Activating transcription factor gene transcriptions
Activating transcription factor (ATF) is a group of bZIP transcription factors, which act as homodimers or heterodimers with a range of other bZIP factors. First, they have been described as members of the CREB/ATF family, whereas it turned out later that some of them might be more similar to AP-1-like factors such as c-Jun or c-Fos. Some of these ATFs, such as ATF3, ATF4, and ATF6 are known to play a role in stress responses. Another example of ATF function would be ATFx that can suppress apoptosis.
"ATF4 is known to regulate transcription by formation of the dimer complexes with the transcription factors of AP-1, Jun and C/EBP (CCAAT-enhancer binding protein) families (Horiguchi et al., 2012; Kilberg et al., 2009). The dimers bind to hybrid C/EBP-ATF responsive elements (CARE), consisting of two half-sites required for binding of C/EBP and ATF family proteins, respectively (Kilberg et al., 2009). By scanning ADM2 promoter region, we did not find potential ATF4 binding sites at reasonable distances upstream of the transcription start site. However a suitable candidate for ATF4-response element (GTTGCATCA corresponding to the consensus XTTXCATCA (Kilberg et al., 2009)) was found at a distance of 30 bp downstream from the ADM2 translation start codon."
"ATF4 regulates transcription of its target genes through the formation of homodimers or heterooligomers with the transcription factors Jun, AP-1 and C/EBP38,39 that bind to CARE (C/EBP-ATF) responsive elements having the consensus sequence XTTXCATCA (where X = G, A or T).39 In the region from -625 to -618 bp relative to the SESN2 translation start codon (from -228 to -221 bp relative to the transcription start site) we found a candidate sequence for the ATF4 binding site TTTTCATCA."

# Human genes
Genes include ATF1, ATF2, ATF3, ATF4, ATF5, ATF6, ATF7, ATFx.
Gene ID: 466 is ATF1 activating transcription factor 1 on 12q13.12: "This gene encodes an activating transcription factor, which belongs to the ATF subfamily and bZIP (basic-region leucine zipper) family. It influences cellular physiologic processes by regulating the expression of downstream target genes, which are related to growth, survival, and other cellular activities. This protein is phosphorylated at serine 63 in its kinase-inducible domain by serine/threonine kinases, cAMP-dependent protein kinase A, calmodulin-dependent protein kinase I/II, mitogen- and stress-activated protein kinase and cyclin-dependent kinase 3 (cdk-3). Its phosphorylation enhances its transactivation and transcriptional activities, and enhances cell transformation. Fusion of this gene and FUS on chromosome 16 or EWSR1 on chromosome 22 induced by translocation generates chimeric proteins in angiomatoid fibrous histiocytoma and clear cell sarcoma. This gene has a pseudogene on chromosome 6."

# Consensus sequences
"The ATF4 binding consensus sequence has been reported as (G/A/C)TT(G/A/T)C(G/A)TCA (38), which matches the ChIP-seq data."
5'-(A/G/T)TT(A/G/T)CATCA-3'
Combined consensus sequences are XTTXCATCA (where X = G, A or T), TTTTCATCA, and (G/A/C)TT(G/A/T)C(G/A)TCA to produce 5'-NTT(A/G/T)C(A/G)TCA-3'.

# Hypotheses
- A1BG has no Activating transcription factor in either promoter.
- A1BG is not transcribed by an Activating transcription factor.
- Activating transcription factors do not participate in the transcription of A1BG.

# Activating transcription factor samplings (Burton)
For the Basic programs testing consensus sequence 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3' (starting with SuccessablesATF.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 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3', 0.
- negative strand, positive direction, looking for 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3', 2, 5'-CTTGCGTCA-3' at 2423, 5'-CTTTCGTCA-3' at 1184.
- positive strand, negative direction, looking for 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3', 1, 5'-ATTTCATCA-3' at 2888.
- positive strand, positive direction, looking for 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3', 0.
- inverse complement, negative strand, negative direction is SuccessablesATFci--.bas, looking for 5'-TGA(C/T)G(A/C/T)AA(C/G/T)-3', 0.
- inverse complement, negative strand, positive direction is SuccessablesATFci-+.bas, looking for 5'-TGA(C/T)G(A/C/T)AA(C/G/T)-3', 1, 5'-TGATGAAAC-3' at 2147.
- inverse complement, positive strand, negative direction is SuccessablesATFci+-.bas, looking for 5'-TGA(C/T)G(A/C/T)AA(C/G/T)-3', 1, 5'-TGACGAAAC-3' at 313.
- inverse complement, positive strand, positive direction is SuccessablesATFci++.bas, looking for 5'-TGA(C/T)G(A/C/T)AA(C/G/T)-3', 1, 5'-TGACGTAAG-3' at 2207.

## ATFB (4560-2846) UTRs
- Positive strand, negative direction: ATTTCATCA at 2888.

## ATFB negative direction (2596-1) distal promoters
- Positive strand, negative direction: TGACGAAAC at 313.

## ATFB positive direction (4050-1) distal promoters
- Negative strand, positive direction: CTTGCGTCA at 2423, TGATGAAAC at 2147, CTTTCGTCA at 1184.
- Positive strand, positive direction: TGACGTAAG at 2207.

# Activating transcription factor (Burton) random dataset samplings
- ATFBr0: 0.
- ATFBr1: 0.
- ATFBr2: 0.
- ATFBr3: 0.
- ATFBr4: 0.
- ATFBr5: 0.
- ATFBr6: 0.
- ATFBr7: 0.
- ATFBr8: 0.
- ATFBr9: 1, GTTTCATCA at 1242.
- ATFBr0ci: 1, TGATGAAAC at 1932.
- ATFBr1ci: 0.
- ATFBr2ci: 0.
- ATFBr3ci: 0.
- ATFBr4ci: 0.
- ATFBr5ci: 0.
- ATFBr6ci: 0.
- ATFBr7ci: 0.
- ATFBr8ci: 0.
- ATFBr9ci: 0.

## ATFBr arbitrary negative direction (evens) (2596-1) distal promoters
- ATFBr0ci: TGATGAAAC at 1932.

## ATFBr alternate negative direction (odds) (2596-1) distal promoters
- ATFBr9: GTTTCATCA at 1242.

## ATFBr arbitrary positive direction (odds) (4050-1) distal promoters
- ATFBr9: GTTTCATCA at 1242.

## ATFBr alternate positive direction (evens) (4050-1) distal promoters
- ATFBr0ci: TGATGAAAC at 1932.

# Activating transcription factor (Burton) analysis and results
"The ATF4 binding consensus sequence has been reported as (G/A/C)TT(G/A/T)C(G/A)TCA (38), which matches the ChIP-seq data."
Comparison:
The occurrences of real activating transcription factor (Burton) UTRs and distals are greater than the randoms. This suggests that the real activating transcription factor (Burton)s are likely active or activable.

# Activating transcription factor samplings (Kilberg)
Copying the consensus for the ATF4: 5'-TTTTCA-3', 5'-CTTTCGTCA-3', or 5'-GTTTCA-3' 5'-GTTTCATC-3' 5'-ATTTCAT-3' (where X = G, A or T) and putting the sequence in "F" finds no, no, no, no, no locations between ZSCAN22 and A1BG and no, one, no, no no, no locations between ZNF497 and A1BG as can be found by the computer programs. Consensus sequence (Kilberg 2009): XTTXCATCA (where X = G, A or T) is 5'-(A/G/T)TT(A/G/T)CATCA-3'.
For the Basic programs testing consensus sequence 5'-(A/G/T)TT(A/G/T)CATCA-3' (starting with SuccessablesATFK.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 5'-(A/G/T)TT(A/G/T)CATCA-3', 0.
- negative strand, positive direction, looking for 5'-(A/G/T)TT(A/G/T)CATCA-3', 0.
- positive strand, negative direction, looking for 5'-(A/G/T)TT(A/G/T)CATCA-3', 1, 5'-ATTTCATCA-3' at 2888.
- positive strand, positive direction, looking for 5'-(A/G/T)TT(A/G/T)CATCA-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-TGATG(A/C/T)AA(A/C/T)-3', 0.
- inverse complement, negative strand, positive direction, looking for 5'-TGATG(A/C/T)AA(A/C/T)-3', 1, 5'-TGATGAAAC-3' at 2147.
- inverse complement, positive strand, negative direction, looking for 5'-TGATG(A/C/T)AA(A/C/T)-3', 0.
- inverse complement, positive strand, positive direction, looking for 5'-TGATG(A/C/T)AA(A/C/T)-3', 0.

## ATFK (4560-2846) UTRs
- Positive strand, negative direction: ATTTCATCA at 2888.

## ATFK positive direction (4050-1) distal promoters
- Negative strand, positive direction: TGATGAAAC at 2147.

# Activating transcription factor (Kilberg) random dataset samplings
- ATFKr0: 0.
- ATFKr1: 0.
- ATFKr2: 0.
- ATFKr3: 0.
- ATFKr4: 0.
- ATFKr5: 0.
- ATFKr6: 0.
- ATFKr7: 0.
- ATFKr8: 0.
- ATFKr9: 1, GTTTCATCA at 1242.
- ATFKr0ci: 1, TGATGAAAC at 1932.
- ATFKr1ci: 0.
- ATFKr2ci: 0.
- ATFKr3ci: 0.
- ATFKr4ci: 0.
- ATFKr5ci: 0.
- ATFKr6ci: 0.
- ATFKr7ci: 0.
- ATFKr8ci: 0.
- ATFKr9ci: 0.

## ATFKr arbitrary negative direction (evens) (2596-1) distal promoters
- ATFKr0ci: TGATGAAAC at 1932.

## ATFKr alternate negative direction (odds) (2596-1) distal promoters
- ATFKr9: GTTTCATCA at 1242.

## ATFKr arbitrary positive direction (odds) (4050-1) distal promoters
- ATFKr9: GTTTCATCA at 1242.

## ATFKr alternate positive direction (evens) (4050-1) distal promoters
- ATFKr0ci: TGATGAAAC at 1932.

# Activating transcription factor (Kilberg) analysis and results
The consensus XTTXCATCA (Kilberg et al., 2009) "having the sequence XTTXCATCA (where X = G, A or T).39 In the region from -625 to -618 bp relative to the SESN2 translation start codon (from -228 to -221 bp relative to the transcription start site) we found a candidate sequence for the ATF4 binding site TTTTCATCA."
Comparison:
The occurrences of real activating transcription factor (Kilberg) UTRs and positive direction distals are greater than the randoms. This suggests that the real activating transcription factor (Kilberg)s are likely active or activable.

# Signal transduction pathways

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