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      Instant Clue: A Software Suite for Interactive Data Visualization and Analysis

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          Abstract

          The development of modern high-throughput instrumentation and improved core facility infrastructures leads to an accumulation of large amounts of scientific data. However, for a majority of scientists the comprehensive analysis and visualization of their data goes beyond their expertise. To reduce this hurdle, we developed a software suite called Instant Clue that helps scientists to visually analyze data and to gain insights into biological processes from their high-dimensional dataset. Instant Clue combines the power of visual and statistical analytics using a straight forward drag & drop approach making the software highly intuitive. Additionally, it offers a comprehensive portfolio of statistical tools for systematic analysis such as dimensional reduction, (un)-supervised learning, clustering, multi-block (omics) integration and curve fitting. Charts can be combined with high flexibility into a main figure template for direct usage in scientific publications. Even though Instant Clue was developed with the omics-sciences in mind, users can analyze any kind of data from low to high dimensional data sets. The open-source software is available for Windows and Mac OS ( http://www.instantclue.uni-koeln.de) and is accompanied by a detailed video tutorial series.

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            The NumPy array: a structure for efficient numerical computation

            In the Python world, NumPy arrays are the standard representation for numerical data. Here, we show how these arrays enable efficient implementation of numerical computations in a high-level language. Overall, three techniques are applied to improve performance: vectorizing calculations, avoiding copying data in memory, and minimizing operation counts. We first present the NumPy array structure, then show how to use it for efficient computation, and finally how to share array data with other libraries.
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              Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling.

              Regulatory protein phosphorylation controls normal and pathophysiological signaling in eukaryotic cells. Despite great advances in mass-spectrometry-based proteomics, the extent, localization, and site-specific stoichiometry of this posttranslational modification (PTM) are unknown. Here, we develop a stringent experimental and computational workflow, capable of mapping more than 50,000 distinct phosphorylated peptides in a single human cancer cell line. We detected more than three-quarters of cellular proteins as phosphoproteins and determined very high stoichiometries in mitosis or growth factor signaling by label-free quantitation. The proportion of phospho-Tyr drastically decreases as coverage of the phosphoproteome increases, whereas Ser/Thr sites saturate only for technical reasons. Tyrosine phosphorylation is maintained at especially low stoichiometric levels in the absence of specific signaling events. Unexpectedly, it is enriched on higher-abundance proteins, and this correlates with the substrate KM values of tyrosine kinases. Our data suggest that P-Tyr should be considered a functionally separate PTM of eukaryotic proteomes. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                h.nolte@uni-koeln.de
                marcus.krueger@uni-koeln.de
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                23 August 2018
                23 August 2018
                2018
                : 8
                : 12648
                Affiliations
                [1 ]ISNI 0000 0000 8580 3777, GRID grid.6190.e, Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), , University of Cologne, ; Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
                [2 ]ISNI 0000 0000 8580 3777, GRID grid.6190.e, Department of Dermatology, , Center for Molecular Medicine Cologne, University of Cologne, ; 50931 Cologne, Germany
                [3 ]ISNI 0000 0000 8580 3777, GRID grid.6190.e, Center for Molecular Medicine (CMMC), , University of Cologne, ; 50931 Cologne, Germany
                Author information
                http://orcid.org/0000-0002-0473-7320
                Article
                31154
                10.1038/s41598-018-31154-6
                6107636
                30140043
                1dcb4733-f301-4a48-a634-b003e0b3fd28
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 15 May 2018
                : 13 August 2018
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