User: gaoteng

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gaoteng10
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Posts by gaoteng

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Answer: A: which form of miRNA corresponding to TCGA?
... According to miRBase, "Distinct precursor sequences and genomic loci that express identical mature sequences get names of the form hsa-mir-121-1 and hsa-mir-121-2". (http://www.mirbase.org/help/nomenclature.shtml) So let-7a-1, let-7a-2, and let-7a-3 are stemloop sequences. I think to get the mature ...
written 4 weeks ago by gaoteng10
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Answer: A: Which kind of microRNAs expression are measured in TCGA?
... I believe that each mature transcript (e.g. hsa-miR-135a-5p, hsa-miR-135a-3p) are identified by a mirBase ID with prefix MIMAT. I think to get the mature transcript expressions, you need to parse the data from TCGA miRNASeq isoform quantification files (ending with .mirbase21.isoforms.quantification ...
written 4 weeks ago by gaoteng10
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Answer: A: miRNAseq isoform-to-mature miRNA quantification
... I think there is a misconception here. According to miRBase, "Distinct precursor sequences and genomic loci that express identical mature sequences get names of the form hsa-mir-121-1 and hsa-mir-121-2". (http://www.mirbase.org/help/nomenclature.shtml) So let-7a-1, let-7a-2, and let-7a-3 are stemloo ...
written 4 weeks ago by gaoteng10
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Answer: A: Selecting One Ensembl Transcript Id For Each Ensembl Gene Id
... I recently ran in to the same problem. You can use Transcript Support Level given by Ensembl and the transcript length to decide which transcript is "canonical" (somewhat subjectively). I wrote a script that achieves this: https://github.com/teng-gao/genomics_utils ...
written 4 weeks ago by gaoteng10
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Answer: A: convert human gene names to ensembl ID
... It seems that there are already many good solutions out there, but here is a python script that I wrote that achieves the same purpose: https://github.com/teng-gao/genomics_utils ...
written 4 weeks ago by gaoteng10

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