updating miRNA library (edge link files) in cytoscape

[BIOMICS]

Hi, 

the two miRNA libraries (edge link files) are not updated in Cytoscape for long. Hence new miRNAs that have been identified in the last 7-9 years are not available in Cytoscape to link with mRNAs. 

The two current miRNA database used by Cytoscape are 

1) miRanda-miRNA-v5 2012-07-19

2) mirecords.umn.edu.validated.miRNAs.2010-11-25

they were last updated in 2012 and 2010 respectively. 

Can anyone help to update this library for miRNAs in Cytoscape. 

Thank you,

Nara

[Alex Pico]

Cytoscape has miRNA libraries??  Cytoscape doesn’t actually have ANY database libraries. It has a few sample files, but that’s it.

Maybe you are referring to a particular Cytoscape App? Check the App Store page and see if you can contact the authors via their email or website links.

 - Alex

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[Narasimhan Kothandaraman]

Hi Alex, thanks for the prompt reply. 

I'm referring to these two sample files which ClueGO uses to create the miRNA-mRNA association network. 

1) miRanda-miRNA-v5 2012-07-19

2) mirecords.umn.edu.validated.miRNAs.2010-11-25

they were last updated in 2012 and 2010 respectively. These files need to be updated as more than few hundred miRNAs have been discovered in the last 5 - 7 years. And we miss them when doing the analysis. 

Thanks,

Nara

---

From: Alex Pico <alex...@gladstone.ucsf.edu>
To: cytoscape...@googlegroups.com
Sent: Thursday, 3 January 2019, 3:44
Subject: Re: [cytoscape-helpdesk] updating miRNA library (edge link files) in cytoscape

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[Alex Pico]

Great. Cc’ing the ClueGO authors here...

 - Alex

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/1665978962.11302412.1546477057261%40mail.yahoo.com.

[Narasimhan Kothandaraman]

Alex, thanks

---

From: Alex Pico <alex...@gladstone.ucsf.edu>

To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Cc: Bernhard <gabriel...@gmail.com>; gabriel...@crc.jussieu.fr
Sent: Thursday, 3 January 2019, 9:12

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/5DD9A92D-A521-4443-AAEF-F047580D6A82%40gladstone.ucsf.edu.

[Bernhard]

Hi Nara,

as you know ClueGO is based on publicly available data. We provide an automatic update for GO and other databases.

If you know a frequently updated resource (publicly available) for miRNAs please let us know.

Best,

[Narasimhan Kothandaraman]

Hi Bernhard, 

thanks for your reply. To start with miRBase would be an ideal one, they have download version also. 

DIANA will be a good source. 

miRanda is another good one and is already in ClueGO except it is updated long while ago. 

There are more than 1000 new miRNAs that have been reported in the last few years. 

If you can help with the updating this would really help with people using CLueGO. 

I list some of the commonly recommended miRNA resources for your reference.  

DIANA, 

miRanda, 

miRBASE, 

miRDB, 

dbDEMC 2.0 (updated database of differentially expressed miRNAs)

miRmine,

mirTarbase ,

miRWalk2.0,

miRecrods 

the last few databases are more recent tools and have a more updated version available. 

Many thanks. 

---

From: Bernhard <gabriel...@gmail.com>
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Monday, 14 January 2019, 18:02
Subject: [cytoscape-helpdesk] Re: updating miRNA library (edge link files) in cytoscape

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[Narasimhan Kothandaraman]

Hi Bernhard, 

Thanks for your reply. 

To start with miRBase would be an ideal one, they have download version also. 

DIANA will be a good source. 

miRanda is another good one and is already in ClueGO except it is updated long while ago. 

There are more than 1000 new miRNAs that have been reported in the last few years. 

If you can help with the updating this would really help with people using CLueGO. 

I list some of the commonly recommended miRNA resources for your reference.  

DIANA, 

miRanda, 

miRBASE, 

miRDB, 

dbDEMC 2.0 (updated database of differentially expressed miRNAs)

miRmine,

mirTarbase ,

miRWalk2.0,

miRecrods 

The last few databases are more recent tools and have a more updated version available. 

If you could help to update the miRNA library it would be of immense help for people who are working in miRNAs. 

Many thanks. 

Nara

[Bernhard]

Hi Nara,

we updated the miR annotations from miRBase v22.1 and the files from miRDB v6.0 (In their experience (see FAQ: http://mirdb.org/faq.html) a predicted target with prediction score > 80 is most likely to be real (0.8 in CluePedia because it has to mapped between 0.0 and 1.0)  ). You can download the annotations via ClueGO (under Ontologies/Pathways) and the prediction file via CluePedia (button next to the EdgeLinks files). Please don't forget to cite the guys from miRDB if you use their predictions for publication (http://mirdb.org/policy.html).

Best

On Wednesday, January 2, 2019 at 2:27:13 PM UTC+1, BIOMICS wrote:

[Nara K]

Hi Bernhard, 

Many thanks for updating the miRNA edge files. I wish to clarify the following 1) I could update the prediction file for  miRBase v22.1 via CluePedia (button next to the EdgeLinks files) and it shows up in the

CluePedia + ClueGO dialog box. However, I could download the annotations via ClueGO (under Ontologies/Pathways) but I could not see the miRBase v22.1 in the ontologies/Pathways dialog box. Same is the case for miRDB v6.0.

Can you please help to troubleshoot why the Ontologies/pathways options for miRBase v22.1 and miRDB v6.0. are not showing up in the ClueGo settings. 

Thankyou

Nara

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[Bernhard]

Hi Nara, it is OK not to see miRBase v22.1, it is not an ontology but an annotation file. It is in the background and should be located in your Source folder for ClueGO. The miRDB v6.0 file you should see in CluePedia as EdgeLink file. So if you start with genes and CluePedia you can then enrich the genes with miRNAs selecting miRDB v6.0 and click on enrich with e.g. 10 genes (in this case with miRs) per gene.

See down the figure with 9 steps to get predicted gene-miR interactions.:

1. Select CluePedia

2. Put your gene/miRs in the text field

3. Start

4-5. Seleced edge files

6. Selected the genes/miRs on the network to enrich

7. Click on Enrich

8. Select "2. Each selected gene" (you can select here what you want) (1. Will enrich your genes/miRs with 10 genes in total with the highest miR-gene score. 2. Will enrich each selected gene/miR. 3. Will find the most interconnected genes/miRs with your selection so Hubs. 4. Will only work on genes that have GO/KEGG associations etc. and will Enrich with terms.)

9. Start enrichment

Now you should see the network with gene-miRs as displayed in the figure down.

Let me know if it is clear.

Best

On Friday, April 26, 2019 at 6:58:38 AM UTC+2, BIOMICS wrote:

Hi Bernhard, 

Many thanks for updating the miRNA edge files. I wish to clarify the following 1) I could update the prediction file for  miRBase v22.1 via CluePedia (button next to the EdgeLinks files) and it shows up in the

CluePedia + ClueGO dialog box. However, I could download the annotations via ClueGO (under Ontologies/Pathways) but I could not see the miRBase v22.1 in the ontologies/Pathways dialog box. Same is the case for miRDB v6.0.

Can you please help to troubleshoot why the Ontologies/pathways options for miRBase v22.1 and miRDB v6.0. are not showing up in the ClueGo settings. 

Thankyou

Nara

On Thu, Apr 25, 2019 at 8:28 PM Bernhard <gabriel...@gmail.com> wrote:

Hi Nara,

we updated the miR annotations from miRBase v22.1 and the files from miRDB v6.0 (In their experience (see FAQ: http://mirdb.org/faq.html) a predicted target with prediction score > 80 is most likely to be real (0.8 in CluePedia because it has to mapped between 0.0 and 1.0)  ). You can download the annotations via ClueGO (under Ontologies/Pathways) and the prediction file via CluePedia (button next to the EdgeLinks files). Please don't forget to cite the guys from miRDB if you use their predictions for publication (http://mirdb.org/policy.html).

Best

On Wednesday, January 2, 2019 at 2:27:13 PM UTC+1, BIOMICS wrote:

Hi, 

the two miRNA libraries (edge link files) are not updated in Cytoscape for long. Hence new miRNAs that have been identified in the last 7-9 years are not available in Cytoscape to link with mRNAs. 

The two current miRNA database used by Cytoscape are 

1) miRanda-miRNA-v5 2012-07-19

2) mirecords.umn.edu.validated.miRNAs.2010-11-25

they were last updated in 2012 and 2010 respectively. 

Can anyone help to update this library for miRNAs in Cytoscape. 

Thank you,

Nara

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