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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 208781_x_at sorting nexin 3 AF062483.18724"gb:AF062483.1 /DEF=Homo sapiens SDP3 mRNA, complete cds. /FEA=mRNA /PROD=SDP3 /DB_XREF=gi:3126978 /UG=Hs.12102 sorting nexin 3 /FL=gb:AF062483.1 gb:AF034546.1 gb:NM_003795.1" SNX3 419.16 452.82 398.17 1.08 0.79 -1.14 -0.84 593.84 708.86 721.05 1.19 0.98 1.21 1.06 "all, " Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression
2 210648_x_at sorting nexin 3 AB047360.18724"gb:AB047360.1 /DEF=Homo sapiens SNX 3A mRNA for sorting nexin 3A, complete cds. /FEA=mRNA /GEN=SNX 3A /PROD=sorting nexin 3A /DB_XREF=gi:12957159 /UG=Hs.12102 sorting nexin 3 /FL=gb:AB047360.1" SNX3 1068.85 1042.01 1023.89 -1.03 -0.8 -1.02 -0.82 1194.93 1371.34 1241.92 1.15 0.95 1.04 0.84 "all, " Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression
3 213545_x_at sorting nexin 3 BE9626158724Consensus includes gb:BE962615 /FEA=EST /DB_XREF=gi:11765691 /DB_XREF=est:601655968R1 /CLONE=IMAGE:3855785 /UG=Hs.12102 sorting nexin 3 SNX3 765.8 736.07 711.8 -1.04 -0.81 -1.03 -0.91 711.22 827.28 810.15 1.16 0.91 1.14 0.88 "all, " Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression
4 200067_x_at sorting nexin 3 AL0785968724"Consensus includes gb:AL078596 /DEF=Human DNA sequence from clone RP3-429G5 on chromosome 6q21-22.1. Contains the NR2E1 gene for nuclear receptor 2E1 (tailless, TLL, TLX, XTLL), the 3 end of the SNX3 gene for sorting nexin 3, ESTs, STSs, GSSs and four predicted CpG islands /FEA=mRNA_2 /DB_XREF=gi:6010168 /UG=Hs.12102 sorting nexin 3 /FL=gb:AF062483.1 gb:AF034546.1 gb:NM_003795.1"  563.89 561.7 530.9 -1 -0.89 -1.06 -0.92 573.59 674.64 570.98 1.18 0.85 -1 -0.79 "all, " Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression

Sample Description:
Culture of human HEK293T cells are treated with cAMP agonist forskolin (FSK) for 1hr. Two control and two forskolin treated samples are collected, together with 2 forskolin treated samples from ACREB plasmid transfected cells. In addition to this data set, a different set of experiments showing FSK effect on 1hr and 4hr treatments is included. The two sets of data in HEK293T were generated at different times with different batch of cells, and comparison should be limited within each set. The cAMP induced genes at 1hr, however, was similar between the two sets. Total RNA was extracted using the Qiagen RNeasy kit.

Microarray Analysis:
Total RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome U133 Array Set HG-U133A array. Array data was analyzed using the dChip software with PM-MM models.

Guidelines for Choosing camp Induced Genes in this Data Set:
The fold change (FC) value is positive for increased expression and negative for decrease expression. There is also a lower bound of fold change (LFC), which is a conservative estimation of the fold change with 90% confidence. For this data set, if a gene was induced by FSK in control samples (LFC>=1) and this induction was inhibited by ACREB ((FSK_ACREB vs FSK) LFC<=-1), we consider it as a good camp induced gene and therefore a potential CREB target. In addition, induction by FSK with the second data set (time series) can further confirm the result from the first data set.