Transcription factor families

We considered families of transcription factors taken from AGRIS and asked if each family was over or under-represented in our total set of differentially expressed genes. The plot here uses the same probability function determined using the Hypergeometric distribution, where we effectively compare the ratio of the number of observed differentially expressed genes in a given transcription factor family to the total number of differentialy expressed transcription factors with the ratio of all the transcription factors in the same family to all the known transcription factors in the genome.
We note that the probes for the ATH1 affymetrix chip does not provide full coverage of these transcription factors. This can have two effects: in the first instance a given transcription factor family might have a larger number of differentially expressed genes than those measured on the Affymetrix chip. This will increase the over-representation of that family. On the other hand, the number of transcription factors in all the other families that are differentially expressed could increase while the number for that given family could remain the same. This would decrease the over-representation of that family. We use these as an upper and lower estimate of the systematic error due to this effect. The error bars are asymmetric and indeed can be zero in some cases since it is possible that for a given transcription factor family all its members are represented in the probe set.





Here's a heat map of the over-represented classes :