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qtran1 / RameshRNA-seq

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Make bar plots for the BAT markers. #3

Open qtran1 opened 9 years ago

qtran1 commented 9 years ago

Use these papers:

Sci Transl Med. 2014 Jul 30;6(247):247ra103. doi: 10.1126/scitranslmed.3008490. ASC-1, PAT2, and P2RX5 are cell surface markers for white, beige, and brown adipocytes. Ussar S1, Lee KY2, Dankel SN3, Boucher J2, Haering MF2, Kleinridders A2, Thomou T2, Xue R2, Macotela Y2, Cypess AM2, Tseng YH2, Mellgren G4, Kahn CR5.

Cell Metabolism 2013 May 7: 17(798-805) A Classical Brown Adipose Tissue mRNA Signature Partly Overlaps with Brite in the Supraclavicular Region of Adult Humans

davebridges commented 9 years ago

Can you also add to the beige markers plot the genes IRX3 and IRX5 based on this paper:

M. Claussnitzer, S. N. Dankel, K.-H. Kim, G. Quon, W. Meuleman, C. Haugen, V. Glunk, I. S. Sousa, J. L. Beaudry, V. Puviindran, N. a. Abdennur, J. Liu, P.-A. Svensson, Y.-H. Hsu, D. J. Drucker, G. Mellgren, C.-C. Hui, H. Hauner, M. Kellis, FTO Obesity Variant Circuitry and Adipocyte Browning in Humans, N. Engl. J. Med. , 150819140043007 (2015).

qtran1 commented 9 years ago

Yep!

On Aug 23, 2015, at 7:37 AM, Dave Bridges notifications@github.com<mailto:notifications@github.com> wrote:

Can you also add to the beige markers plot the genes IRX3 and IRX5 based on this paper:

M. Claussnitzer, S. N. Dankel, K.-H. Kim, G. Quon, W. Meuleman, C. Haugen, V. Glunk, I. S. Sousa, J. L. Beaudry, V. Puviindran, N. a. Abdennur, J. Liu, P.-A. Svensson, Y.-H. Hsu, D. J. Drucker, G. Mellgren, C.-C. Hui, H. Hauner, M. Kellis, FTO Obesity Variant Circuitry and Adipocyte Browning in Humans, N. Engl. J. Med. , 150819140043007 (2015).

— Reply to this email directly or view it on GitHubhttps://github.com/qtran1/RameshRNA-seq/issues/3#issuecomment-133826669.

davebridges commented 9 years ago

These are from this paper:

Wu, J., Boström, P., Sparks, L. M., Ye, L., Choi, J. H., Giang, A.-H., … Spiegelman, B. M. (2012). Beige Adipocytes are a Distinct Type of Thermogenic Fat Cell in Mouse and Human. Cell, 150(2), 366–376. http://doi.org/10.1016/j.cell.2012.05.016

Beige:

Brown:

Pan (Beige and Brown):

Not sure which (after the initial paper but we should check)

If there are ones from the other papers include them too

davebridges commented 9 years ago

See issue #7 as well

davebridges commented 9 years ago

Combined with genes from issue #7 Brown fat:

Beige fat:

White fat:

Mir206, Mir133b will not be detectable in our data set because they are miRNAs