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Old 11-05-2015, 07:47 AM   #1
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Location: Northeastern USA

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Question Trying to find where an Isoform of a gene is expressed in normal tissue

Hello. I have the sequence of a particular isoform of a gene I'm interested in and I am trying to find out where it is normally expressed in the human body. This sequence was found in cancer cells originally. One suggestion was to use the ucsc genome browser, however that did not prove to be a viable option. The other was to download all of these fastq files from illumina bodymap 2.0 which I did and then I would have to download Bowtie 2.0 and allign 68 of these fastq files using this tool and then convert these alignments into SAM files and then convert these to BAM files and then use an application called "R" to search for my coordinates on this giant map, the problem with this approach is that its going to take a long time due to the speed of the computer I am using and because I am not a bioinformatics person. I was wondering if there was an easier way to find this information. I've tried using NCBI Blast and NCBI SRA blast. Are there any other ways to do this quickly and more efficiently?
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Old 11-05-2015, 09:12 AM   #2
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Have you tried searching NCBI GEO with the name of your gene/isoform?
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Old 11-06-2015, 12:46 AM   #3
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Are you asking about the tissue-specificity of your gene or the specific isoform you have?
For the gene, look at the "expression" section in genecards ( For the isoform, search for "ECgene alternative splicing isoforms for" in your genecards results and follow the link. If there is sufficient data on isoform expression available, you will find some tissue-specificities in the "EST clustering result with Confidence Medium level "
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expression, isoform, rnaseq, tissue expression

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