lncRNA target identification
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5.9 years ago

Dear all, I am trying to find out if any of my lncRNA sets (278) can interact with my candidate gene sets (28).

I have obtained lncRNA sequence from a microarray dataset (GSE58043).

I used lncTar website to test their interactions. No interaction was detected.

When I checked the sequence of lncRNAs, I realized that their lengths are shorter than 200nt (60nt).

I checked other lncRNA datasets deposited in GEO and I found out that all lncRNA sequences are 60nt.

I could not find any lncRNA databases that I can obtain the full length of lncRNAs.

My question is if I can rely on lncTar results considering the short length of lncRNAs?

I appreciate any help

Thank you in advance

Nazanin Hosseinkhan

lncRNA Target • 3.0k views
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Perhaps I misunderstood, but how did you obtain the lncRNA sequence from a microarray dataset?

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I hope this would be helpful:

I use GEO2R in GEO to find differential expressed genes between case and control groups.

In output both the IDs and the sequence of all lncRNA are represented.

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Is that the sequence of the probe used in the microarray? No sequence is determined in micro array experiments since it's hybridization-based. Real lncRNAs are far longer than 60nt.

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Assuming you only got partial sequences, you could try identifying the genes they come from by searching the annotated genome of the species they're from e.g if the species is in EnsEMBL, you could blast your sequences against the relevant cDNAs (i.e. transcripts) data.

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I think that you obtained the sequences should be the probe, not the lncRNAs. If you want to get the full-length sequece of lncRNAs, you can download them from some database, such as NCBI, UCSC. You want to find the interaction between lncRNAs and mRNAs, you can calculate the pearson correlation of them using the expression value. You also can check my paper,Functional prediction of differentially expressed lncRNAs in HSV-1 infected human foreskin fibroblasts.

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5.1 years ago

You can download cdna sequence of lncRNAs and mRNAs using biomaRt R package.

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