View Genomic Data Across Multiple Experiments

Key insights can be gained by integrating multiple genomic data sets. Once you see a gene showing interesting pattern in one project, it is very useful look up this gene in other related data sets from your own lab or other published studies. This can be done with a single click in BxGenomicDB.

Let’s look at one example. Here we are interested in finding all the target genes for the transcription factor CREB1 (cAMP response element binding protein). In the classical (and simplified) model, CREB1 dimers bind to cAMP response element (sequences like TGACGTCA) in the promoter region, and when cAMP signal leads to CREB phosphorylation, the target gene is activated.

CREB regulates different genes in different tissues by working together with other regulators.

http://files.bioinforx.com/public/BioInfoRx/BxGenomicDB/CREB1model.JPG

There are many complementary ways to look for target genes, including motif search at the promoter region, promoter occupancy by ChIP-chip or ChIP-Seq, and up-regulation of gene expression when CREB1 is activated by cAMP agonist foskolin (FSK). After we've finished all these experiments, we can now put all the data together to look for bona fide CREB1 target genes.

In the example below, we are showing all these genomic data for NR4A2 gene in a single web page. You can get this page by search the gene symbol, then click “Plot Selected Data” button. Here you can see clearly that there are CRE sites on the promoter of NR4A2, and ChIP-chip with CREB1 antibodies indicates promoter occupancy, and lastly, cAMP agonist FSK induced NR4A2 expression strongly in multiple tissues.

NR4A2 Data from Multiple Experiments

Key insights can be gained by integrating multiple genomic data sets. Once you see a gene showing interesting pattern in one project, it is very useful look up this gene in other related data sets from your own lab or other published studies. This can be done with a single click in BxGenomicDB.