Mercurial > repos > proteore > proteore_expression_levels_by_tissue
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author | proteore |
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date | Fri, 16 Feb 2018 04:22:54 -0500 |
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1 Wrapper for Expression levels by tissue tool | |
2 ========================= | |
3 | |
4 **Authors** | |
5 | |
6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | |
7 | |
8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform | |
9 | |
10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | |
11 | |
12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. | |
13 | |
14 ========================= | |
15 | |
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 | |
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. | |
19 | |
20 The resources from Human Protein Atlas that can be queried are the following: | |
21 | |
22 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays. | |
23 | |
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. | |
27 | |
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. | |
29 | |
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. |