Androgen response element gene transcriptions
"Androgen receptors (ARs) (NR3C4; nuclear receptor subfamily 3, group C, member 4) have a crucial role in the development, function and homeostasis of PCa cells. ARs can be activated as a transcription factor via binding to androgen hormones (either testosterone or dihydrotestosterone). This receptor has two mainfunctional domains: ligand-binding and DNA-binding (DBD).8"
"Androgen response elements structurally consist of a short DNA motif  with  base  sequence  specificity  within  the  promoter upstream of the androgen-responsive genes. The HRE contains a pair of conserved sequences, which are separated by a three-nucleotide spacer. This sequence is determined as 5'-GGTACAnnnTGTTCT-3'10, 11 with 5'-CGG-3' as the spacer in the androgen response element."
"The androgen response element sequence, 5'-GGTACACGGTGTTCT-3', was obtained  from  the  National  Center  of  Biotechnology  Information (NCBI)."
"ARE half sites, benefit from neighboring motifs or cooperating transcription factors in regulating gene expression."
"AREs are well studied but poorly defined and have been shown to contain two hexamers with a three base-pair spacer with an inverted repeat in the second hexamer22."
A "strict ideal 15mer motif search pattern of two hexamers with a 3mer spacer  AGAACANNNTGTTCT ."
"The ideal 15mer model of AGAACANNNTGTTCT had 71 AREs."
"Using the Jaspar motif database, we grouped significant transcription factor logos within a window of 160 bp from the ARE with a p-value of less than 0.05. Top hits included forkhead box (FOX), Kruppel-like factors (KLF), basic helix-loop-helix (BHLH), sterol regulatory element binding factor (SREBF), and v-myc avian myelocytomatosis viral oncogene homolog (MYC) families of transcription factors."
"Taken together, the transcription factor network analysis (top hits in motif enrichment with p-values below 0.05) suggests that KLF, MYC, FOX, and SREBF families of transcription factors have the ability to utilize motifs in the cistrome of AREs and to cooperate with the AR."
"Despite a larger number of weaker ARE half sites found in the proximity of KLF motifs, stronger AREs next to KLF motifs resulted in a larger transcriptional response."
"The KLF family recognizing GC/GT boxes has been implicated in regulation of oncogenic expression signatures in LNCaP and PC3 prostate cancer cell lines85,86."

# Human genes
Gene ID: 367 is AR androgen receptor aka NR3C4 on Xq12: "The androgen receptor gene is more than 90 kb long and codes for a protein that has 3 major functional domains: the N-terminal domain, DNA-binding domain, and androgen-binding domain. The protein functions as a steroid-hormone activated transcription factor. Upon binding the hormone ligand, the receptor dissociates from accessory proteins, translocates into the nucleus, dimerizes, and then stimulates transcription of androgen responsive genes. This gene contains 2 polymorphic trinucleotide repeat segments that encode polyglutamine and polyglycine tracts in the N-terminal transactivation domain of its protein. Expansion of the polyglutamine tract from the normal 9-34 repeats to the pathogenic 38-62 repeats causes spinal bulbar muscular atrophy (SBMA, also known as Kennedy's disease). Mutations in this gene are also associated with complete androgen insensitivity (CAIS). Alternative splicing results in multiple transcript variants encoding different isoforms."

# Gene expressions
"Biased expression in liver (RPKM 12.9), endometrium (RPKM 10.8) and 13 other tissues."

# Consensus sequences
5-GGTACACGGTGTTCT-3
5'-TGGAGAACAGCCTGTTCTCCA-3' or 5'-AGAACAGCCTGTTCT-3' "Using the identified AREs within our experiment a refined extended canonical ARE model is proposed and deposited in transcription factor databases ."

# Hypotheses
- A1BG has no Androgen response elements in either promoter.
- A1BG is not transcribed by an Androgen response element.
- Androgen response element does not participate in the transcription of A1BG.

# Androgen response element1 (Kouhpayeh) samplings
Copying a responsive elements consensus sequence GGTACA and putting the sequence in "F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence GGTACA (starting with SuccessablesAnRE1.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction: 0.
- negative strand, positive direction: 0.
- positive strand, negative direction: 0.
- positive strand, positive direction: 3, GGTACA at 3901, GGTACA at 3336, GGTACA at 2474.
- inverse complement, negative strand, negative direction: 3, TGTACC at 2614, TGTACC at 2152, TGTACC at 1207.
- inverse complement, negative strand, positive direction: 0.
- inverse complement, positive strand, negative direction: 1, TGTACC at 798.
- inverse complement, positive strand, positive direction: 1, TGTACC at 2032.

## AnRE1 negative direction (2811-2596) proximal promoters
- Negative strand, negative direction: TGTACC at 2614.

## AnRE1 negative direction (2596-1) distal promoters
- Negative strand, negative direction: TGTACC at 2152, TGTACC at 1207.
- Positive strand, negative direction: TGTACC at 798.

## AnRE1 positive direction (4050-1) distal promoters
- Positive strand, positive direction: GGTACA at 3901, GGTACA at 3336, GGTACA at 2474, TGTACC at 2032.

# AnRE1 random dataset samplings
- AnRE1r0: 1, GGTACA at 1283.
- AnRE1r1: 2, GGTACA at 3352, GGTACA at 1127.
- AnRE1r2: 0.
- AnRE1r3: 0.
- AnRE1r4: 1, GGTACA at 3774.
- AnRE1r5: 2, GGTACA at 3253, GGTACA at 2244.
- AnRE1r6: 1, GGTACA at 1805.
- AnRE1r7: 0.
- AnRE1r8: 0.
- AnRE1r9: 1, GGTACA at 4067.
- AnRE1r0ci: 0.
- AnRE1r1ci: 0.
- AnRE1r2ci: 0.
- AnRE1r3ci: 0.
- AnRE1r4ci: 2, TGTACC at 4543, TGTACC at 1217.
- AnRE1r5ci: 1, TGTACC at 4395.
- AnRE1r6ci: 1, TGTACC at 4193.
- AnRE1r7ci: 0.
- AnRE1r8ci: 2, TGTACC at 2780, TGTACC at 455.
- AnRE1r9ci: 0.

## AnREr arbitrary (evens) (4560-2846) UTRs
- AnRE1r4: GGTACA at 3774.
- AnRE1r4ci: TGTACC at 4543.
- AnRE1r6ci:  TGTACC at 4193.

## AnRE1r alternate (odds) (4560-2846) UTRs
- AnRE1r1: GGTACA at 3352.
- AnRE1r5: GGTACA at 3253.
- AnRE1r9: GGTACA at 4067.
- AnRE1r5ci: TGTACC at 4395.

## AnRE1r arbitrary positive direction (odds) (4445-4265) core promoters
- AnRE1r5ci: TGTACC at 4395.

## AnRE1r arbitrary negative direction (evens) (2811-2596) proximal promoters
- AnRE1r8ci: TGTACC at 2780.

## AnRE1r arbitrary positive direction (odds) (4265-4050) proximal promoters
- AnRE1r9: GGTACA at 4067.

## AnRE1r alternate positive direction (evens) (4265-4050) proximal promoters
- AnRE1r6ci: TGTACC at 4193.

## AnRE1r arbitrary negative direction (evens) (2596-1) distal promoters
- AnRE1r0: GGTACA at 1283.
- AnRE1r6: GGTACA at 1805.
- AnRE1r4ci: TGTACC at 1217.
- AnRE1r8ci: TGTACC at 455.

## AnRE1r alternate negative direction (odds) (2596-1) distal promoters
- AnRE1r1: GGTACA at 1127.
- AnRE1r5: GGTACA at 2244.

## AnRE1r arbitrary positive direction (odds) (4050-1) distal promoters
- AnRE1r1: GGTACA at 3352, GGTACA at 1127.
- AnRE1r5: GGTACA at 3253, GGTACA at 2244.

## AnRE1r alternate positive direction (evens) (4050-1) distal promoters
- AnRE1r0: GGTACA at 1283.
- AnRE1r4: GGTACA at 3774.
- AnRE1r6: GGTACA at 1805.
- AnRE1r4ci: TGTACC at 1217.
- AnRE1r8ci: TGTACC at 2780, TGTACC at 455.

# Androgen response element1 analysis and results
"The HRE contains a pair of conserved sequences, which are separated by a three-nucleotide spacer. This sequence is determined as 5'-GGTACAnnnTGTTCT-3'10, 11 with 5'-CGG-3' as the spacer in the androgen response element."
Comparison:
The occurrences of real androgen response element1s (AnRE1) are greater than the randoms. This suggests that the real AnRE1s are likely active or activable.

# Androgen response element2 (Kouhpayeh) samplings
For the Basic programs testing consensus sequence TGTTCT (starting with SuccessablesAnRE2.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction: 4, TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
- negative strand, positive direction: 1, TGTTCT at 108.
- positive strand, negative direction: 1, TGTTCT at 45.
- positive strand, positive direction: TGTTCT, 0.
- inverse complement, negative strand, negative direction: 1, AGAACA at 281.
- inverse complement, negative strand, positive direction: 2, AGAACA at 4068, AGAACA at 3094.
- inverse complement, positive strand, negative direction: 2, AGAACA at 3668, AGAACA at 287.
- inverse complement, positive strand, positive direction: 0.

## AnRE2 (4560-2846) UTRs
- Negative strand, negative direction: TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
- Positive strand, negative direction: AGAACA at 3668.

## AnRE2 positive direction (4265-4050) proximal promoters
- Negative strand, positive direction: AGAACA at 4068.

## ARnE2 negative direction (2596-1) distal promoters
- Negative strand, negative direction: AGAACA at 281.
- Positive strand, negative direction: AGAACA at 287, TGTTCT at 45.

## AnRE2 positive direction (4050-1) distal promoters
- Negative strand, positive direction: AGAACA at 3094, TGTTCT at 108.

# AnRE2 random dataset samplings
- AnRE2r0: 1, TGTTCT at 1979.
- AnRE2r1: 1, TGTTCT at 1218.
- AnRE2r2: 0.
- AnRE2r3: 0.
- AnRE2r4: 0.
- AnRE2r5: 2, TGTTCT at 2442, TGTTCT at 958.
- AnRE2r6: 1, TGTTCT at 827.
- AnRE2r7: 1, TGTTCT at 1886.
- AnRE2r8: 1, TGTTCT at 217.
- AnRE2r9: 1, TGTTCT at 1534.
- AnRE2r0ci: 0.
- AnRE2r1ci: 2, AGAACA at 4240, AGAACA at 2607.
- AnRE2r2ci: 1, AGAACA at 908.
- AnRE2r3ci: 0.
- AnRE2r4ci: 0.
- AnRE2r5ci: 1, AGAACA at 1196.
- AnRE2r6ci: 1, AGAACA at 646.
- AnRE2r7ci: 0.
- AnRE2r8ci: 1, AGAACA at 4495.
- AnRE2r9ci: 0.

## AnRE2r arbitrary (evens) (4560-2846) UTRs
- AnRE2r8ci: AGAACA at 4495.

## AnRE2r alternate (odds) (4560-2846) UTRs
- AnRE2r1ci: AGAACA at 4240.

## AnRE2r alternate negative direction (odds) (2811-2596) proximal promoters
- AnRE2r1ci: AGAACA at 2607.

## AnRE2r arbitrary positive direction (odds) (4265-4050) proximal promoters
- AnRE2r1ci: AGAACA at 4240.

## AnRE2r arbitrary negative direction (evens) (2596-1) distal promoters
- AnRE2r0: TGTTCT at 1979.
- AnRE2r6: TGTTCT at 827.
- AnRE2r8: TGTTCT at 217.
- AnRE2r2ci: AGAACA at 908.
- AnRE2r6ci: AGAACA at 646.

## AnRE2r alternate negative direction (odds) (2596-1) distal promoters
- AnRE2r1: TGTTCT at 1218.
- AnRE2r5: TGTTCT at 2442, TGTTCT at 958.
- AnRE2r7: TGTTCT at 1886.
- AnRE2r9: TGTTCT at 1534.
- AnRE2r5ci: AGAACA at 1196.

## AnRE2r arbitrary positive direction (odds) (4050-1) distal promoters
- AnRE2r1: TGTTCT at 1218.
- AnRE2r5: TGTTCT at 2442, TGTTCT at 958.
- AnRE2r7: TGTTCT at 1886.
- AnRE2r9: TGTTCT at 1534.
- AnRE2r1ci: AGAACA at 2607.
- AnRE2r5ci: AGAACA at 1196.

## AnRE2r alternate positive direction (evens) (4050-1) distal promoters
- AnRE2r0: TGTTCT at 1979.
- AnRE2r6: TGTTCT at 827.
- AnRE2r8: TGTTCT at 217.
- AnRE2r2ci: AGAACA at 908.
- AnRE2r6ci: AGAACA at 646.

# Androgen response element2 analysis and results
This sequence is determined as 5'-GGTACAnnnTGTTCT-3'10, 11 with 5'-CGG-3' as the spacer in the androgen response element." Here, AnRE2 is TGTTCT.
Comparison:
The occurrences of real AnRE2s are greater than the randoms. This suggests that the real AnRE2s are likely active or activable.

# Full AnRE (Kouhpayeh)
- negative strand, negative direction, looking for 5'-GGTACANNNTGTTCT-3', 0.
- positive strand, positive direction, looking for 5'-GGTACANNNTGTTCT-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-AGAACANNNTGTACC-3', 0.
- inverse negative strand, negative direction, looking for 5'-TCTTGTNNNACATGG-3', 0.
- inverse negative strand, positive direction, looking for 5'-TCTTGTNNNACATGG-3', 0.

# Androgen response element (Wilson) samplings
Copying a responsive elements consensus sequence TGATTCGTGAG and putting the sequence in "F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs. Ideal consensus sequence is AGAACANNNTGTTCT.
For the Basic programs testing consensus sequence AGAACANNNTGTTCT (starting with SuccessablesAnREW.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction, looking for AGAACANNNTGTTCT, 0.
- negative strand, positive direction, looking for AGAACANNNTGTTCT, 0.
- positive strand, negative direction, looking for AGAACANNNTGTTCT, 0.
- positive strand, positive direction, looking for AGAACANNNTGTTCT, 0.
- complement, negative strand, negative direction, looking for TCTTGTNNNACAAGA, 0.
- complement, negative strand, positive direction, looking for TCTTGTNNNACAAGA, 0.
- complement, positive strand, negative direction, looking for TCTTGTNNNACAAGA, 0.
- complement, positive strand, positive direction, looking for TCTTGTNNNACAAGA, 0.
The inverse complement is the same as the initial direct.
The inverse is the same as the initial direct complement.

## AnREW (4560-2846) UTRs
- Negative strand, negative direction: TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
- Positive strand, negative direction: AGAACA at 3668.

## AnREW positive direction (4265-4050) proximal promoters
- Negative strand, positive direction: AGAACA at 4068.

## AnREW negative direction (2596-1) distal promoters
- Negative strand, negative direction: AGAACA at 281.
- Positive strand, negative direction: AGAACA at 287, TGTTCT at 45.

## AnREW positive direction (4050-1) distal promoters
- Negative strand, positive direction: AGAACA at 3094, TGTTCT at 108.

# AnREW ACAAGA and TGTTCT random dataset samplings
- AnRE2r0: 1, TGTTCT at 1979.
- AnRE2r1: 1, TGTTCT at 1218.
- AnRE2r2: 0.
- AnRE2r3: 0.
- AnRE2r4: 0.
- AnRE2r5: 2, TGTTCT at 2442, TGTTCT at 958.
- AnRE2r6: 1, TGTTCT at 827.
- AnRE2r7: 1, TGTTCT at 1886.
- AnRE2r8: 1, TGTTCT at 217.
- AnRE2r9: 1, TGTTCT at 1534.
- AnREWr0: 0.
- AnREWr1: 2, AGAACA at 4240, AGAACA at 2607.
- AnREWr2: 1, AGAACA at 908.
- AnREWr3: 0.
- AnREWr4: 0.
- AnREWr5: 1, AGAACA at 1196.
- AnREWr6: 1, AGAACA at 646.
- AnREWr7: 0.
- AnREWr8: 1, AGAACA at 4495.
- AnREWr9: 0.

## AnREWr arbitrary (evens) (4560-2846) UTRs
- AnREWr8: AGAACA at 4495.

## AnREWr alternate (odds) (4560-2846) UTRs
- AnREWr1: AGAACA at 4240.

## AnREWr alternate negative direction (odds) (2811-2596) proximal promoters
- AnREWr1: AGAACA at 2607.

## AnREWr arbitrary positive direction (odds) (4265-4050) proximal promoters
- AnREWr1: AGAACA at 4240.

## AnREWr arbitrary negative direction (evens) (2596-1) distal promoters
- AnRE2r0: TGTTCT at 1979.
- AnRE2r6: TGTTCT at 827.
- AnRE2r8: TGTTCT at 217.
- AnREWr2: AGAACA at 908.
- AnREWr6: AGAACA at 646.

## AnREWr alternate negative direction (odds) (2596-1) distal promoters
- AnRE2r1: TGTTCT at 1218.
- AnRE2r5: TGTTCT at 2442, TGTTCT at 958.
- AnRE2r7: TGTTCT at 1886.
- AnRE2r9: TGTTCT at 1534.
- AnREWr5: AGAACA at 1196.

## AnREWr arbitrary positive direction (odds) (4050-1) distal promoters
- AnRE2r1: TGTTCT at 1218.
- AnRE2r5: TGTTCT at 2442, TGTTCT at 958.
- AnRE2r7: TGTTCT at 1886.
- AnRE2r9: TGTTCT at 1534.
- AnREWr1: AGAACA at 2607.
- AnREWr5: AGAACA at 1196.

## AnREWr alternate positive direction (evens) (4050-1) distal promoters
- AnRE2r0: TGTTCT at 1979.
- AnRE2r6: TGTTCT at 827.
- AnRE2r8: TGTTCT at 217.
- AnREWr2: AGAACA at 908.
- AnREWr6: AGAACA at 646.

# Androgen response element (Wilson) analysis and results
A "strict ideal 15mer motif search pattern of two hexamers with a 3mer spacer  AGAACANNNTGTTCT ."
Comparison:
The occurrences of real AnREWs are greater than the randoms. This suggests that the real AnREWs are likely active or activable.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.