Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper

Workflow Type: Galaxy

version 1.0, 160318, published at https://github.com/Stortebecker/secretome_prediction

Associated Tutorial

This workflows is part of the tutorial Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper, available in the GTN

Thanks to...

Tutorial Author(s): Florian Christoph Sigloch, Björn Grüning

gtn star logo followed by the word workflows

Steps

ID Name Description
3 UniProt Retrieves Fasta files for all proteins in the input list. toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1
4 Select Removes comment lines at the head of the Uniprot Go database file. Grep1
5 Get subontology from a given OBO term GO:0043230 "extracellular organelle" get_subontology_from
6 Get subontology from a given OBO term GO:0005576 "extracellular region" get_subontology_from
7 Get subontology from a given OBO term GO:0005887 "integral component of plasma membrane" get_subontology_from
8 Get subontology from a given OBO term GO:0009986 "cell surface" get_subontology_from
9 Get subontology from a given OBO term GO:0005764 "lysosome" get_subontology_from
10 WoLF PSORT Predicts subcellular localization of all proteins in the input list. toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.8
11 Join Annotates input protein list with GO annotations. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0
12 Get all the term IDs and term names of a given OBO ontology GO:0043230 "extracellular organelle" term_id_vs_term_name
13 Get all the term IDs and term names of a given OBO ontology GO:0005576 "extracellular region" term_id_vs_term_name
14 Get all the term IDs and term names of a given OBO ontology GO:0005887 "integral component of plasma membrane" term_id_vs_term_name
15 Get all the term IDs and term names of a given OBO ontology GO:0009986 "cell surface" term_id_vs_term_name
16 Get all the term IDs and term names of a given OBO ontology GO:0005764 "lysosome" term_id_vs_term_name
17 Filter Filters all proteins that are predicted to reside extracellularly. Filter1
18 Filter Filters all proteins that are predicted to reside in lysosomes. Filter1
19 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0
20 Join Combines all GO annotations for "integral to plasma membrane" and "cell surface" toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0
21 Join Combines all proteins in the input list that are predicted by WolfPsort to be lysosomal and/or extracellular. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0
22 Join Combines all GO annotations for "extracellular region", "integral to plasma membrane" and "cell surface" excluding "extracellular organelle" toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0
23 Convert Extracts uniprot accessions from all proteins in the input list that are predicted by WolfPsort to be lysosomal and/or extracellular. Convert characters1
24 Join Combines all GO annotations for "lysosome", "extracellular region", "integral to plasma membrane" and "cell surface" excluding "extracellular organelle" toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0
25 Cut Deletes all columns but the one containing uniprot accessions of extracellular proteins as predicted by WoLF PSORT. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0
26 Compare two Datasets filters out all proteins in the input protein list of interest that are annotated as "extracellular region" and "lysosome" and "plasma membrane" excluding "extracellular organelle" and "cytoplasmic side of plasma membrane" comp1
27 Unique cleans up the protein list for unique entries toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3
28 Cut Deletes all columns but the one containing uniprot accessions of secreted and shed (i.e. "secretome") proteins. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0
29 Join Combines all proteins that are either predicted by WoLF PSORT to be shed or secreted or annotated in the GO database to be shed or secreted. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0
30 Unique Final output. Unique entries of all proteins that are either predicted by WoLF PSORT to be shed or secreted or annotated in the GO database to be shed or secreted. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0

Version History

3.0 (latest) Created 16th Jul 2024 at 14:07 by Helena Rasche

Added/updated 4 files


Open master f5af0bb

5.0 (earliest) Created 25th Jun 2024 at 11:03 by Helena Rasche

Added/updated 4 files


Frozen 5.0 2b2881d
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Views: 569   Downloads: 167

Created: 25th Jun 2024 at 11:03

Last updated: 25th Jun 2024 at 11:03

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