutrition</a> </i> &nbsp;
In this study, the soluble proteome quantitation data (LC-MS/MS) of the food-isolated strain E. faecalis D27 (dairy-isolate) was compared with the soluble proteome quantitation data of the pathogenic E  ...  From one side they are used as food starters, bio-control agents and probiotics to improve human or animal health.  ...  Thanks to the Voronoi treemaps, it is possible to visualize the bacterial proteome, grouping the proteins according to their function, sub-function or specific protein name (the functional prediction is  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fnut.2019.00071">doi:10.3389/fnut.2019.00071</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31157229">pmid:31157229</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6533484/">pmcid:PMC6533484</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i2dz3xxtqjfw5fhu3knc7zccbm">fatcat:i2dz3xxtqjfw5fhu3knc7zccbm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200214174328/https://fjfsdata01prod.blob.core.windows.net/articles/files/439025/pubmed-zip/.versions/1/.package-entries/fnut-06-00071/fnut-06-00071.pdf?sv=2015-12-11&amp;sr=b&amp;sig=hBuTblefP3OK%2F974KGwuX90seYZlLNxMql1H82XhH44%3D&amp;se=2020-02-14T17%3A43%3A57Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fnut-06-00071.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/e2/4c/e24c1465d5caea3b2793c50297513acc492f3cb7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fnut.2019.00071"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533484" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Metabolic Labeling Strategy for Relative Protein Quantification in Clostridioides difficile

Anke Trautwein-Schult, Sandra Maaß, Kristina Plate, Andreas Otto, Dörte Becher
<span title="2018-10-16">2018</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/67anf6qgandy5adz4rakospiuq" style="color: black;">Frontiers in Microbiology</a> </i> &nbsp;
Hence, quantitative proteome analyses could only be carried out by label free or chemical labeling methods so far. In this paper, a ML approach for C. difficile is described.  ...  A detailed analysis of the proteome may provide new targets for drug development or therapeutic strategies to combat this pathogen.  ...  For a better visualization a legend of the Voronoi treemaps is shown in Supplementary Figure S5 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2018.02371">doi:10.3389/fmicb.2018.02371</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30386308">pmid:30386308</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6198727/">pmcid:PMC6198727</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vpekmd55tnedrf5ijja6tg6fea">fatcat:vpekmd55tnedrf5ijja6tg6fea</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304082052/http://pdfs.semanticscholar.org/d87c/76e7f1ddac840b4ef30918c6cf0a81585d16.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/d8/7c/d87c76e7f1ddac840b4ef30918c6cf0a81585d16.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2018.02371"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198727" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

Fran Supek, Matko Bošnjak, Nives Škunca, Tomislav Šmuc, Cynthia Gibas
<span title="2011-07-18">2011</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 semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views.  ...  Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and  ...  Introduction Today's high-throughput experiments measure the expression of thousands of genes simultaneously using microarrays, RNA-Seq or various proteomics approaches.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0021800">doi:10.1371/journal.pone.0021800</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21789182">pmid:21789182</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3138752/">pmcid:PMC3138752</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b52krkfyzfdtlm2a6lpf6jul6m">fatcat:b52krkfyzfdtlm2a6lpf6jul6m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191107073437/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3138752&amp;blobtype=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/5f/9e/5f9e7f6d8a87db40ec1e395d57a69bd286af1d41.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0021800"> <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/PMC3138752" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Proteomic Charting of Imipenem Adaptive Responses in a Highly Carbapenem Resistant Clinical Enterobacter roggenkampii Isolate

Suruchi Nepal, Sandra Maaß, Stefano Grasso, Francis M Cavallo, Jürgen Bartel, Dörte Becher, Erik Bathoorn, Jan Maarten van Dijl
<span title="2021-04-28">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7qjwjjvzkje2tjpdspmnfvu4ve" style="color: black;">Antibiotics</a> </i> &nbsp;
for quantitative mass spectrometry.  ...  Our present study was therefore aimed at charting the responses of the E. roggenkampii ST232 isolate to the carbapenem imipenem, using a 'stable isotope labeling of amino acids in cell culture' approach  ...  Figure 3 . 3 Voronoi treemaps presenting the functional categories of all proteins of E. roggenkampii ST232 as identified in our quantitative proteome analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/antibiotics10050501">doi:10.3390/antibiotics10050501</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33924830">pmid:33924830</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gda522m5lbgzfoaaqxx7fnx2x4">fatcat:gda522m5lbgzfoaaqxx7fnx2x4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715040921/https://pure.rug.nl/ws/files/170403492/Proteomic_Charting_of_Imipenem_Adaptive_Responses_in_a_Highly_Carbapenem_Resistant_Clinical_Enterobacter_roggenkampii_Isolate.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/aa/4a/aa4a95cef99b7cd95fc5d31f9c3f4ee67f3357df.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/antibiotics10050501"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Genomic Analysis of Intrinsically Disordered Proteins in the Genus Camelus

Manal A. Alshehri, Manee M. Manee, Mohamed B. Al-Fageeh, Badr M. Al-Shomrani
<span title="2020-06-03">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
Our findings indicate that the human proteome is more disordered than the Camelus proteome.  ...  The study includes the prediction of disordered proteins/regions in Camelus species and in humans using multiple state-of-the-art prediction tools.  ...  as a treemap ( Figure 5 ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21114010">doi:10.3390/ijms21114010</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32503351">pmid:32503351</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7312968/">pmcid:PMC7312968</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/okuauy4nxnc2nhl5mmycgwomxq">fatcat:okuauy4nxnc2nhl5mmycgwomxq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201103154755/https://res.mdpi.com/d_attachment/ijms/ijms-21-04010/article_deploy/ijms-21-04010-v2.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/b4/0d/b40d0c202f8ee51e71b499b22e842a3befc6d28c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21114010"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7312968" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Allicin inhibits SARS-CoV-2 replication and abrogates the antiviral host response in the Calu-3 proteome [article]

Kirstin Mösbauer, Verena Nadin Fritsch, Lorenz Adrian, Jörg Bernhardt, Martin Clemens Horst Gruhlke, Alan John Slusarenko, Daniela Niemeyer, Haike Antelmann
<span title="2021-05-16">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Proteome analyses of infected Calu-3 cells revealed a strong induction of the antiviral interferon-stimulated gene (ISG) signature (e.g. cGAS, Mx1, IFIT, IFIH, IFI16, IFI44, OAS and ISG15), pathways of  ...  Allicin abrogated the ISG host response and reverted the host cellular pathways to levels of uninfected Calu-3 cells, confirming the antiviral and immunomodulatory activity of allicin in the host proteome  ...  The treemaps visualize the following proteome changes: A) SARS-CoV-2 infection/ Mock, B) SARS-CoV-2 infection + Allicin/ Mock and D) SARS-CoV-2 infection -/ + Allicin.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.15.444275">doi:10.1101/2021.05.15.444275</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ojwsy5e2crbsfnhnut7w2kqwom">fatcat:ojwsy5e2crbsfnhnut7w2kqwom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210707171520/https://www.biorxiv.org/content/biorxiv/early/2021/05/16/2021.05.15.444275.full.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.15.444275"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Phosphoproteomics reveals network rewiring to a pro-adhesion state in annexin-1-deficient mammary epithelial cells

Asfa Alli-Shaik, Sheena Wee, Lina H. K. Lim, Jayantha Gunaratne
<span title="">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jbglhnqkwfee7n3dmmcag7huuu" style="color: black;">Breast Cancer Research</a> </i> &nbsp;
Methods: Quantitative phosphoproteomics analysis of mammary gland epithelial cells derived from ANXA1-heterozygous and ANXA1-deficient mice was carried out using stable isotope labeling with amino acids  ...  Comparative analysis of regulated global proteome and phosphoproteome highlighted key differences in translational and post-translational effects of ANXA1, and suggested closely coordinated rewiring of  ...  The predicted transcription factors that were significantly enriched (p value <0.05) were visualized using the Treemap package from R.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13058-017-0924-4">doi:10.1186/s13058-017-0924-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29233185">pmid:29233185</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5727667/">pmcid:PMC5727667</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/byuhloabgjedjgjkmt5jqtwpsq">fatcat:byuhloabgjedjgjkmt5jqtwpsq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720005156/https://breast-cancer-research.biomedcentral.com/track/pdf/10.1186/s13058-017-0924-4?site=breast-cancer-research.biomedcentral.com" 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/0e/f0/0ef04cb990119457f212ba81724b579c1ecb892c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13058-017-0924-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727667" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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