how to visualize locations of lncRNA close to my gene of interest

angel-sakura · 11-30-2014, 03:38 AM

Hi, everyone, I am looking for the lncRNAs of some specific genes.
Q1: Now I have extracted all predicted lncRNAs (using PLEK) that close to my target genes (500 KB upstream or downstream). I can do blastn to get the location of those lncRNAs on gene scaffold I extracted from genomic sequence (my target gene +/-500KB). But I don't know how to visualize them. Could someone please show me the software or protocol?
Q2: Is there any lncRNA database or lncRNA database with consensus sequences that I can blast with?
Q3: Is there any software or command that I can predict structure/function/lncRNA-protein, lncRNA-DNA,lncRNA-microRNA interaction of lncRNAs (with multiple sequences as input)?

Thank you very much!
Y

dpryan · 12-01-2014, 12:58 AM

1. I'd use IGV and make either a BED or GTF file describing the lncRNA locations in the scaffold. If you add your gene of interest to it too then you can easily visualize where things are relative to each other (you can also do this in R with packages like Gviz, but I think just using IGV will be a bit easier for your needs).
2. RNAcentral has the lncRNA sequences from Ensembl and lincRNAdb, so have a look at it. It's interface isn't great at the moment, so you'll have to download and parse the fasta file (I actually have some tools to do this that I need to post on github).
3. No clue, hopefully someone else knows.

angel-sakura · 12-01-2014, 02:22 AM

Thank you very much for your kind reply!
Could you also recommend some commands or softwares that I can use to transfer lncRNAs (fasta format) into BED or GTF format?

dpryan · 12-01-2014, 02:26 AM

The simplest thing is to probably use blast to align them to you either the genome or the targeted region and then use some of the replies in this thread over at Biostars to convert that to GFF/GTF. I should note that I've not personally done this, so I can't say how easy/difficult it is...but it should at least work well in theory (famous last words!).

angel-sakura · 12-02-2014, 04:47 AM

lol, I haven't done this before either, but it is worth trying it.
Thank you !

docnj · 12-28-2014, 06:35 AM

Hi angel-sakura, You said that you have extracted all predicted lncRNAs that close to the target genes by using PLEK. I'm confronted with the same problem myself, too. I have one interested target gene, but don't know how to find lncRNAs close to it. May I ask how you conducted the prediction through using PLEK? If you can also provide procedures in details, that would be appreciated very much!! Thank you!

angel-sakura · 01-02-2015, 09:24 PM

Quote:

Originally Posted by docnj

Hi angel-sakura, You said that you have extracted all predicted lncRNAs that close to the target genes by using PLEK. I'm confronted with the same problem myself, too. I have one interested target gene, but don't know how to find lncRNAs close to it. May I ask how you conducted the prediction through using PLEK? If you can also provide procedures in details, that would be appreciated very much!! Thank you!

Hi, sorry for the late reply, I was on holidays.

Check this link:http://sourceforge.net/projects/plek/files/
You can downloand the PLEK and its manual from above link. The PLEK is straight forward, you just input the fasta file, then it will produce an output containing coding and non-coding genes.
As for finding lncRNAs close to your gene of interet. The steps are: 1. extract the upstream and downstream sequences (such as 500kb) of your target gene. 2. Blast RNAseq data to fragment extracted from step 1. 3. predict the blast result with PLEK.

Cheers

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11-30-2014, 03:38 AM	#1
angel-sakura Member Location: Aus Join Date: Nov 2014 Posts: 23	how to visualize locations of lncRNA close to my gene of interest Hi, everyone, I am looking for the lncRNAs of some specific genes. Q1: Now I have extracted all predicted lncRNAs (using PLEK) that close to my target genes (500 KB upstream or downstream). I can do blastn to get the location of those lncRNAs on gene scaffold I extracted from genomic sequence (my target gene +/-500KB). But I don't know how to visualize them. Could someone please show me the software or protocol? Q2: Is there any lncRNA database or lncRNA database with consensus sequences that I can blast with? Q3: Is there any software or command that I can predict structure/function/lncRNA-protein, lncRNA-DNA,lncRNA-microRNA interaction of lncRNAs (with multiple sequences as input)? Thank you very much! Y

12-01-2014, 12:58 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	1. I'd use IGV and make either a BED or GTF file describing the lncRNA locations in the scaffold. If you add your gene of interest to it too then you can easily visualize where things are relative to each other (you can also do this in R with packages like Gviz, but I think just using IGV will be a bit easier for your needs). 2. RNAcentral has the lncRNA sequences from Ensembl and lincRNAdb, so have a look at it. It's interface isn't great at the moment, so you'll have to download and parse the fasta file (I actually have some tools to do this that I need to post on github). 3. No clue, hopefully someone else knows. Last edited by dpryan; 12-01-2014 at 01:02 AM.

12-01-2014, 02:22 AM	#3
angel-sakura Member Location: Aus Join Date: Nov 2014 Posts: 23	Thank you very much for your kind reply! Could you also recommend some commands or softwares that I can use to transfer lncRNAs (fasta format) into BED or GTF format?

12-01-2014, 02:26 AM	#4
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	The simplest thing is to probably use blast to align them to you either the genome or the targeted region and then use some of the replies in this thread over at Biostars to convert that to GFF/GTF. I should note that I've not personally done this, so I can't say how easy/difficult it is...but it should at least work well in theory (famous last words!).

12-02-2014, 04:47 AM	#5
angel-sakura Member Location: Aus Join Date: Nov 2014 Posts: 23	lol, I haven't done this before either, but it is worth trying it. Thank you !

12-28-2014, 06:35 AM	#6
docnj Junior Member Location: Nanjing，PR China Join Date: Dec 2014 Posts: 1	Hi angel-sakura, You said that you have extracted all predicted lncRNAs that close to the target genes by using PLEK. I'm confronted with the same problem myself, too. I have one interested target gene, but don't know how to find lncRNAs close to it. May I ask how you conducted the prediction through using PLEK? If you can also provide procedures in details, that would be appreciated very much!! Thank you!