Cell Type–Specific Hypoxia Response

(A and B) Hierarchical clustering of a total of 5,432 array elements showing a cell type-specific hypoxia response that are selected by multiclass SAM using zero-transformed gene expression with a FDR of 3.7% (A). The orange vertical bar marks clusters of genes induced only in RPTECs and is expanded with the names of representative genes (B).

(C) The number of genes (y-axis) with fold inductions greater than those indicated (x-axis) in all six hypoxic samples (6, 12, and 24 h at 2% and 0% O2) are shown for SMCs (SM, blue curve), HMECs (pink curve), and RPTEC#1 (orange curve).

(D) Comparison of the gene expression pattern of VHL-reconstituted RCCs (A498 cells) to the hypoxia response of RPTEC#1. We compared the expression of genes affected by VHL reconstitution of VHL-deficient RCC A498 cells (from [38] and in the sample marked “VHL repression”) to the expression of those same genes in RPTEC#1 with hypoxia treatments (samples marked “RPTEC#1 hypoxia”). Genes showing concurrent induction (vertical red bar), concurrent repression (vertical green bar), and VHL-specific response (vertical black bar) are shown with selected gene names. (Complete data can be found at: http://microarray-pubs.stanford.edu/hypoxia)