A Quick Tutorial on Integrating ChIP-Seq and Gene Expression Microarray Data Sets
GSE88896 is a study of the transcription factor TFEB and consists of two subseries. One is TFEB ChIP-Seq, and the other is microarray data profiling the effect of TFEB knockdown. This quick tutorial shows how to analyze the multi-omics datasets integratively.
In this tutorial, we identify differentially expressed genes by TFEB knockdown and separate them into two groups: those with TFEB peaks near their TSS and those without. They are supposed to be the direct target of TFEB and the indirect effects. We also compare experimentally detected target genes with predicted targets from the DNA sequence.
Although you can follow the steps to grab the workflow, we have omitted some of the detailed steps in this movie. We instead provide the SSA file so that you can import the data and easily follow the operations. It also enables further analysis by yourselves.
On the other hand, even if you do not have ChIP-seq data for your transcription factor of interest, you may still be able to use publicly available ChIP-seq datasets. In Using ChIP-Atlas to Interpret RNA-Seq Results , we explain how to import transcription factor binding peaks into Subio Platform, compare them with RNA-Seq expression patterns, and identify candidate upstream regulators from differentially expressed genes.