Guide to database entries and calculations

Yeast Deletion Project

Two timecourses were performed. Each timecourse is defined by its starting pool (the collection of deletion strains at time 0). The medias that were monitored in each timecourse are listed in a table.

We calculated growth rates by regression analysis. Regression lines were fit to the log of the intensity values and 1.0 was added to each slope for readability.

The number of probes indicates the number of probes on the Affymetrix chip that interrogate a particular strain.

The number of measurements indicates the total number of data values upon which the regression calculation is based. For example, for a typical strain with 4 probes and 20 timepoints, 80 measurements were collected per media condition. However, only the timepoints up to and including the first measurement below three-fold above background were considered meaningful and used for the regression fits.

The maximum difference is the difference between medias of the highest and lowest growth rates. For each strain and each timecourse, an F-statistic and associated p-value were calculated to determine whether differences in growth rates between media conditions are significant.

Mitochondrial Proteomics Project

We prepared samples from 20 different experiments and 4 different growth conditions, with either a fermentable or a non-fermentable carbon source added. All ypl* samples were cultured under complex Yeast Peptone media with lactate as the non-fermentable carbon source, which was also supplemented to synthetic complete media samples scl*. Samples assigned with ypd* and scd* were cultured under fermentable growth conditions.

Mitochondria were isolated by differential centrifugation followed by a Nycodenz density gradient purification (*DG*). All other samples were purified by a zone electrophoretic separation (ZE) using a ProTeam FFE TM Free-Flow Electrophoresis apparatus (Tecan, Grödig, Austria).

Fractionation of matrix and membrane was achieved by mitochondrial disruption using zirconia beads, and membrane proteins were extracted using CHAPS solution. Tryptic digested peptides were analyzed consequently by LC/tandem mass spectrometry (MS/MS) and by high sensitivity, high dynamic range LC/Fourier Transform-Ion Cyclotron Resonance mass spectrometry (FT-ICR MS). Each LC/MS/MS experiment identified a list of potential mass and time (PMT) tags, which were used to define protein assignments through a yeast proteome database search. Samples marked with *FT were independently measured by LC/FT-ICR MS to confirm the PMTs as accurate mass and time (AMT) tags.

See Table S1 for a description of the sample names.

The values in the database indicate the number of tags detected for each protein.

Expression Project

Each sample was done in duplicate. Log phase cultures were grown overnight to O.D. of 1 in 100 ml of YPD, YPL, SCD, SCL medium. Total RNA was isolated using a hot phenol glass beads protocol. PolyA+ mRNA was purified using Qiagen oligotex kit. 4.5ug of polyA+ mRNA were reverse transcribed to generate single stranded cDNA. Product was fragmented to 50bp using Dnase digestion, biotin end labeled and hybridized to Affymetrix S98 arrays as described in the Affymetrix user handbook (Affymetrix, Santa Clara). Hybridization's were normalized and duplicate samples integrated to arrive at an estimate of absolute transcript abundance using the dChip computational package (Harvard University). For genes with multiple probe sets on the array only the probe set with the highest signal was used. The values in the table show absolute expression values of a probe as determined by the Affymetrix array. Ratios of YPL/YPD, and SCL/SCD give the difference in absolute expression values between these two conditions (fold-change), which were calculated using the Dchip program.

Web site © 2003 Stanford Genome Technology Center

In addition to original data, this web site and its associated links contain information gleened from public data. While the public data has been faithfully downloaded into the YDPM database, no representations are made regarding the accuracy of the public data.

Web site administrator