Mercurial > repos > proteore > proteore_expression_levels_by_tissue
comparison sel_ann_hpa.xml @ 4:f294fd77b143 draft
planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
| author | proteore |
|---|---|
| date | Wed, 14 Mar 2018 12:22:51 -0400 |
| parents | d7f909ae24d9 |
| children | f7e93829327e |
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| 3:d7f909ae24d9 | 4:f294fd77b143 |
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| 49 </param> | 49 </param> |
| 50 </when> | 50 </when> |
| 51 <when value="file" > | 51 <when value="file" > |
| 52 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of ENSG IDs" help="" /> | 52 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of ENSG IDs" help="" /> |
| 53 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> | 53 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> |
| 54 <param name="ncol" type="text" label="The column number of ENSG IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> | 54 <param name="ncol" type="text" value="c1" label="The column number of ENSG IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> |
| 55 </when> | 55 </when> |
| 56 </conditional> | 56 </conditional> |
| 57 <conditional name="options"> | 57 <conditional name="options"> |
| 58 <param name="database" type="select" label="Human Protein Atlas (data from normal or tumor tissue)"> | 58 <param name="database" type="select" label="Human Protein Atlas (data from normal or tumor tissue)"> |
| 59 <option value="normal">Human Normal Tissue</option> | 59 <option value="normal">Human Normal Tissue</option> |
| 66 <column name="value" index="2" /> | 66 <column name="value" index="2" /> |
| 67 <filter type="remove_value" meta_ref="proteinatlas" key="name" value="Full Human Protein Atlas" /> | 67 <filter type="remove_value" meta_ref="proteinatlas" key="name" value="Full Human Protein Atlas" /> |
| 68 <filter type="remove_value" meta_ref="proteinatlas" key="name" value="HPA Tumor Tissue" /> | 68 <filter type="remove_value" meta_ref="proteinatlas" key="name" value="HPA Tumor Tissue" /> |
| 69 </options> | 69 </options> |
| 70 </param> | 70 </param> |
| 71 <param name="normal_tissue" type="select" label="Keep and annotate genes present in the following tissue(s)" multiple="True" display="checkboxes" optional="False"> | 71 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False"> |
| 72 <option value="adrenal gland" >Adrenal gland</option> | 72 <option value="adrenal gland" >Adrenal gland</option> |
| 73 <option value="appendix" >Appendix</option> | 73 <option value="appendix" >Appendix</option> |
| 74 <option value="bone marrow" >Bone marrow</option> | 74 <option value="bone marrow" >Bone marrow</option> |
| 75 <option value="breast" >Breast</option> | 75 <option value="breast" >Breast</option> |
| 76 <option value="bronchus" >Bronchus</option> | 76 <option value="bronchus" >Bronchus</option> |
| 116 <option value="thyroid gland" >Thyroid gland</option> | 116 <option value="thyroid gland" >Thyroid gland</option> |
| 117 <option value="tonsil" >Tonsil</option> | 117 <option value="tonsil" >Tonsil</option> |
| 118 <option value="urinary bladder" >Urinary bladder</option> | 118 <option value="urinary bladder" >Urinary bladder</option> |
| 119 <option value="vagina" >Vagina</option> | 119 <option value="vagina" >Vagina</option> |
| 120 </param> | 120 </param> |
| 121 <param name="level" type="select" label="Expression value" display="checkboxes" multiple="True" optional="False"> | 121 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False"> |
| 122 <option value="High" selected="true">High</option> | 122 <option value="High" selected="true">High</option> |
| 123 <option value="Medium" selected="true">Medium</option> | 123 <option value="Medium">Medium</option> |
| 124 <option value="Low" selected="true">Low</option> | 124 <option value="Low">Low</option> |
| 125 <option value="Not detected" selected="true">Not detected</option> | 125 <option value="Not detected">Not detected</option> |
| 126 </param> | 126 </param> |
| 127 <param name="reliability" type="select" label="The gene reliability of the expression value" display="checkboxes" multiple="True" optional="False"> | 127 <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False"> |
| 128 <option value="Approved" selected="true">Approved</option> | 128 <option value="Enhanced" selected="true">Enhanced</option> |
| 129 <option value="Supported" selected="true">Supported</option> | 129 <option value="Supported" selected="true">Supported</option> |
| 130 <option value="Uncertain" selected="true">Uncertain</option> | 130 <option value="Approved">Approved</option> |
| 131 <option value="Uncertain">Uncertain</option> | |
| 131 </param> | 132 </param> |
| 132 </when> | 133 </when> |
| 133 <when value="tumor"> | 134 <when value="tumor"> |
| 134 <param name="proteinatlas" type="select" label="Human Protein Atlas" > | 135 <param name="proteinatlas" type="select" label="Human Protein Atlas" > |
| 135 <options from_file="proteinatlas.loc" > | 136 <options from_file="proteinatlas.loc" > |
| 186 <param name="not_mapped" value="true" /> | 187 <param name="not_mapped" value="true" /> |
| 187 <output name="hpa_output" file="Expres_levels_Lacombe_et_al_2017_OK.txt"/> | 188 <output name="hpa_output" file="Expres_levels_Lacombe_et_al_2017_OK.txt"/> |
| 188 </test> | 189 </test> |
| 189 </tests> | 190 </tests> |
| 190 <help><![CDATA[ | 191 <help><![CDATA[ |
| 191 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. | 192 This tool retrieve information from Human Protein Atlas (https://www.proteinatlas.org/) |
| 192 | 193 regarding the expression profiles of human genes both on the mRNA and protein level. |
| 193 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. | 194 |
| 195 A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file), | |
| 196 if it's not the case, please use the ID_Convert tool from ProteoRE. | |
| 194 | 197 |
| 195 The resources from Human Protein Atlas that can be queried are the following: | 198 The resources from Human Protein Atlas that can be queried are the following: |
| 196 | 199 |
| 197 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays. | 200 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays. |
| 198 | 201 |
| 203 * **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. | 206 * **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. |
| 204 | 207 |
| 205 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"). | 208 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"). |
| 206 | 209 |
| 207 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38. | 210 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38. |
| 211 | |
| 212 ----- | |
| 213 | |
| 214 **Reliability score** | |
| 215 | |
| 216 Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect | |
| 217 to the definitions from HPA: | |
| 218 | |
| 219 Enhanced - One or several antibodies with non-overlapping epitopes targeting the same gene | |
| 220 have obtained enhanced validation based on orthogonal or independent antibody validation method. | |
| 221 | |
| 222 Supported - Consistency with RNA-seq and/or protein/gene characterization data, | |
| 223 in combination with similar staining pattern if independent antibodies are available. | |
| 224 | |
| 225 Approved - Consistency with RNA-seq data in combination with inconsistency with, or lack of, | |
| 226 protein/gene characterization data. Alternatively, consistency with protein/gene characterization data | |
| 227 in combination with inconsistency with RNA-seq data. If independent antibodies are available, | |
| 228 the staining pattern is partly similar or dissimilar. | |
| 229 | |
| 230 Uncertain - Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, | |
| 231 in combination with dissimilar staining pattern if independent antibodies are available. | |
| 208 | 232 |
| 209 ----- | 233 ----- |
| 210 | 234 |
| 211 .. class:: infomark | 235 .. class:: infomark |
| 212 | 236 |