Table 7.
Data sets used in Bayes’ analysis to address the question, “What transcription factors (TFs) are most likely among all known TFs to be involved in regulation of Aqp2 gene transcription?”
| Data Set | Rationale | Assignment of Likelihood Values: P(B|A) | URL |
|---|---|---|---|
| All transcription factors (TFs) in rat | TFs that regulate AQP2 must include one or more of the TFs on this list. | 1/1,375 of total transcription factors as initial probability of each transcription factor | http://www.bioguo.org/AnimalTFDB/ |
| Rat IMCD transcriptome | The ability of a transcription factor to regulate transcription of Aqp2 gene depends on whether or not it is expressed in IMCD cells. | Complements of minimum Bayes’ factors (Z* = signal value/noise value where intrinsic noise is 0.4) | https://esbl.nhlbi.nih.gov/IMCD-transcriptome |
| Rat IMCD proteome | Ability of a transcription factor to regulate transcription of Aqp2 gene depends on whether or not it is expressed in IMCD cells. | Complements of minimum Bayes’ factors from χ2 test using number of data sources among 20 IMCD proteome databases published previously (null hypothesis: 0/20) | https://hpcwebapps.cit.nih.gov/ESBL/Database/IMCD_Proteome_Database/ |
| Rat IMCD nuclear proteome | Ability of a transcription factor to regulate transcription of Aqp2 gene depends on whether or not it is present in nuclei of IMCD cells. | If found in both nuclear extract and nuclear pellet fractions, P = 0.95; if found one of two fractions, P = 0.8; if not found, P = 0.4 | https://helixweb.nih.gov/ESBL/Database/IMCD_Nucleus/NE_NP_Webpage_TF.html |
| Transcription factor binding sites in promoter of rat Aqp2 gene | Ability of a transcription factor to regulate transcription of Aqp2 gene depends on whether or not it binds to specific DNA sites in the promoter of rat Aqp2 gene | Complements of minimum Bayes’ factors from the nucleotide probability of random expectation (expected occurrences of the match in a random sequence of the same length as the query sequence according to the dissimilarity index) | http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3 |
See Supplemental Table S1 (online) for full details of calculation.