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Table 1 AR targets identified in this study

From: Identification of novel androgen receptor target genes in prostate cancer

CD Primers1

Band2

Ava II – Ava II3

Nearby Genes4

Position of CD Hit Relative to gene

ChIP validation5

     

C4-2B

LNCaP

AT, TA

1p35.2

30,152,547 – 30,152,728

Nearest gene is 626-kb away

4

2

AA, TC

1q25.2

178,433,288 – 178,433,456

QSCN6[63, 67]

exon 13

3

1

   

LHX4 [68]

32.7-kb 5'

  
   

CEP350

84.2-kb3'

  
   

ACBD6

90.6-kb 3'

  

AT, AT

2q37.3

241,348,804 – 241,348,990

KIF1A

intron 23/exon 24

3

1

   

AQP12

62.4-kb 3'

  

TT, TT

3p21.1

53,169,093 – 53,169,401

PRKCD[51, 53]

0.8-kb 5'

4

nd

AT, AC

4p16.1

6,644,411 – 6,644,619

MAN2B2

intron 5

3

3

   

MRFAP1

48.7-kb 5'

  

AA, TC

7q11.23

72,483,118 – 72,483,317

FZD9[69]

2.7-kb 5'

4

nd

   

BAZ1B

10k-b 3'

  

AT, AG

7q11.23

72,922,165 – 72,922,474

WBSCR28

4-kb 3'

4

2

   

WBSCR27

27.4-kb 5'

  
   

CLDN4 [70]

37.2-kb 3'

  

AA, AG

8q24.3

143,094,298 – 143,094,518

Nearest gene is 197kb away [64]

3

2

AC, TC

10p12.1

24,584,349 – 24,584,579

KIAA1217

intron 2

4

3

AT, AG

10q26.13

126,072,189 – 126,072,473

OAT

3.4-kb 3'

2

0

   

LHPP

67.9-kb 5'

  

AC, TC

11p15.4

1,017,234 – 1,017,529

MUC6[58]

10-kb 5'

3

3

   

AP2A2

15-kb 3'

  

AT, AT

11q12.3

62,532,814 – 62,532,977

SLC22A8

intron 2

5

2

   

SLC22A6

23.9-kb 5'

  
   

CHRM1

87.3-kb 5'

  

AT, AT

11q25

134,102,859 – 134,103,167

Nearest gene is 315-kb away

2

3

AT, AT

14q31.3

86,510,091 – 86,510,360

Nearest gene is 959-kb away

3

2

AT, AC

17p13.2

3,446,846 – 3,447,080

TRPV1

exon 1/intron 1

3

1

   

CARKL

11.4-kb 3'

  
   

TRPV3 [60, 61]

39-kb 5'

  

AC, TG

17q25.3

77,480,155 – 77,480,527

MAFG

1.5-kb 5'

4

2

   

PYCR1 [36, 50]

2.5-kb 3'

  
   

SIRT7 [71, 72]

12-kb 5'

  

AA, AA

22q11.23

22,655,127 – 22,655,462

GSTT2[62]

exon 4/intron 4

3

2

   

DDT

3.1-kb 5'

  

AG, AG

22q13.1

38,101,611 – 38,101,989

SYNGR1

intron 2

3

2

   

MAP3K7IP1

25-kb 5'

  

AC, TC

22q13.3

48,707,684 – 48,707,956

CRELD2

1-kb 3'

3

1

   

ALG12

10-kb 5'

  
  1. 1CD primers are defined based on two variable nucleotides as described in Methods.
  2. 2Cytogenetic band containing the CD hit.
  3. 3Absolute positions of the Ava II sites flanking the fragment displayed by PAGE.
  4. 4The nearest Refseq gene annotated in Ensembl [65] is shown in bolded and italicized text. Published papers suggesting relevance to cancer are referenced near the respective gene name.
  5. 5Number of independent conventional ChIP assays in which AR occupancy was confirmed. nd, not determined.