Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

annotate README.rst @ 10:07858c6dbbff draft

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author proteore
date Wed, 22 Jan 2020 15:26:11 +0000
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1 Wrapper for Add expression data to your protein list Tool
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2 =========================================================
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3 **Authors**
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5 Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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7 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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9 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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11 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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13 ---------------------------------------------------------
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15 This tool adds expression information (RNAseq- or antibody-based experiments) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your protein list.
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17 **Input**
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19 Input can be either a list of Ensembl gene ids (copy/paste) or a file containing multiple fields but with **at least one column of Ensembl gene IDs**. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs.
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21 **Databases**
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23 HPA source file: http://www.proteinatlas.org/download/proteinatlas.tab.gz
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25 **Annotation**
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27 - Gene name: according to the HGNC (Hugo Gene Nomenclature Committee)
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29 - Gene description: entry description (full text)
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31 - Evidence: at protein level, at transcript level or no evidence
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33 - Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF
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35 - RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna .
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37 - IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .
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39 - IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih .
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41 - Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa
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43 - RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts.
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45 - RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
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47 **Outputs**
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49 The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose.