Proteomic tools

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(PAGE UNDER CONSTRUCTION)

General organization

A total of 492 files, 150 absolute value data, 342 relative expression data, were created and integrated in the Listeriomics website. For every experiment, relative expression data were always available whereas absolute expression data was found only in a quarter of the data.


Transcriptomic database

We downloaded the 64 Listeria related ArrayExpress experiments in MAGE-TAB standard. Every MAGE-TAB file included an IDF (Investigation Description Format) file giving general information about the experiment, SDRF (Sample and Data Relationship Format) file giving data relationship, and processed data. We manually curated every SDRF file and integrated the different information about the data.

ID</td><td>Pubmed Accession</td><td>Title</td><td>Day/Month/Year</td><td>Processed Data</td><td>Comment</td> <tr>1</td><td>15378702</td><td>Two-dimensional electrophoresis database of Listeria monocytogenes EGDe proteome and proteomic analysis of mid-log and stationary growth phase cells.</td><td>08/03/2004</td><td>http://onlinelibrary.wiley.com/doi/10.1002/pmic.200300841/abstract</td><td></td></tr> <tr>2</td><td>15838904</td><td>Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species.</td><td>10/09/2004</td><td>http://onlinelibrary.wiley.com/doi/10.1002/pmic.200401024/abstract</td><td></td></tr> <tr>3</td><td>15627966</td><td>Analysis of the Listeria cell wall proteome by two-dimensional nanoliquid chromatography coupled to mass spectrometry.</td><td>24/06/2004</td><td>http://onlinelibrary.wiley.com/doi/10.1002/pmic.200400936/abstract</td><td></td></tr> <tr>4</td><td>15966022</td><td>"""LaneSpector"", a tool for membrane proteome profiling based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis/liquid chromatography-tandem mass spectrometry analysis: application to Listeria monocytogenes membrane proteins."</td><td>10/06/2005</td><td>http://onlinelibrary.wiley.com/doi/10.1002/elps.200410348/abstract</td><td></td></tr> <tr>5</td><td>16381897</td><td>LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.</td><td>08/10/2005</td><td>http://nar.oxfordjournals.org/content/34/suppl_1/D402.long</td><td></td></tr> <tr>6</td><td>18836007</td><td>Comparative analysis of extracellular and intracellular proteomes of Listeria monocytogenes strains reveals a correlation between protein expression and serovar.</td><td>10/12/2008</td><td>http://aem.asm.org/content/74/23/7399.long</td><td>Cannot processed data has it is a mix of strains</td></tr> <tr>7</td><td>18065622</td><td>Proteomic analyses of a Listeria monocytogenes mutant lacking sigmaB identify new components of the sigmaB regulon and highlight a role for sigmaB in the utilization of glycerol.</td><td>10/02/2008</td><td>http://aem.asm.org/content/74/3/594.long</td><td></td></tr> <tr>8</td><td>19834917</td><td>Isolation and 2-D-DIGE proteomic analysis of intracellular and extracellular forms of Listeria monocytogenes.</td><td>10/12/2009</td><td>http://onlinelibrary.wiley.com/doi/10.1002/pmic.200900503/abstract</td><td></td></tr> <tr>9</td><td>19028911</td><td>Comparative proteomic analysis of Listeria monocytogenes strains F2365 and EGD.</td><td>10/01/2009</td><td>http://aem.asm.org/content/75/2/366.long</td><td></td></tr> <tr>10</td><td>19694553</td><td>Differential expression of proteins in Listeria monocytogenes under thermotolerance-inducing, heat shock, and prolonged heat shock conditions.</td><td>10/11/2009</td><td>http://online.liebertpub.com/doi/abs/10.1089/fpd.2009.0286?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed</td><td></td></tr> <tr>11</td><td>20620249</td><td>Proteomics for the elucidation of cold adaptation mechanisms in Listeria monocytogenes.</td><td>23/06/2010</td><td>http://www.sciencedirect.com/science/article/pii/S1874391910001892</td><td></td></tr> <tr>12</td><td>21350852</td><td>Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms.</td><td>25/02/2011</td><td>http://link.springer.com/article/10.1007%2Fs00253-011-3172-z</td><td>No data available, and the strain used is not sequenced</td></tr> <tr>13</td><td>21605710</td><td>Proteomic expression profiles of virulent and avirulent strains of Listeria monocytogenes isolated from macrophages.</td><td>11/05/2011</td><td>http://www.sciencedirect.com/science/article/pii/S1874391911001990</td><td></td></tr> <tr>14</td><td>22526570</td><td>Carbon catabolite control is important for Listeria monocytogenes biofilm formation in response to nutrient availability.</td><td>10/07/2012</td><td>http://link.springer.com/article/10.1007%2Fs00284-012-0125-4</td><td></td></tr> <tr>15</td><td>23558187</td><td>Listeria monocytogenes dairy isolates show a different proteome response to sequential exposure to gastric and intestinal fluids.</td><td>14/03/2013</td><td>http://www.sciencedirect.com/science/article/pii/S0168160513001219</td><td>Cannot processed data has it is a mix of strains</td></tr> <tr>16</td><td>23970489</td><td>Proteomic identification of Listeria monocytogenes surface-associated proteins.</td><td>20/07/2013</td><td>http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200449/abstract</td><td></td></tr> <tr>18</td><td>24564473</td><td>Proteomic analysis of cross protection provided between cold and osmotic stress in Listeria monocytogenes.</td><td>24/02/2014</td><td>http://pubs.acs.org/doi/abs/10.1021/pr401004a</td><td></td></tr> <tr>17</td><td>23977379</td><td>Transcription Factor ?B Plays an Important Role in the Production of Extracellular Membrane-Derived Vesicles in Listeria monocytogenes</td><td>20/08/2013</td><td>http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073196</td><td></td></tr> <tr>19</td><td>25056936</td><td>A systematic proteomic analysis of Listeria monocytogenes house-keeping protein secretion systems.</td><td>13/11/2014</td><td>http://www.mcponline.org/content/13/11/3063.long</td><td></td></tr> <tr>20</td><td>25516393</td><td>Attached and Planktonic Listeria monocytogenes Global Proteomic Responses and Associated Influence of Strain Genetics and Temperature.</td><td>09/01/2015</td><td>http://pubs.acs.org/doi/suppl/10.1021/pr501114e</td><td></td></tr> <tr>21</td><td>25578509</td><td>Comparison of five methods for direct extraction of surface proteins from Listeria monocytogenes for proteomic analysis by orbitrap mass spectrometry</td><td>09/01/2015</td><td>http://www.sciencedirect.com/science/article/pii/S0167701215000056</td><td></td></tr> <tr>22</td><td>21846725</td><td>Association of ActA to peptidoglycan revealed by cell wall proteomics of intracellular Listeria monocytogenes.</td><td>16/12/2011</td><td>http://www.jbc.org/cgi/pmidlookup?view=long&pmid=21846725</td><td></td></tr> <tr>23</td><td>23657685</td><td>Occurrence of mutations impairing sigma factor B (SigB) function upon inactivation of Listeria monocytogenes genes encoding surface proteins.</td><td>08/05/2013</td><td>http://mic.sgmjournals.org/cgi/pmidlookup?view=long&pmid=23657685</td><td></td></tr> <tr>24</td><td>20839850</td><td>Comprehensive appraisal of the extracellular proteins from a monoderm bacterium: theoretical and empirical exoproteomes of Listeria monocytogenes EGD-e by secretomics.</td><td>01/10/2010</td><td>http://pubs.acs.org/doi/abs/10.1021/pr1003642</td><td></tr></td></tr> <tr>25</td><td>23291529</td><td>Exoproteomic analysis of the SecA2-dependent secretion in Listeria monocytogenes EGD-e.</td><td>27/03/2013</td><td>http://www.sciencedirect.com/science/article/pii/S1874391912007968</td><td></td></tr> <tr>26</td><td>22912771</td><td>Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses.</td><td>09/08/2012</td><td>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415414/</td><td></td></td></tr> </table>
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