Figure 5B shows the SPR baseline shift with and without bevacizumab regulation obtained from three similar experiments with different batch of SKOV-3 cells.
Informed consent according to institutional regulations was obtained from all patients before study entry.
For String, gene regulations with score >= 800 were collected; for TRANSFAC, binding site quality <= 5 was the criterion; and for TRED, only gene regulations not obtained from computational predicted method were collected.
The authors compared performance of the method with gene regulation networks inferred from microarray data (other than the analyzed) and with gene regulation networks obtained from KEGG database.
Information on gene regulation was obtained from RegulonDB [ 45].
Additional evidence for TF regulation was obtained from literature search and the Transcriptional Regulatory Element Database (TRED) [ 108].
Interactions associated with transcriptional regulation were obtained from experimental validation protein-DNA binding relationships licensed from the TransFac [ 97] and TRRD [ 98] databases.
In the past, many data on mTOR regulation were obtained from ectopic overexpression experiments in transformed cells or using in vitro kinase assays.
An additional result supporting the notion that CpGlow promoters have a higher potential for combinatorial regulation was obtained from the analysis of FR values of 200 randomly selected oligomers.
To sum up, our network inference approach provided us with the knowledge that the most regulations which were obtained from the literature were also present in our trastuzumab cell system and novel regulations might have potential role in the observed phenotype of the cells.
