Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Cell type–specific gene expression differences in complex tissues


We describe cell type–specific significance analysis of microarrays (csSAM) for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. First, we validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejection, which revealed hundreds of differentially expressed genes that were otherwise undetectable.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Overview of csSAM.
Figure 2: Statistical deconvolution of complex tissues yields accurate estimates of pure tissue-subset expression.
Figure 3: csSAM reveals cell type–specific differential expression undetectable at heterogeneous tissue level.


  1. 1

    Whitney, A.R. et al. Proc. Natl. Acad. Sci. USA 100, 1896–1901 (2003).

    CAS  Article  Google Scholar 

  2. 2

    Cobb, J.P. et al. Proc. Natl. Acad. Sci. USA 102, 4801–4806 (2005).

    CAS  Article  Google Scholar 

  3. 3

    Palmer, C., Diehn, M., Alizadeh, A.A. & Brown, P.O. BMC Genomics 7, 115 (2006).

    Article  Google Scholar 

  4. 4

    Feezor, R.J. et al. Physiol. Genomics 19, 247–254 (2004).

    CAS  Article  Google Scholar 

  5. 5

    Debey, S. et al. Pharmacogenomics J. 4, 193–207 (2004).

    CAS  Article  Google Scholar 

  6. 6

    Stuart, R.O. et al. Proc. Natl. Acad. Sci. USA 101, 615–620 (2004).

    CAS  Article  Google Scholar 

  7. 7

    Lahdesmaki, H., Shmulevich, L., Dunmire, V., Yli-Harja, O. & Zhang, W. BMC Bioinformatics 6, 54 (2005).

    Article  Google Scholar 

  8. 8

    Wang, M., Master, S.R. & Chodosh, L.A. BMC Bioinformatics 7, 328 (2006).

    Article  Google Scholar 

  9. 9

    Lu, P., Nakorchevskiy, A. & Marcotte, E.M. Proc. Natl. Acad. Sci. USA 100, 10370–10375 (2003).

    CAS  Article  Google Scholar 

  10. 10

    Abbas, A.R., Wolslegel, K., Seshasayee, D., Modrusan, Z. & Clark, H.F. PLoS One 4, e6098 (2009).

    Article  Google Scholar 

  11. 11

    Tusher, V.G., Tibshirani, R. & Chu, G. Proc. Natl. Acad. Sci. USA 98, 5116–5121 (2001).

    CAS  Article  Google Scholar 

Download references


We thank N. Hartmann, M. Letzkus and E.J. Oakeley for support with mixing experiments; A. Morgan, B. Narasimhan, R. Olshen, E. Eden, members of Stanford Molecular Profiling Colloquium and Biostats forum for enlightening discussions; O. Goldberger, M. Drukker, G. Nestorova, X. Ji and D. Hirschberg for generating mixture datasets; A. Skrenchuk and B. Oskotsky for computer support; and the Lucile Packard Foundation for Children's Health and the Hewlett Packard Foundation for support and computational resources. S.S.S.-O., M.M.D. and A.J.B. are supported by the US National Institutes of Health (NIH) (U19 AI057229). S.S.S.-O. was also supported by the Brennan family. R.T. is supported by the National Science Foundation (DMS-9971405) and NIH (contract N01-HV-28183). P.K. and M.M.S. are supported by NIH (U01 AI077821 and R21 AI075256). T.H. is supported by the National Science Foundation (DMS-0505676) and NIH (2R01 CA 72028-07).

Author information




S.S.S.-O., R.T., D.L.B., F.S., M.M.D. and A.J.B. designed the experiments. S.S.S.-O., R.T., T.H. and P.K. developed the algorithms. M.M.S., F.S. and D.L.B. generated the data. S.S.S.-O., R.T., P.K., N.M.P. and D.L.B. analyzed the data. S.S.S.-O., R.T., P.K., M.M.D. and A.J.B. wrote the manuscript.

Corresponding authors

Correspondence to Mark M Davis or Atul J Butte.

Ethics declarations

Competing interests

D.L.B. and F.S. are employees of Novartis. M.M.D. is a paid consultant to Novartis. A.J.B. is or has served as a scientific advisor and/or consultant to NuMedii, Genstruct, Prevendia, Tercica, Eli Lilly and Company, and Johnson and Johnson.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Tables 1–3, Supplementary Notes 1–2 (PDF 5148 kb)

Supplementary Data

Source code for csSAM (ZIP 1040 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Shen-Orr, S., Tibshirani, R., Khatri, P. et al. Cell type–specific gene expression differences in complex tissues. Nat Methods 7, 287–289 (2010).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing