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date Tue, 18 Dec 2018 09:48:29 -0500
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1 Wrapper for Get expression data by tissue Tool 1 Wrapper for Get expression profiles by tissue Tool
2 ================================================= 2 =================================================
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4 **Authors** 4 **Authors**
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6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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14 ------------------------------------------------- 14 -------------------------------------------------
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16 This tool retrieve information from Human Protein Atlas (https://www.proteinatlas.org/) 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.
17 regarding the expression profiles of human genes both on the mRNA and protein level.
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19 A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file), 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.
20 if it's not the case, please use the ID_Convert tool from ProteoRE.
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22 The resources from Human Protein Atlas that can be queried are the following: 20 The resources from Human Protein Atlas that can be queried are the following:
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24 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays. 22 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays.
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30 * **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. 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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32 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"). 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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34 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38. 32 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
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36 -----
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38 **Reliability score**
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40 Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect
41 to the definitions from HPA:
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43 Enhanced - One or several antibodies with non-overlapping epitopes targeting the same gene
44 have obtained enhanced validation based on orthogonal or independent antibody validation method.
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46 Supported - Consistency with RNA-seq and/or protein/gene characterization data,
47 in combination with similar staining pattern if independent antibodies are available.
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49 Approved - Consistency with RNA-seq data in combination with inconsistency with, or lack of,
50 protein/gene characterization data. Alternatively, consistency with protein/gene characterization data
51 in combination with inconsistency with RNA-seq data. If independent antibodies are available,
52 the staining pattern is partly similar or dissimilar.
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54 Uncertain - Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data,
55 in combination with dissimilar staining pattern if independent antibodies are available.