Hi, I have a FPKM matrix of 9644 columns and 15 rows from a RNA-seq expression experiment. The columns are the gene and the rows represents expression of the gene at different time points. My basic idea is to identify transcription factor binding site (TFBS) upstream of target gene. I want to do de-novo motif discovery based on over-represented sequence search in regulatory regions of target gene along with a group of co-expressed gene. Therefore, my first idea is to search genes co-expressed with my target gene. How can I do the co-expression analysis in R. How can I visualize the results? Please help me with R scripts. Let us consider the data name is ‘Rdata.csv’
If it is time-series data, I would suggest using the TCAP method (temporal clustering by affinity propagation): http://bioinformatics.oxfordjournals.org/content/26/3/355.short
You can do time series gene expression using your target genes along with all other genes and look for your target gene in the time series profiles. Your target gene along with other genes will be clustered in particular profile or pattern of expression, which confirms the co-expressing genes with same pattern of expression as your target.
Use this program: STEM
Hope that I understood your question properly.