Question: how to obtain detailed pathways?
gravatar for tim.gallengor
4.9 years ago by
United States
tim.gallengor10 wrote:

I am new to bioinformatics and have a problem that I am sure almost everyone has faced or is facing. I know that my question is an over simplification, but any pointers in the right direction would be much appreciated.

I would simply like to query (compare/contrast/word search/etc.) multiple biological pathways.

I have used Cytoscape and imported pathways from databases/tools such as Reactome,  KEGG, STRING, Agilent Literature search,  but the two main limitations are:

1. Limited pathways to choose from

2. Interactions are not well defined

3. Difficult to compare large number of pathways on specific parameters

Does a tool/database exist that incorporates more pathways and  detailed interactions? GO annotations and more descriptions on the single gene/molecule itself would not be helpful. I am focusing mainly on the interactions in the pathway. 

I can't imagine having to manually annotate or even create 1000s of pathways. I also know that this is not a unique problem, so creating a database or tool would probably be redundant.

How have any of you solved the problem of getting a greater number of detailed pathways?

Giving names of any other tools/database, areas of research, etc. would be helpful.



ADD COMMENTlink modified 4.9 years ago by AndreiR50 • written 4.9 years ago by tim.gallengor10

Have you tried to merge pathways on cytoscape?

ADD REPLYlink written 4.9 years ago by AndreiR50

Yeah, that's a pretty neat feature, but still doesn't contain the information I need. For example, when importing Reactome pathways with ReactomeFIPlugIn, usually only gene entities are imported, not molecules. I end up exporting the table to mySQL adding additional entities and annotations, and then importing back to cytoscape.

. The annotations and entities I am adding are not that specific. Usually I am just adding if a gene product "activates", "inhibits", or "modulates" a channel and what ions a channel conducts. These seem like simple annotations, but can't seem to find a database that I can easily import this information from.

Maybe there's another tool or plugin?

ADD REPLYlink written 4.9 years ago by tim.gallengor10

Have you tried to retrieve pathway - Import -> Network from webservices -> options -> full model? And after import, look at node attribute browser and select all fields.

Another thing is that you can use annotation directly into cytoscape via import node attributes (i.e. csv file) in order to avoid exporting and importing back pathways.

I have just imported "Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell (Reactome)" and found on node attribute browser -

biopax.entity_type (i.e. biochemical reaction, catalysis, complex, physical entity, protein, small molecule, etc);

biopax.entity.comment (i.e. FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degradation by the proteasome. Inhibits p53/TP53- and p73/TP73-mediated cell cycle arrest and apoptosis by binding its transcriptional activation domain... etc.)

ADD REPLYlink written 4.9 years ago by AndreiR50

Those annotations seem really useful! Although, I'm not sure how to get them, as I am using cytoscape 3.2.1, and I can only find descriptions on node attribute browser by looking at earlier versions of cytoscape. Do you know of another way to get these files? I have not used BioPAX before, but am looking into it.

ADD REPLYlink written 4.9 years ago by tim.gallengor10
gravatar for AndreiR
4.9 years ago by
AndreiR50 wrote:

On cytoscape 3.2.1-

File -> import -> network -> public databases (alt+L -on linux)

search by id (second combo), select and import the pathway.

After that you can add info to the pathway by:

File -> import -> Ontology and annotation

annotation data source for the specie and

ontology for the type of data you need.

However, I can see no trouble in using older versions of cytoscape such 2.8.3 and, if you need plugins from 3.2.1, export in 2.8.3 and import in 3.2.1



ADD COMMENTlink written 4.9 years ago by AndreiR50
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