Question: lncRNA target identification
0
gravatar for nazaninhoseinkhan
3.5 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan390 wrote:

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

target lncrna • 2.3k views
ADD COMMENTlink modified 2.7 years ago by zhangjunpeng_4110 • written 3.5 years ago by nazaninhoseinkhan390

Perhaps I misunderstood, but how did you obtain the lncRNA sequence from a microarray dataset?

ADD REPLYlink written 3.5 years ago by WouterDeCoster43k

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.

ADD REPLYlink written 3.5 years ago by nazaninhoseinkhan390

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.

ADD REPLYlink written 3.5 years ago by WouterDeCoster43k

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.

ADD REPLYlink written 3.5 years ago by Jean-Karim Heriche21k

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.

ADD REPLYlink written 2.7 years ago by Ben50
0
gravatar for zhangjunpeng_411
2.7 years ago by
China
zhangjunpeng_4110 wrote:

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

ADD COMMENTlink written 2.7 years ago by zhangjunpeng_4110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1184 users visited in the last hour