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annotate README.rst @ 11:6e85f07c20ee draft

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date Wed, 13 Mar 2019 09:30:12 -0400
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1 Wrapper for Get expression profiles by tissue Tool
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2 =================================================
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4 **Authors**
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6 David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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14 -------------------------------------------------
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16 This tool retrieve information from Human Protein Atlas (https://www.proteinatlas.org/) regarding the expression profiles of human genes both on the mRNA and protein level.
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18 A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file), if it's not the case, please use the ID_Convert tool from ProteoRE.
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20 The resources from Human Protein Atlas that can be queried are the following:
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22 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays.
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24 The tab-separated file includes Ensembl gene identifier ("Gene"), tissue name ("Tissue"), annotated cell type ("Cell type"), expression value ("Level"), and the gene reliability of the expression value ("Reliability").
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26 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
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28 * **Human tumor tissue data**: staining profiles for proteins in human tumor tissue based on immunohistochemisty using tissue micro arrays and log-rank P value for Kaplan-Meier analysis of correlation between mRNA expression level and patient survival.
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30 The tab-separated file includes Ensembl gene identifier ("Gene"), gene name ("Gene name"), tumor name ("Cancer"), the number of patients annotated for different staining levels ("High", "Medium", "Low" & "Not detected") and log-rank p values for patient survival and mRNA correlation ("prognostic - favourable", "unprognostic - favourable", "prognostic - unfavourable", "unprognostic - unfavourable").
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32 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.