Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper
Visit source
Download RO-Crateversion 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
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
masterf5af0bb
5.0 (earliest) Created 25th Jun 2024 at 11:03 by Helena Rasche
Added/updated 4 files
Frozen
5.02b2881d
Creators and Submitter
Views: 614 Downloads: 175
Created: 25th Jun 2024 at 11:03
Last updated: 25th Jun 2024 at 11:03
Tags AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
