Galaxy | ProteoRE | Accessible Workflow | ProteoRE_ProteomeAnnotation_Tutorial (release 1.1)

ProteoRE_ProteomeAnnotation_Tutorial (release 1.1)

Annotation:

Step	Annotation
Step 1: Input dataset Lacombe_et_al_2017.txt select at runtime
Step 2: Input dataset Bredberg.txt select at runtime
Step 3: Input dataset Mucilli.txt select at runtime
Step 4: Retrieve tissue-specific expression data Please choose experimental data source (antibody- or RNAseq-based) Expression profiles based on immunohistochemisty Select tissue by clicking the dropdown menu below Bronchus Lung Expression level High Medium Low Reliability score Enhanced Supported
Step 5: Filter by keywords or numerical value Input file Output dataset 'output' from step 1 Does your input file contain header? True Please select an operator to combine your filters (if more than one) OR If you want to sort the result files by values from a column, please enter a column number Empty. Sort in descending order ? False Filter by keywords Filter by keywords 1 Please specify the column number of the input file on which you want to apply the filter c1 Would you like to search for exact match? False Filter by keyword Enter keywords (copy/paste) Copy/paste keywords to be filtered out P04264;P35908;P13645; Q5D862 ;Q5T749; Q8IW75;P81605;P22531; P59666; P78386 Filter by values Filter by range of values
Step 6: ID Converter Enter IDs Input file containing IDs Select your file Output dataset 'output' from step 4 Does file contain header? True Column number of IDs to map c1 Species Human (Homo sapiens) Release /home/proteore/galaxy/tool-data/id_mapping/Human_id_mapping_16-06-2021.tsv Type/source of IDs UniProt accession number (e.g. P31946) Target type: Target type of IDs you would like to map to UniProt accession number (e.g. P31946) - reviewed entries only
Step 7: ID Converter Enter IDs Input file containing IDs Select your file Output dataset 'output1' from step 5 Does file contain header? True Column number of IDs to map c1 Species Human (Homo sapiens) Release /home/proteore/galaxy/tool-data/id_mapping/Human_id_mapping_16-06-2021.tsv Type/source of IDs UniProt accession number (e.g. P31946) Target type: Target type of IDs you would like to map to UniProt accession number (e.g. P31946) - reviewed entries only
Step 8: JVenn diagram Lists to compares Lists to compare 1 Please provide your identifiers Input file containing your identifiers Choose a file that contains your list of IDs Output dataset 'output1' from step 5 Does your input file contain header? True Please specify the column where you would like to apply the comparison c1 Please enter the name of this list Lacombe et al Lists to compare 2 Please provide your identifiers Input file containing your identifiers Choose a file that contains your list of IDs Output dataset 'output' from step 2 Does your input file contain header? False Please specify the column where you would like to apply the comparison c1 Please enter the name of this list Bredberg et al Lists to compare 3 Please provide your identifiers Input file containing your identifiers Choose a file that contains your list of IDs Output dataset 'output' from step 3 Does your input file contain header? False Please specify the column where you would like to apply the comparison c1 Please enter the name of this list Mucilli et al
Step 9: Add expression data HPA source file version /home/proteore/galaxy/tool-data/protein_atlas/HPA_full_atlas_14-06-2024.tsv No value found for 'HPA source file version'. Using default: '/home/proteore/galaxy/tool-data/protein_atlas/HPA_full_atlas_14-06-2024.tsv'. Enter your IDs (Ensembl gene IDs only, e.g. ENSG00000064787) Input file containing your IDs Select your file Output dataset 'output' from step 7 Column IDs (e.g : Enter c1 if ENSG ID are in column n°1) c4 Does file contain header? True RNAseq/Ab-based expression data: Select information to add to your list Gene name
Step 10: Filter by keywords or numerical value Input file Output dataset 'output' from step 9 Does your input file contain header? True Please select an operator to combine your filters (if more than one) OR If you want to sort the result files by values from a column, please enter a column number Empty. Sort in descending order ? False Filter by keywords Filter by keywords 1 Please specify the column number of the input file on which you want to apply the filter c8 Would you like to search for exact match? False Filter by keyword Enter keywords (copy/paste) Copy/paste keywords to be filtered out salivary Filter by values Filter by range of values
Step 11: Reactome Input identifiers (Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157) or gene name (e.g. AQP7) Input file containing your identifiers Input file containing your identifiers Output dataset 'output1' from step 10 Does your input file contain header? True Please specify the column number where are your IDs (e.g : Enter c1 for column n°1) c1
Step 12: Classification and enrichment analysis Enter your IDs (UniProt Accession number or Gene ID) Input file containing your IDs Choose a file that contains your list of IDs Output dataset 'output1' from step 10 Does file contain header? True Column number of IDs c1 Select type/source of IDs UniProt accession number (e.g. P31946) Species Human (Homo sapiens) parameter 'species': an invalid option (u'human') was selected (valid options: org.Hs.eg.db,org.Rn.eg.db,org.Mm.eg.db) Using default: 'org.Hs.eg.db'. Select GO terms category Cellular Component Biological Process Molecular Function Perform GO categories representation analysis? True Ontology level (the higher this number, the deeper the GO level, up to 3) 3 Perform GO categories enrichment analysis? True P-value cut off 0.01 Q-value cut off 0.05 Define your own background IDs? True Enter your background IDs (UniProt Accession number or Entrez Gene ID) Input file containing your background IDs Select file that contains your background IDs list Output dataset 'output' from step 6 Does file contain header? True Column number of IDs c7 Select type of IDs of your background UniProt Accession number Graphical display dot-plot

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