Galaxy | ProteoRE | Published Workflow | Workflow constructed from history 'MiMB_GO_Protocol_ProteoRE_2021'

Workflow constructed from history 'MiMB_GO_Protocol_ProteoRE_2021'

Step	Annotation
Step 1: Input dataset BreastCancer_DE_S4_Pozniak_MiMB.txt select at runtime
Step 2: Input dataset BreastCancer_Background_S2_Pozniak_MiMB.tab select at runtime
Step 3: ID Converter Enter IDs Input file containing IDs Select your file Output dataset 'output' from step 1 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_24-08-2020.tsv Type/source of IDs Gene Name (e.g. YWHAB) Target type: Target type of IDs you would like to map to UniProt accession number (e.g. P31946) - reviewed entries only Entrez gene ID (e.g. 7529) Ensembl gene ID (e.g. ENSG00000166913)
Step 4: ID Converter Enter IDs Input file containing IDs Select your file Output dataset 'output' from step 2 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_24-08-2020.tsv Type/source of IDs Gene Name (e.g. YWHAB) Target type: Target type of IDs you would like to map to UniProt accession number (e.g. P31946) - reviewed entries only Entrez gene ID (e.g. 7529) Ensembl gene ID (e.g. ENSG00000166913)
Step 5: Filter by keywords and/or numerical value Input file Output dataset 'output' from step 3 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 c5 Search for exact match? True Enter keywords copy/paste Copy/paste keywords to find (keep or discard) NA Filter by numerical values Filter by range of numerical values Sort by column ? False
Step 6: Add protein features Enter your IDs (neXtProt or UniProt; e.g. NX_P05090 or P05090) Input file containing your IDs Select your file Output dataset 'kept_lines' from step 5 Column IDs (e.g : Enter c1 for column n°1) c5 Does input file have header? True Type of IDs UniProt accession number Features/Annotation Number of transmembrane domains Subcellular Location Pathway(s) Release of neXtProt reference file to use tool-data/nextprot_ref_31-07-2020.tsv
Step 7: Enrichment analysis Enter your IDs (Ensembl Gene Id) Input file containing your IDs Select your file Output dataset 'kept_lines' from step 5 Column number of IDs c7 Does file contain header? True Use your own background (ID list) ? True Enter your background IDs (Ensembl gene IDs) Input file containing your background IDs Select file that contains your background IDs list Output dataset 'output' from step 4 Does file contain header ? True Column number of IDs c4 Species (human, mouse, rat) Human (Homo sapiens) GO terms category Biological Process Select GO scoring method (read user doc section) Classic Fisher test p-value threshold (e.g : 1e-3) 1e-15 Multiple testing procedure (p-value adjustment) Benjamini and Hochberg Graphical display dot-plot
Step 8: Enrichment analysis Enter your IDs (Ensembl Gene Id) Input file containing your IDs Select your file Output dataset 'kept_lines' from step 5 Column number of IDs c7 Does file contain header? True Use your own background (ID list) ? True Enter your background IDs (Ensembl gene IDs) Input file containing your background IDs Select file that contains your background IDs list Output dataset 'output' from step 4 Does file contain header ? True Column number of IDs c4 Species (human, mouse, rat) Human (Homo sapiens) GO terms category Biological Process Select GO scoring method (read user doc section) Weight01 p-value threshold (e.g : 1e-3) 1e-5 Multiple testing procedure (p-value adjustment) Benjamini and Hochberg Graphical display dot-plot
Step 9: Filter by keywords and/or numerical value Input file Output dataset 'kept_lines' from step 5 Does file contain header? True Operation Keep 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 c4 Search for exact match? False Enter keywords copy/paste Copy/paste keywords to find (keep or discard) upregulated Filter by numerical values Filter by range of numerical values Sort by column ? False
Step 10: Biological theme comparison List to compares List to compare 1 Enter your ID list (Entrez gene ID, e.g. 2810) Input file containing your list of IDs Choose a file that contains your list of IDs Output dataset 'kept_lines' from step 9 Does file contain header? True Column number of IDs c6 name of your list Up List to compare 2 Enter your ID list (Entrez gene ID, e.g. 2810) Input file containing your list of IDs Choose a file that contains your list of IDs Output dataset 'discarded_lines' from step 9 Does file contain header? True Column number of IDs c6 name of your list Down Species Human (Homo sapiens) Select GO terms category Biological Process

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yvdb

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