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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 202316_x_at "ubiquitination factor E4B (UFD2 homolog, yeast)" AW24171510277Consensus includes gb:AW241715 /FEA=EST /DB_XREF=gi:6575469 /DB_XREF=est:xn74b08.x1 /CLONE=IMAGE:2700183 /UG=Hs.24594 ubiquitination factor E4B (homologous to yeast UFD2) /FL=gb:AF043117.1 gb:NM_006048.1 UBE4B 77.11 87.08 77.12 1.13 0.74 -1.13 -0.73 58.35 70.63 65.91 1.21 0.66 1.13 0.5 "all, " Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression
2 215533_s_at "ubiquitination factor E4B (UFD2 homolog, yeast)" AF091093.110277"Consensus includes gb:AF091093.1 /DEF=Homo sapiens clone 686 unknown mRNA, complete sequence. /FEA=mRNA /PROD=unknown /DB_XREF=gi:3860023 /UG=Hs.24594 ubiquitination factor E4B (homologous to yeast UFD2)" UBE4B 90.09 90.82 62.19 1.01 0.66 -1.46 -1.05 82.11 91.62 88.81 1.12 0.77 1.08 0.69 "all, " Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression
3 210685_s_at "ubiquitination factor E4B (UFD2 homolog, yeast)" AB028839.110277"gb:AB028839.1 /DEF=Homo sapiens HDNB1(homzygously deleted in neuroblastoma-1)UFD2 mRNA, complete cds. /FEA=mRNA /GEN=HDNB1UFD2 /PROD=homzygously deleted in neuroblastoma-1UFD2 /DB_XREF=gi:13516466 /UG=Hs.24594 ubiquitination factor E4B (homologous to yeast UFD2) /FL=gb:AB028839.1" UBE4B 174.13 165.63 111.93 -1.05 -0.86 -1.48 -1.27 114.25 141.45 127.03 1.24 0.85 1.11 0.83 "all, " Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression
4 202317_s_at "ubiquitination factor E4B (UFD2 homolog, yeast)" NM_006048.110277"gb:NM_006048.1 /DEF=Homo sapiens ubiquitination factor E4B (homologous to yeast UFD2) (UBE4B), mRNA. /FEA=mRNA /GEN=UBE4B /PROD=ubiquitination factor E4B (homologous to yeastUFD2) /DB_XREF=gi:5174482 /UG=Hs.24594 ubiquitination factor E4B (homologous to yeast UFD2) /FL=gb:AF043117.1 gb:NM_006048.1" UBE4B 169.23 151.03 85.68 -1.12 -0.89 -1.76 -1.35 126.23 140.7 131.61 1.11 0.79 1.04 0.68 "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.