Quick tour
How to use the database:
Choose the species, select the table your want to search, leave field as it as ('All') and type in the gene you want to search. A table listing the search results will be returned, followed by the description of the table. If no search result is returned, don't give up yet, try use the official gene symbol or gene ID (locuslink number) from NCBI Entrez Gene.
How to interpret the result:
When the promoter of a gene is occupied by CREB protein, we call it a CREB target gene. In each tissue or cell type, only a small yet distinct subset of CREB target gene are activated by cAMP. Before we look at the result, please keep in mind a few important concepts here:
1) It seems CREB occupancy is very similar across tissues. If you see CREB
binding in HEK293T cells from the ChIP-on-chip result, it is likely this is
also true in the tissue you are interested in.
2) However, only a small subset of CREB occupied promoters are responsive to
cAMP in each tissue. If you see a CREB target gene being induced by cAMP in
liver, it does not say anything about whether the gene will be incuded in brain.
3) The sensitivity of the ChIP-chip assay is only about 50%. For genes below
the threshold, it could still be a perfect CREB target if there is strong evidence
from other sources.
We will use some examples to give you a feeling about how to use the database and interpret the result.
a) DUSP1, a typical CREB target gene, which shows CREB occupancy on promoter, induction in HEK293T cells and presence of good CRE on the promoter.
b) NR4A2, a gene highly induced by cAMP in HEK293T cells and contain good CRE sites in the promoter. The ChIP-chip signal is not strong, but based on the other evidence, it is still a good CREB target.
c) FDPS, whose promoter is bound by CREB and contain good CRE sites. The gene in not induced by cAMP in the two tissues we have tested.
Now let's look at some real examples:
a) DUSP1, a typical CREB target gene, which shows CREB occupancy on promoter, induction in HEK293T cells and presence of good CRE on the promoter.
Let's say we want to check dual specificity phosphatase 1. To do this, just
search the gene symbol DUSP1 in "human ChIP-chip" table. Two genes
were returned, the first one was DUSP12, and the second hit was what we want.
The p-value and binding ratio for DUSP1 in HEK293T cells are good, meaning CREB
is proably on the promoter.
No | ID | Symbol | Gene Name | Alias Symbols | Accession | Official Symbol | LocusLink | Probe Type | Ave. HEK CREB p-value | Ave. HEK CREB Binding Ratio | Hepatocyte_CREB p-value | Hepatocyte_CREB Binding Ratio | Hepatocyte_P-CREB p-value | Hepatocyte_P-CREB Binding Ratio | Islet_P-CREB p-value | Islet_P-CREB Binding Ratio | HEK_0h_CREB p-value | HEK_0h_CREB Binding Ratio | HEK_1h_CREB p-value | HEK_1h_CREB Binding Ratio | HEK_4h_CREB p-value | HEK_4h_CREB Binding Ratio | HEK_0h_P-CREB p-value | HEK_0h_P-CREB Binding Ratio | HEK_1h_P-CREB p-value | HEK_1h_P-CREB Binding Ratio | HEK_4h_P-CREB p-value | HEK_4h_P-CREB Binding Ratio | CRE prediction | CREflag | Chr. Location | Note | Link |
1 | Hp1_66_3_6 | DUSP12 | dual specificity phosphatase 12 | DUSP1;YVH1 | NM_007240 | DUSP12 | 11266 | promoter | 9.1E-08 | 3.0 | 4.5E-01 | 1.0 | 2.2E-01 | 1.2 | 1.3E-02 | 1.2 | 7.0E-07 | 3.0 | 5.6E-08 | 2.9 | 4.3E-06 | 3.2 | 9.2E-06 | 2.1 | 1.1E-07 | 2.7 | 2.9E-06 | 2.4 | others | none | chr1_171113511_171114511 | "all, CREBtarget" | HEK293T_Expression Human_CRE_prediction Pancreatic_Islet_Expression |
2 | Hp1_112_7_5 | DUSP1 | dual specificity phosphatase 1 | CL100;HVH1;MKP-1;PTPN10 | NM_004417 | DUSP1 | 1843 | promoter | 7.1E-05 | 2.1 | 2.0E-03 | 1.7 | 1.6E-06 | 2.6 | 9.3E-04 | 2.1 | 2.3E-02 | 1.4 | 1.2E-05 | 2.2 | 3.9E-05 | 2.4 | CRE_TATA | 1FT 3HT 8ht 10h | chr5_178058796_178059796 | "all, CREBtarget" | HEK293T_Expression Human_CRE_prediction Pancreatic_Islet_Expression |
Now we want to see if DUSP1 is induced by cAMP in HEK293T cells. We can search
DUSP1 in HEK293T_expression table, but a faster way is to click the link from
the last column in the table. Now we get the expression result in HEK293T cells.
There are two probe sets for DUSP1 on the Affymetrix array, we can take the
first one, which has higher expression values and is therefor more reliable.
The induction by cAMP agonist FSK in very big, and this effect is blocked by
dominant negative ACREB.
No | probe set | gene | Accession | LocusLink | Description | Symbol | CTRL | FSK | ACREB_FSK | (FSK vs CTRL) FC | (FSK vs CTRL) LFC | (ACREB_FSK vs FSK) FC | (ACREB_FSK vs FSK) LFC | 0hr | 1hr_FSK | 4hr_FSK | (1hr_FSK vs 0hr) FC | (1hr_FSK vs 0hr) LFC | (4hr_FSK vs 0hr) FC | (4hr_FSK vs 0hr) LFC | notes | Link |
1 | 201041_s_at | dual specificity phosphatase 1 | NM_004417.2 | 1843 | "gb:NM_004417.2 /DEF=Homo sapiens dual specificity phosphatase 1 (DUSP1), mRNA. /FEA=mRNA /GEN=DUSP1 /PROD=dual specificity phosphatase 1 /DB_XREF=gi:7108342 /UG=Hs.171695 dual specificity phosphatase 1 /FL=gb:NM_004417.2" | DUSP1 | 195 | 2037.1 | 376.23 | 10.45 | 8.44 | -5.41 | -4.69 | 180.89 | 1972.82 | 339.96 | 10.91 | 8.45 | 1.88 | 1.4 | "all, CREBtarget" | Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression |
2 | 201044_x_at | dual specificity phosphatase 1 | AA530892 | 1843 | Consensus includes gb:AA530892 /FEA=EST /DB_XREF=gi:2273598 /DB_XREF=est:ni97d11.s1 /CLONE=IMAGE:984789 /UG=Hs.171695 dual specificity phosphatase 1 /FL=gb:NM_004417.2 | DUSP1 | -29.55 | 92.41 | -38.7 | 92.41 | 1.68 | -92.41 | -1.64 | 27.78 | 97.34 | 15.14 | 3.5 | 1.17 | -1.84 | 0 | "all, CREBtarget" | Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression |
Now we may also want to check if there is a good CREB on the promoter. To do
this, search DUSP1 in CRE_Preditcion table or just click the link from the last
column. We can see that there is indeed a good full site at -113 and another
half site at -163, and there is a good TATA box following these sites. All look
good.
No | Symbol | Gene Name | Accession | LocusLink | Alias Symbols | CRE Prediction | CRE Flag | Full Site | Half Site | Conserved CRE | CREcluster | pHMM+Pos | Chrom | Strand | Pos | Note | Link |
1 | DUSP1 | dual specificity phosphatase 1 | NM_004417 | 1843 | CL100;HVH1;MKP-1;PTPN10 | CRE_TATA | FT HT ht h | FT_-113 | h_97 ht_-102 HT_-163 ht_-1239 | FT_-113_86 HT_-163_136 | |H_-163_F_-113_h_-102_1 | chr5 | - | 172179126 | "all, CREBtarget" | HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression |
b) NR4A2, a gene highly induced by cAMP in HEK293T cells and
contain good CRE sites in the promoter. The ChIP-chip signal is not strong,
but based on the other evidence, it is still a good CREB target.
Let's say we noticed that NR4A2 is highly induced by cAMP in HEK293T cells.
Search NR4A2 in HEK293T_Expression table and you will get the following. All
three probe sets show good induction by cAMP agonist FSK and this effect is
blocked by dominant negative ACREB.
No | probe set | gene | Accession | LocusLink | Description | Symbol | CTRL | FSK | ACREB_FSK | (FSK vs CTRL) FC | (FSK vs CTRL) LFC | (ACREB_FSK vs FSK) FC | (ACREB_FSK vs FSK) LFC | 0hr | 1hr_FSK | 4hr_FSK | (1hr_FSK vs 0hr) FC | (1hr_FSK vs 0hr) LFC | (4hr_FSK vs 0hr) FC | (4hr_FSK vs 0hr) LFC | notes | Link |
1 | 216248_s_at | "nuclear receptor subfamily 4, group A, member 2" | S77154.1 | 4929 | "Consensus includes gb:S77154.1 /DEF=TINUR= NGFI-Bnur77 beta-type transcription factor homolog human, T lymphoid cell line, PEER, mRNA, 2469 nt. /FEA=mRNA /GEN=TINUR /DB_XREF=gi:913966 /UG=Hs.82120 nuclear receptor subfamily 4, group A, member 2" | NR4A2 | 24.95 | 536.85 | 22.99 | 21.51 | 14.14 | -23.36 | -12.37 | 18.03 | 269.72 | 36.06 | 14.96 | 6.09 | 2 | 0.87 | "all, CREBtarget" | Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression |
2 | 204622_x_at | "nuclear receptor subfamily 4, group A, member 2" | NM_006186.1 | 4929 | "gb:NM_006186.1 /DEF=Homo sapiens nuclear receptor subfamily 4, group A, member 2 (NR4A2), mRNA. /FEA=mRNA /GEN=NR4A2 /PROD=nuclear receptor subfamily 4, group A, member 2 /DB_XREF=gi:5453821 /UG=Hs.82120 nuclear receptor subfamily 4, group A, member 2 /FL=gb:NM_006186.1" | NR4A2 | 29.2 | 512.99 | 31.57 | 17.57 | 9.62 | -16.25 | -10.76 | 13.49 | 199.61 | 45.55 | 14.8 | 5.44 | 3.38 | 1.09 | "all, CREBtarget" | Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression |
3 | 204621_s_at | "nuclear receptor subfamily 4, group A, member 2" | AI935096 | 4929 | "Consensus includes gb:AI935096 /FEA=EST /DB_XREF=gi:5673966 /DB_XREF=est:wp13e10.x1 /CLONE=IMAGE:2464746 /UG=Hs.82120 nuclear receptor subfamily 4, group A, member 2 /FL=gb:NM_006186.1" | NR4A2 | 4.57 | 286.18 | 20.98 | 62.67 | 8.87 | -13.64 | -6.52 | 62.58 | 340.37 | 78.92 | 5.44 | 2.83 | 1.26 | 0.4 | "all, CREBtarget" | Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression |
When we check the promoter by clicking Human_CRE_prediction at the last column, four splice variants of NR4A2 show up. They have the same start site and there are a bunch of conserved CREs on the promoter. These CREs form clusters and they are also positionally conserved.
No | Symbol | Gene Name | Accession | LocusLink | Alias Symbols | CRE Prediction | CRE Flag | Full Site | Half Site | Conserved CRE | CREcluster | pHMM+Pos | Chrom | Strand | Pos | Note | Link |
1 | NR4A2 | "nuclear receptor subfamily 4, group A, member 2" | NM_006186 | 4929 | HZF-3;NOT;NURR1;RNR1;TINUR | CRE_TATA | FT HT H h | FT_-163 | HT_-71 HT_-81 h_-493 H_-1936 H_-2033 H_-2053 | FT_-163_134 HT_-71_42 HT_-81_52 H_-1936_496 H_-2033_593 H_-2053_613 | |H_-2053_H_-2033_0|H_-81_H_-71_1 | FF_human_6.6_-2671_mouse_6.6_-2645 | chr2 | - | 157391745 | "all, CREBtarget" | HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression |
2 | NR4A2 | "nuclear receptor subfamily 4, group A, member 2" | NM_173171 | 4929 | HZF-3;NOT;NURR1;RNR1;TINUR | CRE_TATA | FT HT H h | FT_-163 | HT_-71 HT_-81 h_-493 H_-1936 H_-2033 H_-2053 | FT_-163_134 HT_-71_42 HT_-81_52 H_-1936_496 H_-2033_593 H_-2053_613 | |H_-2053_H_-2033_0|H_-81_H_-71_1 | chr2 | - | 157391745 | "all, CREBtarget" | HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression | |
3 | NR4A2 | "nuclear receptor subfamily 4, group A, member 2" | NM_173172 | 4929 | HZF-3;NOT;NURR1;RNR1;TINUR | CRE_TATA | FT HT H h | FT_-163 | HT_-71 HT_-81 h_-493 H_-1936 H_-2033 H_-2053 | FT_-163_134 HT_-71_42 HT_-81_52 H_-1936_496 H_-2033_593 H_-2053_613 | |H_-2053_H_-2033_0|H_-81_H_-71_1 | chr2 | - | 157391745 | "all, CREBtarget" | HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression | |
4 | NR4A2 | "nuclear receptor subfamily 4, group A, member 2" | NM_173173 | 4929 | HZF-3;NOT;NURR1;RNR1;TINUR | CRE_TATA | FT HT H h | FT_-163 | HT_-71 HT_-81 h_-493 H_-1936 H_-2033 H_-2053 | FT_-163_134 HT_-71_42 HT_-81_52 H_-1936_496 H_-2033_593 H_-2053_613 | |H_-2053_H_-2033_0|H_-81_H_-71_1 | chr2 | - | 157391745 | "all, CREBtarget" | HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression |
However, when we check the ChIP-on-Chip data (click the quick link 'human_ChIP_chip' from the last column), the numbers did not meet the criteria as CREB target genes. This could be due to a variant of reasons, but considering the strong evidence from the two tables above, NR4A2 is still likely a good CREB tagets. Indeed, in our manual ChIP data, NR4A2 promoter is verified to be CREB positive.
No | ID | Symbol | Gene Name | Alias Symbols | Accession | Official Symbol | LocusLink | Probe Type | Ave. HEK CREB p-value | Ave. HEK CREB Binding Ratio | Hepatocyte_CREB p-value | Hepatocyte_CREB Binding Ratio | Hepatocyte_P-CREB p-value | Hepatocyte_P-CREB Binding Ratio | Islet_P-CREB p-value | Islet_P-CREB Binding Ratio | HEK_0h_CREB p-value | HEK_0h_CREB Binding Ratio | HEK_1h_CREB p-value | HEK_1h_CREB Binding Ratio | HEK_4h_CREB p-value | HEK_4h_CREB Binding Ratio | HEK_0h_P-CREB p-value | HEK_0h_P-CREB Binding Ratio | HEK_1h_P-CREB p-value | HEK_1h_P-CREB Binding Ratio | HEK_4h_P-CREB p-value | HEK_4h_P-CREB Binding Ratio | CRE prediction | CREflag | Chr. Location | Note | Link |
1 | Hp1_73_1_3 | NR4A2 | "nuclear receptor subfamily 4, group A, member 2" | HZF-3;NOT;NURR1;RNR1;TINUR | NM_006186 | NR4A2 | 4929 | promoter | 1.4E-01 | 1.4 | 4.2E-02 | 1.4 | 3.2E-01 | 1.1 | 7.7E-01 | 0.8 | CRE_TATA | 1FT 3HT 6H 10h | chr2_155360200_155361200 | "all, " | HEK293T_Expression Human_CRE_prediction Pancreatic_Islet_Expression |
c) FDPS, whose promoter is bound by CREB and contain good CRE sites. The gene in not induced by cAMP in the two tissues we have tested.
The promoter of FDPS shows very good ChIP-chip signal (search FDPS in human_ChIP_chip table). The values are good in all ChIP experiments we tested.
No | ID | Symbol | Gene Name | Alias Symbols | Accession | Official Symbol | LocusLink | Probe Type | Ave. HEK CREB p-value | Ave. HEK CREB Binding Ratio | Hepatocyte_CREB p-value | Hepatocyte_CREB Binding Ratio | Hepatocyte_P-CREB p-value | Hepatocyte_P-CREB Binding Ratio | Islet_P-CREB p-value | Islet_P-CREB Binding Ratio | HEK_0h_CREB p-value | HEK_0h_CREB Binding Ratio | HEK_1h_CREB p-value | HEK_1h_CREB Binding Ratio | HEK_4h_CREB p-value | HEK_4h_CREB Binding Ratio | HEK_0h_P-CREB p-value | HEK_0h_P-CREB Binding Ratio | HEK_1h_P-CREB p-value | HEK_1h_P-CREB Binding Ratio | HEK_4h_P-CREB p-value | HEK_4h_P-CREB Binding Ratio | CRE prediction | CREflag | Chr. Location | Note | Link |
1 | Hp1_5_1_11 | FDPS | "farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)" | FPS | NM_002004 | FDPS | 2224 | promoter | 1.4E-10 | 4.6 | 1.6E-05 | 2.2 | 2.9E-06 | 3.1 | 3.5E-02 | 1.2 | 8.0E-10 | 5.0 | 5.2E-11 | 4.6 | 1.6E-07 | 4.3 | 2.7E-10 | 3.4 | 2.4E-11 | 4.0 | 1.9E-09 | 3.9 | CRE_TATA | 3HT 8ht | chr1_157499889_157500889 | "all, CREBtarget" | HEK293T_Expression Human_CRE_prediction Pancreatic_Islet_Expression |
By clicking the human_CRE_prediction link at the last column, we can see that the promoter contains a conserved half CRE site.
No | Symbol | Gene Name | Accession | LocusLink | Alias Symbols | CRE Prediction | CRE Flag | Full Site | Half Site | Conserved CRE | CREcluster | pHMM+Pos | Chrom | Strand | Pos | Note | Link |
1 | FDPS | "farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)" | NM_002004 | 2224 | FPS | CRE_TATA | HT ht | h_-3986 ht_-312 HT_-263 | HT_-263_135 | |h_-312_H_-263_1 | chr1 | + | 152495546 | "all, CREBtarget" | HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression |
When we check the expression of FDPS in HEK293T cells by clicking the link, however, this gene was not induced by cAMP agonist FSK. This is not surprising. Actually only a small subset of CREB target genes are induced by cAMP in each tissues. The genes that do not repsond to cAMP here may become repsonsive in another tissue, or they respond to a differnt sitmulus. Alternatively, CREB may play a role in basal transcription. Actually FDPS expression is reduced by ACREB treatment, suggesting CREB may be involvled in basel transcription of this gene.
No | probe set | gene | Accession | LocusLink | Description | Symbol | CTRL | FSK | ACREB_FSK | (FSK vs CTRL) FC | (FSK vs CTRL) LFC | (ACREB_FSK vs FSK) FC | (ACREB_FSK vs FSK) LFC | 0hr | 1hr_FSK | 4hr_FSK | (1hr_FSK vs 0hr) FC | (1hr_FSK vs 0hr) LFC | (4hr_FSK vs 0hr) FC | (4hr_FSK vs 0hr) LFC | notes | Link |
1 | 201275_at | "farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)" | NM_002004.1 | 2224 | "gb:NM_002004.1 /DEF=Homo sapiens farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) (FDPS), mRNA. /FEA=mRNA /GEN=FDPS /PROD=farnesyl diphosphate synthase (farnesylpyrophosphate synthetase, dimethylallyltranstransferase,geranyltranstransferase) /DB_XREF=gi:4503684 /UG=Hs.77393 farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) /FL=gb:J05262.1 gb:D14697.1 gb:NM_002004.1" | FDPS | 696.38 | 668.18 | 405.5 | -1.04 | -0.85 | -1.65 | -1.26 | 393.01 | 484.14 | 394.28 | 1.23 | 0.83 | 1 | 0.66 | "all, " | Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression |
Similarly, FDPS is not incuded by FSK in human pancreatic islet culture either.
No | probe set | Gene Name | Accession | LocusLink | Symbol | Alias Symbols | Description | CTRL | FSK | (FSK vs CTRL) FC | (FSK vs CTRL) LFC | Note | Link |
1 | 201275_at | "farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)" | NM_002004 | 2224 | FDPS | FPS | "gb:NM_002004.1 /DB_XREF=gi:4503684 /GEN=FDPS /FEA=FLmRNA /CNT=295 /TID=Hs.77393.0 /TIER=FL+Stack /STK=106 /UG=Hs.77393 /LL=2224 /DEF=Homo sapiens farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) (FDPS), mRNA. /PROD=farnesyl diphosphate synthase (farnesylpyrophosphate synthetase, dimethylallyltranstransferase,geranyltranstransferase) /FL=gb:NM_002004.1 gb:D14697.1 gb:J05262.1" | 1086.88 | 972.11 | -1.12 | -1.03 | "all, " | HEK293T_Expression Human_ChIP_chip Human_CRE_prediction |