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Tip: To quickly search the same gene in another data set, click the links from the last column. The locuslink number will be used as query.
|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||206115_at||early growth response 3||NM_004430.1||1960||"gb:NM_004430.1 /DEF=Homo sapiens early growth response 3 (EGR3), mRNA. /FEA=mRNA /GEN=EGR3 /PROD=early growth response 3 /DB_XREF=gi:4758251 /UG=Hs.74088 early growth response 3 /FL=gb:NM_004430.1"||EGR3||65.88||58.87||44.57||-1.12||-0.81||-1.32||-0.81||50.81||60.18||50.44||1.18||0.87||-1.01||-0.66||"all, "||Human_ChIP_chip Human_CRE_prediction Pancreatic_Islet_Expression|
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.
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
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.