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I have a list of 100 lncRNAs (long non-coding RNAs). For each of these RNAs, I would like to query GEO to find any experiments that used a high throughput sequencing platform and detected expression levels of that RNA in FPKM. To filter further, I'd like to have those expression levels found in controls only. The last filter is to find experiments which found the specific RNA's expression in smooth muscle tissue.

Here are some example lncRNAs:

  • CDC37L1-AS1
  • LCMT1-AS1
  • FLJ21408
  • CDIPT-AS1
  • LINC00920
  • TAT-AS1
  • SUZ12P1

Is there any way to do any of this? Any help would be appreciated.

Thanks.

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  • $\begingroup$ You cannot query GEO or SRA using the gene names that are present in an expression data. You have to manually do this. Or you can download selected datasets. Otherwise, as Maxim has pointed out, you should refer to papers/databases that have collected information from different datasets. $\endgroup$ – WYSIWYG Mar 7 '16 at 6:27
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  1. You could look at supplementary and methods section of "The Landscape of Long Noncoding RNAs in the Human Transcriptome" paper. They've collected RNASeq samples from TCGA, ENCODE and MCTP and processed it with their pipeline (most of it are filtering and GSEA) to detect novel lncRNAs and associate them with cancer pathogenesis. Their statistics, processing and cross-validation look clean and accurate.

  2. To extract signatures from GEO, you could use GEO2Enrichr. Then calculate the differential expression of tissue-specific libraries in Enrichr. Also, you could submit gene list to Enrichr's Crowd libraries and find GEO entries with a reasonable number of mapped genes first.

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  • $\begingroup$ That paper had some great baseline FPKMs of interest. Using R, I was able to grab their data and work with it nicely. Thanks for the help. $\endgroup$ – aaiezza Mar 7 '16 at 16:58

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