Identification of putative AR target genes for inclusion on the Agilent oligoarray

a. Retrieve AR binding regions from a genome-wide AR ChIP-chip study on prostate cancer cells

- a list of AR binding regions (hg18 build) from LNCaP cells treated for 4 hours with 100nM DHT was downloaded from the Brown laboratory website (http://research4.dfci.harvard.edu/brownlab/, file: AR data file 21809p1E-4_LNCaP_AR_4hr.bed.xls) (1) 

- AR binding regions with p≤1e-4 were considered 

b. Define location of AR binding sites relative to transcriptional start sites (TTSs)

- genomic coordinates for TSSs of human RefSeq transcripts were obtained from the UCSC genome browser (hg18 build) 

- the nearest AR binding region for each human RefSeq gene TSS was identified using a PERL script

c. Define androgen-responsive genes harboring AR binding site(s) within 300 KB of TTS

-  genes reported as androgen-responsive in LNCaP cells were retrieved from literature (2-9) 

- genes associated with an AR binding site(s) under b. were cross-matched with androgen-responsive genes  

- androgen-responsive genes harboring an AR binding region(s) within 300Kb of their TSS(s) were withheld for inclusion on a custom oligoarray

References

1.    Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J, et al. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 2009;138(2):245-56.

2.    DePrimo SE, Diehn M, Nelson JB, Reiter RE, Matese J, Fero M, et al. Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biol. 2002;3(7):RESEARCH0032.

3.    Nelson PS, Clegg N, Arnold H, Ferguson C, Bonham M, White J, et al. The program of androgen-responsive genes in neoplastic prostate epithelium. Proc Natl Acad Sci U S A. 2002;99(18):11890-5.

4.    Segawa T, Nau ME, Xu LL, Chilukuri RN, Makarem M, Zhang W, et al. Androgen-induced expression of endoplasmic reticulum (ER) stress response genes in prostate cancer cells. Oncogene. 2002;21(57):8749-58.

5.    Febbo PG, Lowenberg M, Thorner AR, Brown M, Loda M, Golub TR. Androgen mediated regulation and functional implications of fkbp51 expression in prostate cancer. J Urol. 2005;173(5):1772-7.

6.    Velasco AM, Gillis KA, Li Y, Brown EL, Sadler TM, Achilleos M, et al. Identification and validation of novel androgen-regulated genes in prostate cancer. Endocrinology. 2004;145(8):3913-24.

7.    Ngan S, Stronach EA, Photiou A, Waxman J, Ali S, Buluwela L. Microarray coupled to quantitative RT-PCR analysis of androgen-regulated genes in human LNCaP prostate cancer cells. Oncogene. 2009;28(19):2051-63.

8.    Waghray A, Feroze F, Schober MS, Yao F, Wood C, Puravs E, et al. Identification of androgen-regulated genes in the prostate cancer cell line LNCaP by serial analysis of gene expression and proteomic analysis. Proteomics. 2001;1(10):1327-38.

9.    Xu LL, Su YP, Labiche R, Segawa T, Shanmugam N, McLeod DG, et al. Quantitative expression profile of androgen-regulated genes in prostate cancer cells and identification of prostate-specific genes. Int J Cancer. 2001;92(3):322-8.