S.1.1: The Transcription Factor Regulatory Network in E. coli and Yeast
Click here to download the TF regulatory network for E. coli
Click here to download the TF regulatory network for Yeast
Fig S.1.1: (A) The Transcription factor (TF) regulatory network in E. coli. This is a fraction of the known network in E. coli
where the regulated gene is also a TF. This network consists of 129 interactions and 85 TFS
(69 interactions and 63 TFs when one does not consider the 60 autoregulatory interactions).
(B) The graph shows the distribution of the number of other TFs regulated by a TF in the network for E. coli
(including and excluding autoregulatory interactions). Note that CRP regulates 15 other TFs and many
TFs regulate only one other TF. In other words, it is evident from (A) and (B) that the
E. coli TF regulatory network is not uniformly connected, but has a few TFs that regulate many other
genes and many TFs that regulate a few other genes. (C) The TF regulatory network in
Yeast where the regulated gene is also a TF. This network consists of 70 interactions and 51 transcription
factors (60 interactions nd 48 TFs when one does not consider the 10 autoregulatory interactions).
(D)The graph shows the distribution of the number of other TFs regulated by a TF in the network for Yeast
(including and excluding autoregulatory interactions). Note that the distribution is not as extreme as in the case of the
E. coli network. There are many TFs that regulate more than 2 other TFs and there are no major regulatory
hubs like CRP in E. coli, indicating that the TF regulatory network in Yeast is more uniformly connected than the
E. coli network. An obvious manifestation of such a characteristic is the fact that the Yeast network contains more
Feed-Forward motifs than E. coli.
S.1.2: Direct and Indirect Number of Genes/Operons/TFs Regulated by E. coli and Yeast Transcription Factors
Click here to download the data used to plot the above graphs.
Fig S.1.2: (A) Direct and indirect number of operons regulated by E. coli transcription factors (TFs). Since the connections
amongst the TFs were poor in the TF regulatory network (see, Fig S2A), there are not many operons that are indirectly regulated.
(B) Direct and inderect number of TFs regulated by E. coli TFs. Note that not many TFs indirectly regulate other TFs.
(C) Direct and indirect number of genes regulated by Yeast TFs. The number of indirectly regulated genes is much more for Yeast than E. coli
because of the fact that the TF regulatory network is more uniformly interconnected (see, Fig S2C)
and hence each TF is able to influence many more genes than it actually regulates. (D) Direct and indirect number of TFs regulated by Yeast TFs.
This graph clearly shows that Yeast TFs can also indirectly regulate more TFs than E. coli and hence amplify/influence their regulatory
effect more effectively.