|
Size: 571
Comment:
|
Size: 2198
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| # Cell-Cell Interactions | = Cell-Cell Interactions = <<TableOfContents(5)>> == Overview == Cell-Cell interactions were computed by a similar method as described by Qiao et al([[ref1|1]]). Using a set of proteins designated as receptors, and ligands defined with a set of GO terms and other data sources calculate the set of interactions that represent cell-cell interactions (for example Ligand-receptor, receptor-receptor, ...). This analysis is not limited to Cell-Cell interactions. You can define your own protein types, either manually or by choosing different go terms, and create your customized protein-protein interaction network. |
| Line 5: | Line 9: |
| ## Overview | {{attachment:ligand_receptor_flowchart.png|Network creation flowchart|align="center"}} |
| Line 7: | Line 11: |
| Using a set of proteins designated as receptors, and ligands defined with a set of GO terms calculate the set of interactions that represent cell-cell interactions (for example Ligand-receptor, receptor-receptor, ...). This analysis is not limited to Cell-Cell interactions. You can define your own protein types, either manually or by choosing different go terms, and create your customized protein-protein interaction network. | == Defining Receptor and Ligands == Receptor genes were defined based on 1. a set of GO terms: * GO:0043235 - receptor complex, * GO:0008305 - integrin complex, * GO:0072657 - protein localized to membrane * GO:0043113 - receptor clustering * GO:0004872 -receptor activity, * GO:0009897 - external side of plasma membrane) 1. Uniprot annotations * search term -"Receptor [KW-0675]" go:0005886 organism:human. |
| Line 9: | Line 23: |
| {{attachment:ligand_receptor_flowchart.png|Network creation flowchart}}<<BR>> | Ligand genes were defined based on 1. the GO terms: * GO:0005102 - receptor binding 1. the set of proteins labelled as secreted in the Secretome dataset (http://www.proteinatlas.org/humanproteome/secretome)[PMID:: 25613900]. '''Receptor and ligand lists were further manually curated''' * removing genes that were neither receptors or ligands and * moving misclassified genes were moved to the correct list (i.e. receptors found on the ligand list or vice versa) Using the curated list of receptors and ligands interactions from irefindex (version 14)[PMID:18823568] were filtered to only included interaction that contained receptor-ligand, receptor - receptor, or ligand-ligand interactions. == References == 1. <<Anchor(ref1)>> Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW '''Intercellular network structure and regulatory motifs in the human hematopoietic system'''<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25028490|Pubmed]] |
Cell-Cell Interactions
Overview
Cell-Cell interactions were computed by a similar method as described by Qiao et al(1). Using a set of proteins designated as receptors, and ligands defined with a set of GO terms and other data sources calculate the set of interactions that represent cell-cell interactions (for example Ligand-receptor, receptor-receptor, ...). This analysis is not limited to Cell-Cell interactions. You can define your own protein types, either manually or by choosing different go terms, and create your customized protein-protein interaction network.
![[ATTACH]](/CellCellInteractions?action=AttachFile&do=upload_form&ticket=00681cf613.9c049d23ca638d75bb72d6fa4bec3f0068136752&target=ligand_receptor_flowchart.png "[ATTACH]"){kind=small}
Defining Receptor and Ligands
Receptor genes were defined based on
- a set of GO terms:
GO:0043235 - receptor complex,
GO:0008305 - integrin complex,
GO:0072657 - protein localized to membrane
GO:0043113 - receptor clustering
GO:0004872 -receptor activity,
GO:0009897 - external side of plasma membrane)
- Uniprot annotations
- search term -"Receptor [KW-0675]" go:0005886 organism:human.
Ligand genes were defined based on
- the GO terms:
GO:0005102 - receptor binding
the set of proteins labelled as secreted in the Secretome dataset (http://www.proteinatlas.org/humanproteome/secretome)[PMID:: 25613900].
Receptor and ligand lists were further manually curated
- removing genes that were neither receptors or ligands and
- moving misclassified genes were moved to the correct list (i.e. receptors found on the ligand list or vice versa)
Using the curated list of receptors and ligands interactions from irefindex (version 14)[PMID:18823568] were filtered to only included interaction that contained receptor-ligand, receptor - receptor, or ligand-ligand interactions.
References
Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW Intercellular network structure and regulatory motifs in the human hematopoietic system
Pubmed