Filtering for some GO terms

[beginner984]

Hi

I got a question which I was not able to solve yet

If I am only interested in lncRNAs related to Angiogenesis GO term how to download such a list please?

I searched for Angiogenesis in search bar and some results came out and I see for instance 123 of lncRNAs are here and I want to download them as a list but I don't know how

[AntonPetrov]

@beginner984 Thank you for your question! Currently you can download search results as FASTA or JSON files or as a list of RNAcentral IDs:

I would like to note that when you search with a term like Angiogenesis, you will find all entries that mention angiogenesis, not only those annotated with an angiogenesis-related GO term.

You will also notice that most of the results in your search are microRNAs. This is because they are the best-annotated sequences. In fact, there are several groups that manually annotate microRNAs with GO terms using RNAcentral IDs.

I do have a suggestion that you may find helpful. If you search for pub_title:"angiogenesis" you will see additional entries where the term angiogenesis occurs in one of the associated publication titles.

https://rnacentral.org/search?q=pub_title:%22angiogenesis%22%20AND%20so_rna_type_name:%22LncRNA%

The pub_title field is not searched by default because through experience we found that such results are not always relevant, so you might want to inspect the results with additional care.

I hope this helps!

[beginner984]

Thank you so much for your help

I am not much familiar with JASON or FASTA

In a forum somebody helped to download the results in such a format as I attached by link

http://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/gencode.tsv

Is the anyway to download the results in this format please?

[AntonPetrov]

I am afraid the tsv format is not supported in the text search export because RNAcentral entries have a lot of data and the tsv format is not flexible enough to represent it.

What information are you trying to extract? Ensembl IDs for any of the matching sequences?

[beginner984]

Thank you so much download gives IDs like URS0000000055 while I need something equal to that like ZNF451-AS1

But I don't know how to retrieve that in such identifier instead of RNAcentral identifiers

[AntonPetrov]

Okay, I see. Currently there is no way to download this info from the web interface but it can be done using the id_mapping.tsv.gz file that contains all external IDs linked to each URS accession: http://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/

You can search this file with a tool like grep or by writing a script. Alternatively, you can connect to the public Postgres database and write an SQL query but that also requires some programming.

I can do this for you as a one-off task if you send me a URL of a search result that you want exported in this format.

[beginner984]

Thanks a million

I have attached a list of lncRNA here

Is it possible to get from this list any lncRNA related to angiogenesis and immune response please? d.txt

[AntonPetrov]

I am afraid that I don't understand the contents of the file. I thought you needed a mapping between URS ids and other accessions, but the file contains only ids like:

linc-HMGCS1:antisense
linc-FAM19A1-2:copy2

It does not look like these IDs are from RNAcentral.

[beginner984]

hank you so much

Might be non sense, do you know a software giving pathways related to a list of lncRNAs ?

I found LncPath R package which uses a networks of lncRNA-mRNA for getting pathways

Have you heard about a software directly giving pathways or GO terms related to a list of lncRNAs please?

In RNAcentral if we search for a lncRNA we may find a related GO term but this demands one by one checking 🙁

Thanks a lot anyway

[AntonPetrov]

In general I would not recommend using RNAcentral for lncRNA GO annotations, the coverage is very far from comprehensive at the moment. It's okay for microRNAs but not lncRNAs.

I have not used it but you could try LncSEA for lncRNA GO enrichment analysis.

Sorry that I cannot help more!

[beginner984]

Thanks a million

[AntonPetrov]

No worries, let us know if we can help with anything else.