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Gtf or GFF with target genes regulated by ncRNAs

I was wondering if there is a gtf containing target genes regulated by ncRNAs. In databases like GENECODE i can download a gff/gtf with the gene_ids which corresponds to the id of the lncRNA. Is it possible to find or create gtf file with the target genes regualted by ncRNAs (lncRNAs, miRNAs etc ) ?

databases ncrnas genes gtf
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written by dzisis1986 • dzisis1986

If you had a list of which lncRNA regulates what, I guess you could do a little bit of data wrangling to add an extra field. But I don't think they produce this from GENECODE, and probably GTF/GFF might not be the best wat to contain this data (maybe a table?)

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written by biofalconch biofalconch

i want to connect GWAS variants with target genes regulated by ncRNAs. So what I did until now is to create a file that connects my variants with ncRNAs for example from GENECODE but intersecting my vcf with gtf. But what i obtained is my variants related with the gene ids of each lncRNA for example. How can i find target genes for those lncRNAs? Is any list of genes regulated by lncRNAs for example ?

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written by dzisis1986 • dzisis1986

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