Comparison of two sets of miRNAs

Giorgio C · 03-30-2012, 04:02 AM

Hi all,

i have two sets A and B of miRNAs. How i can make a comparison of them considering common elements and not ?

Is there any tool that makes this type of comparison ?

Thanks in advance for your help

NicoBxl · 03-30-2012, 06:32 AM

which type of data ? explain a little bit more about your problem

Giorgio C · 03-30-2012, 07:31 AM

There are two sets of miRNAs one coming out from a leaf and the other from the flower of the same Orchid. I have to know what are the differences between these two sets:
Elements in common and not. They are both in fasta format and in replicate (trimmed, filtered and collapsed with galaxy tools) originally coming out from a 454 platform.

they apper like this:

>1-8490
ACGTCACTCTCTCC..
>2-7990
CGTCAATCGCCTCC..
>3-6696
ACGTGCACTGCATG..

the first number is the Id , the second represents the number of occurences.

I need to evidence what are the differences fromt he two sets. Do you have any advice ??

tnx

NicoBxl · 03-30-2012, 07:37 AM

Ok

First annotate your reads : align them against mirbase databse (with blats per example) and then count for each miR, the number of reads.

After that in R create a matrix : each line represent one miR, each column a sample. Then use DESeq or edgeR for the DE analysis

Giorgio C · 03-30-2012, 07:39 AM

thank you very much for your fast reply. Is a problem that most of the miRNAs are novel and have no match with the database ??

NicoBxl · 03-30-2012, 07:42 AM

maybe try miRDeep before DE analysis

Giorgio C · 03-30-2012, 07:47 AM

Yes, i'v just done it with mirDeep but being this type of Orhichid not yet annotated i have a lot of no matching elements

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03-30-2012, 04:02 AM	#1
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	Comparison of two sets of miRNAs Hi all, i have two sets A and B of miRNAs. How i can make a comparison of them considering common elements and not ? Is there any tool that makes this type of comparison ? Thanks in advance for your help

03-30-2012, 06:32 AM	#2
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	which type of data ? explain a little bit more about your problem

03-30-2012, 07:31 AM	#3
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	There are two sets of miRNAs one coming out from a leaf and the other from the flower of the same Orchid. I have to know what are the differences between these two sets: Elements in common and not. They are both in fasta format and in replicate (trimmed, filtered and collapsed with galaxy tools) originally coming out from a 454 platform. they apper like this: >1-8490 ACGTCACTCTCTCC.. >2-7990 CGTCAATCGCCTCC.. >3-6696 ACGTGCACTGCATG.. the first number is the Id , the second represents the number of occurences. I need to evidence what are the differences fromt he two sets. Do you have any advice ?? tnx

03-30-2012, 07:37 AM	#4
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	Ok First annotate your reads : align them against mirbase databse (with blats per example) and then count for each miR, the number of reads. After that in R create a matrix : each line represent one miR, each column a sample. Then use DESeq or edgeR for the DE analysis

03-30-2012, 07:39 AM	#5
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	thank you very much for your fast reply. Is a problem that most of the miRNAs are novel and have no match with the database ??

03-30-2012, 07:42 AM	#6
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	maybe try miRDeep before DE analysis

03-30-2012, 07:47 AM	#7
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	Yes, i'v just done it with mirDeep but being this type of Orhichid not yet annotated i have a lot of no matching elements