Genome Dependence

Genome Dependence: constitutive mutants

An estimate of the genome-wide requirement for a transcription factor was made for the constitutive mutant experiments (deletion or enzymatically dead mutants) by adding the number of genes in the 2-fold up and 2-fold down list and dividing this by the total of scored genes. This number is expressed as a percentage and represents the portion of genes in the genome whose expression is significantly affected by the mutation.

Genome Dependence: temperature sensitive mutants

An estimate of the genome-wide requirement for transcription factors analyzed through temperature sensitive mutations was made by estimating the number of genes whose transcription showed the same dependence on a given transcription factor as on core RNA polymerase itself. The portion of genes in the genome whose expression is equivalently dependent on RPB1 and the factor is expressed as a percentage. This was calculated as described below.

Genes Compared to Rpb1

Those mRNAs whose levels are called in both the rpb1-1 experiment and in the experiment involving ts factor X were collected. Transcripts whose levels drop less than 2-fold in the rpb1-1 experiment are not included in the analysis because the decay rates are not sufficient to provide a meaningful comparison.

Genes Equivalent Dependence

To determine the number of genes whose expression is as dependent on a transcription factor as it is on core RNA polymerase II itself, we used the following criteria. For the subset of rpb1-1 transcripts where the average decrease was greater than two-fold (Genes Compared to Rpb1), a comparison was made between the apparent half-life in rpb1-1 and that observed in the other ts factor experiment. A gene is determined to be equivalently dependent on Rpb1 and the factor of interest, and is incorporated into the "Genes Equivalent Dependence" group, if its transcript decays to a level which is within one apparent half-life of the decrease observed with rpb1-1 cells.