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Expression quantification/differential expression gene analysis by RNA-Seq chenjy Bioinformatics 12 08-02-2013 03:06 AM

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Old 10-13-2014, 02:50 AM   #1
jeni
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Default How to get expression of one gene from 10 RNA-Seq datasets?

Hello guys,

I am trying to fetch gene expression level of one gene from 10 different samples in human and mouse. I think its very straight forward but I dont know any of such browser where I can get it. I know about UCSC, Epigenome browser but not able to get the gene expression value for the specific gene of my interest.
Therefore, please help me in this regard.

Thanks.
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Old 10-13-2014, 02:54 AM   #2
A.N.Other
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What format do you have the files in? Do you know what (if any) processing the reads have had to get them into the state you have?
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Old 10-13-2014, 02:57 AM   #3
jeni
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Thanks A.N.Other for your response.

I do not have any sequenced data. I am trying it from the publically available dataset. And therefore, please suggest me some tool or genome browser name, so that I can directly save for the expression level of few specific genes.

Last edited by jeni; 10-13-2014 at 03:07 AM.
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Old 10-13-2014, 03:13 AM   #4
dpryan
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That's likely not directly possible. If you get lucky, perhaps the datasets are available all aligned to the same reference genome (with the same aligner and similar preprocessing) in BAM format, though in practice this is unlikely. The reality is that it's typically only the fastq files (i.e., raw reads) that are uploaded to the public databases. You then have to align things yourself and get the read count that way.

Edit: BTW, raw expression levels of a single gene across multiple datasets is likely useless. You might just want to mention what your goal is.
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Old 10-13-2014, 04:00 AM   #5
GenoMax
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@jeni: If data you are looking at is related to cancer you may be able to find the information you need here: http://www.cbioportal.org/public-portal/ if the study has RNA-seq/Microarry data. Data would be z-scores (as Devon already said raw values probably are useless).
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Old 10-13-2014, 04:54 AM   #6
jeni
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Actually, I am looking for a browser or tool where I can directly get the gene expression information + cell line information.

Last edited by jeni; 10-14-2014 at 01:34 AM.
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Old 10-14-2014, 12:43 PM   #7
amitm
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hi,
One easy resource would be BioGPS website (http://biogps.org/)
It is an old data, microarray, but quite rich in terms of tissues covered in humans and mouse. And the expression values can be easily browsed.
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