Table 1.
List of mRNA data sets (above the midline) and protein concentration data sets (below the midline). If the data set has multiple measurements, the number of replicates in each data set is given after the technology name, in parentheses. ‘2D gel’ stands for two-dimensional gel electrophoresis, and ‘MS’ for mass-spectrometry. The last column is the missingness rate out of the 5,308 genes in our data set.
| ID | Reference | Technology (measurements) | Missing |
|---|---|---|---|
| CAUS | Causton et al. (2001) | commercial microarray (×5) | 19–22% |
| DUD | Dudley et al. (2002) | custom microarray (×4) | 5% |
| GARC | García-Martínez et al. (2004) | custom microarray | 1% |
| HOLS | Holstege et al. (1998) | commercial microarray | 12% |
| ING1 | Ingolia et al. (2009) | RNA-Seq (mRNA rich) (×2) | 9–10% |
| ING2 | Ingolia lab, unpublished, 2010 | RNA-Seq (rq) (×2) | 4–5% |
| ING3 | Ingolia lab, unpublished, 2010 | RNA-Seq (ca) (×2) | 6–8% |
| LIP1 | Lipson et al. (2009) | RNA-Seq (×6) | 1% |
| LIP2 | Lipson et al. (2009) | commercial microarray | 4% |
| MAC | MacKay et al. (2004) | custom microarray | 28% |
| MIUR | Miura et al. (2008) | cPCR (×4) | 26–29% |
| NGAL | Nagalakshmi et al. (2008) | RNA-Seq | 22% |
| PELE | Pelechano and Pérez-Ortín (2010) | custom microarray | 14% |
| ROTH | Roth et al. (1998) | commercial microarray (×2) | 59–70% |
| VELC | Velculescu et al. (1997) | SAGE | 58% |
| YASS | Yassour et al. (2009) | RNA-Seq (×4) | 5% |
| FUTR | Futcher et al. (1999) | 2D gel | 99% |
| GHAM | Ghaemmaghami et al. (2003) | Western blot | 34% |
| GODO | de Godoy et al. (2008) | LC MS/MS | 25% |
| GYGI | Gygi et al. (1999) | 2D gel | 98% |
| LEE | Lee et al. (2011) | LC MS/MS (×3) | 67–76% |
| LU | Lu et al. (2007) | LC MS/MS | 83% |
| NGAR | Nagaraj et al. (2012) | LC MS/MS (×6) | 31% |
| NEWM | Newman et al. (2006) | GFP | 60% |
| PENG | Peng et al. (2003) | LC MS/MS | 74% |
| THAK | Thakur et al. (2011) | LC MS/MS (×3) | 84–85% |
| WASH | Washburn et al. (2001) | LC MS/MS | 77% |