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05-17-2014, 07:48 AM
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#1 |
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Member
Location: Germany Join Date: Nov 2013
Posts: 20
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Which kind of microRNA expression are measured in TCGA?
Hi all,
I have download the mRNA and microRNA NGS data from TCGA for BRCA. for downloading the microRNA data, I choosed the miRNASeq from filter setting. Now I have the expression level of miRNA in diffrent samples. The question for is that, which kind of microRNA they are quantified ? is it all mature miRNA ? or mirna precursor are also there ? They seqenced miRNA which they got from gel electrophoresis ?(to be sure that, all of them have same length in case of mature miRNA). But when I look at the miRNA IDs; there is some problem: for example : they have expression level for hsa-mir-135a-2 , which when I search for it in miRBase, it's stem loop and it's mature form in miRbase is hsa-miR-135a-5p . so now I'm really in trouble to undersrand that expression level of which type of miRNA are quantified ? would someone clarify it more ? |
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11-22-2014, 03:50 AM
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#2 |
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Registered Vendor
Location: San Francisco, CA Join Date: Mar 2014
Posts: 18
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If you look at the "DESCRIPTION.TXT" files included in each package, there is the following description:
This data archive contains the miRNA expression data for cancer samples of The Cancer Genome Atlas (TCGA) project. The experiments were performed by the BCCA Genome Sciences Centre in BC using the miRNA-Seq approach on the Illumina platform. Please see DESCRIPTION.txt in the mage-tab for algorithm description of the data protocols. The .adf file format describing miRNA annotations is as follows: MiRNA ID miRBase version genome version and coordinates as <version>:<Chromosome>:<Start position>-<End position>:<Strand> precursor sequence mature strand coordinates relative to precursor coordinates, as <relative start>-<relative end> mature strand accession alternate mature strand coordinates, if provided by miRBase alternate mature form accession star strand name, if provided by miRBase star strand form accession The .mirna.quantification.txt data file describing summed expression for each miRNA is as follows: miRNA name raw read count reads per million miRNA reads cross-mapped to other miRNA forms (Y or N) The .isoform.quantification.txt data file describing every individual sequence isoform observed is as follows: miRNA name alignment coordinates as <version>:<Chromosome>:<Start position>-<End position>:<Strand> raw read count reads per million miRNA reads cross-mapped to other miRNA forms (Y or N) region within miRNA ------------------ When one looks at the associated files such as *.isoform.quantification.txt and *.mirna.quantification.txt, one can get a sense of the coordinates for which counts were calculated. As an example, let's take a look at "hsa-let-7a-1" below. You'll notice that the mature and star forms are mentioned in the last column. If you look at column two, you'll see that the reads all align to a range of 25 nucleotides (hg19:9:96938242-96938267:+) for the mature miRNA of hsa-let-7a-1 and a range of 25 nucleotides (hg19:9:96938292-96938317:+) for the star miRNA of hsa-let-7a-1. From *.isoform.quantification.txt for one sample: hsa-let-7a-1 hg19:9:96938242-96938264:+ 4 1.495846 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938242-96938266:+ 4 1.495846 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938243-96938264:+ 8 2.991692 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938243-96938265:+ 4 1.495846 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938243-96938266:+ 6 2.243769 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938244-96938263:+ 157 58.711957 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938244-96938264:+ 5196 1943.104000 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938244-96938265:+ 3954 1478.643806 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938244-96938266:+ 7029 2628.575446 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938244-96938267:+ 278 103.961299 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938244-96938268:+ 18 6.731307 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938245-96938264:+ 9 3.365654 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938245-96938265:+ 16 5.983384 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938245-96938266:+ 44 16.454306 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938245-96938267:+ 3 1.121885 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938246-96938264:+ 1 0.373962 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938247-96938265:+ 2 0.747923 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938247-96938266:+ 10 3.739615 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938247-96938267:+ 2 0.747923 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938248-96938266:+ 1 0.373962 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938248-96938267:+ 2 0.747923 N mature,MIMAT0000062 hsa-let-7a-1 hg19:9:96938292-96938311:+ 1 0.373962 N star,MIMAT0004481 hsa-let-7a-1 hg19:9:96938295-96938314:+ 3 1.121885 N star,MIMAT0004481 hsa-let-7a-1 hg19:9:96938295-96938315:+ 6 2.243769 N star,MIMAT0004481 hsa-let-7a-1 hg19:9:96938295-96938316:+ 13 4.861500 N star,MIMAT0004481 hsa-let-7a-1 hg19:9:96938295-96938317:+ 20 7.479230 N star,MIMAT0004481 hsa-let-7a-1 hg19:9:96938296-96938316:+ 3 1.121885 N star,MIMAT0004481 hsa-let-7a-1 hg19:9:96938296-96938317:+ 1 0.373962 N star,MIMAT0004481 From *.mirna.quantification.txt for the same sample miRNA_ID read_count reads_per_million_miRNA_mapped cross-mapped hsa-let-7a-1 16795 6280.683542 N ================== The count of 16795 in *.mirna.quantification.txt for hsa-let-7a-1 is literally the sum of all the counts mapped to the 25-nucleotide-ranges for the mature and star regions of hsa-let-7a-1. So in conclusion, the values represent expression for the mature miRNAs, not the stem loops. Incidentally, if you're interested, we have imported all of the miRNA-Seq data along with all of the other TCGA assays into GenePool and linked in all of the patient & sample metadata. GenePool makes it very simple to slice and dice the samples according to patient characteristics and clinical metadata, then run analyses. Here are the links to related threads: http://seqanswers.com/forums/showthread.php?t=48485 http://seqanswers.com/forums/showthread.php?t=42471 Good Luck! ------------------------------ GenePool is making genomics data management, analysis, and sharing easier! Products @ www.stationxinc.com Last edited by GenePool; 11-23-2014 at 09:26 PM. |
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02-02-2015, 01:01 AM
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#3 | |
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Junior Member
Location: Shanghai,China Join Date: Feb 2015
Posts: 1
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Hey
Hey, this problem troubles me too. However, after I checked as what you said, it seemed that the values represent expression for the mature miRNAs, ADDING the stem loops and PRECURSOR.
Quote:
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| Tags |
| bioinformatic analaysis, ngs 3g, ngs data analysis, rna sequencing, tcga |
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