Gene expression and chromatin state
I want to compare the expression of a list of genes (mouse) in a specific organ e.g. lung. Also, the chromatin state e.g. which regions are repressed or transcriptionally active.
I think MGI gene expression database for gene expression and ENCODE for chromatin?
But I cannot figure out how to get chromatin information from ENCODE database...
I had a try at MGI expression database. does cM here means expression? how do I search for tissue specific expression?
MGI Gene ID Gene Symbol Gene Name Type Chr Genome Location-GRCm38 cM Strand
MGI:97363 Notch1 notch 1 protein coding gene 2 26457902-26503822 18.91 -
MGI:98834 Trp53 transformation related protein 53 protein coding gene 11 69580359-69591873 42.83 +
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Hi, most of your questions so far went unanswered/uncommented, and I think the reason is that they have been a bit unspecific and open-ended. Biostars is usually good to answer precise technical questions, but people are usually reluctant to guide you through an analysis. The lung is an organ, that is true, but there are plenty of celltypes involved, so I think you oversimplify the task you are up to by assuming that a single value will give you a meaningful information. What is exactly the question you are after, and which chromatin features do you need? There is open chromatin, histone modifications, TF binding, all types of stuff. Try to be more precise, that might help getting you valuable answers.
I don't know for certain, but my guess would be that cM stands for CentiMorgan, which is an old fashioned genetic measure of distance. In this case distance from the centromere I think?.