Up: Component summary
Up: Component summary
Component
PINAFinds the interacting proteins of query proteins for a list of query Uniprot ACs. Optionally also produces interactions between interactors.
| Version | 1.1 |
|---|---|
| Bundle | microarray |
| Categories | Annotation |
| Authors | Jianmin Wu (jianmin.wu@gmail.com), Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | commons-codec-1.3.jar (jar) ; commons-httpclient-3.0.1.jar (jar) ; commons-logging-1.1.1.jar (jar) |
| Source files | component.xml Interactome.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| query | CSV | Mandatory | If query partners of proteins, it must contain the column named by the parameter "column" that contains query Uniprot IDs. If query whether interactions existing, it must contain two columns named by parameters "column" and "column2". |
Outputs| Name | Type | Description |
|---|---|---|
| interactions | CSV | There are two columns including queryProtein and interactingProtein. Each row corresponds to one protein interaction. |
| network | GraphML | Ouput interactions in graphML format with Gene Ontology annoation. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| WS_URL | string | "http://cbg.garvan.unsw.edu.au/pina/batchDownload" | URL for PINA web service. |
| column | string | "Uniprot" | Column name in the input CSV file that contains Uniprot IDs. |
| column2 | string | "Uniprot" | Column name in the input CSV file that contains Uniprot IDs. |
| extend | boolean | false | If true, also query interactions between interactors of query proteins. |
| findPartners | boolean | true | If true, fetch partners of query proteins, otherwise check whether query interactions are known in PINA. |
| outputCSV | boolean | true | If true, produce content for interactions output. |
| outputGraphML | boolean | false | If true, produce content for network output. |
Test cases| Test case | Parameters▼ | IN query |
OUT interactions |
OUT network |
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|---|---|---|---|---|---|---|
| case1 | properties | query | interactions | network | ||
|
column=MyUniprotColumn, |
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| case2 | properties | query | interactions | network | ||
|
column=UniProtA, |
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| case3 | properties | query | interactions | network | ||
|
column=MyUniprotColumn, |
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| case4 | properties | query | interactions | network | ||
|
column=MyUniprotColumn, |
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| case5 | properties | query | interactions | network | ||
|
column=MyUniprotColumn, |
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| case6 | properties | query | (missing) | (missing) | ||
|
column=Uniprot/SWISSPROT |
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