Galaxy | ProteoRE | Published Workflow | Tutorial_ProteoRE_ProteinList_Annotation (release 2.0)

Tutorial_ProteoRE_ProteinList_Annotation (release 2.0)

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: Filter by keywords and/or numerical value Input file Output dataset 'output' from step 1 Does file contain header? True Operation Discard Select an operator to combine your filters (if more than one) OR Filter by keywords Filter by keywords 1 Column number on which to apply the filter c1 Search for exact match? False Enter keywords copy/paste Copy/paste keywords to find (keep or discard) P04264 P35908 P13645 Q5D862 Q5T749 Q8IW75 P81605 P22531 P59666 P78386 Filter by numerical values Filter by range of numerical values Sort by column ? False
Step 5: ID Converter Enter IDs Input file containing IDs Select your file Output dataset 'kept_lines' 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 Ensembl gene ID (e.g. ENSG00000166913)
Step 6: Venn diagram List to compares List to compare 1 Enter your list Input file containing your list Select your file Output dataset 'kept_lines' from step 4 Does file contain header? True Column number on which apply the comparison c1 Enter the name of this list Lacombe et al List to compare 2 Enter your list Input file containing your list Select your file Output dataset 'output' from step 2 Does file contain header? True Column number on which apply the comparison c1 Enter the name of this list Bredberg et al List to compare 3 Enter your list Input file containing your list Select your file Output dataset 'output' from step 3 Does file contain header? True Column number on which apply the comparison c1 Enter the name of this list Mucilli et al
Step 7: Add expression data HPA source file version /home/proteore/galaxy/tool-data/protein_atlas/HPA_full_atlas_17-06-2021.tsv Enter your IDs (Ensembl gene IDs only, e.g. ENSG00000064787) Input file containing your IDs Select your file Output dataset 'output' from step 5 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 Gene description RNA tissue category RNA tissue specificity abundance in 'Transcript Per Million'
Step 8: Filter by keywords and/or numerical value Input file Output dataset 'output' from step 7 Does file contain header? True Operation Discard Select an operator to combine your filters (if more than one) OR Filter by keywords Filter by keywords 1 Column number on which to apply the filter c8 Search for exact match? False Enter keywords copy/paste Copy/paste keywords to find (keep or discard) salivary Filter by numerical values Filter by range of numerical values Sort by column ? False
Step 9: 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 'kept_lines' from step 8 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) 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? False Graphical display dot-plot
Step 10: Pathway enrichment analysis Input IDs (UniProt Accession number, Entrez Gene ID, Gene Name) Input file containing your IDs Input file containing your IDs Output dataset 'kept_lines' from step 8 Does file contain header? True Column number of IDs (e.g : Enter c1 for column n°1) c1 Species (human, mouse, rat) Human (Homo sapiens)

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