yeast: Yeast Cell Cycle Dataset

In spls: Sparse Partial Least Squares (SPLS) Regression and Classification

Description

This is the Yeast Cell Cycle dataset used in Chun and Keles (2010).

Usage

 data(yeast) 

Format

A list with two components:

x

ChIP-chip data. A matrix with 542 rows and 106 columns.

y

Cell cycle gene expression data. A matrix with 542 rows and 18 columns.

Details

Matrix y is cell cycle gene expression data (Spellman et al., 1998) of 542 genes from an α factor based experiment. Each column corresponds to mRNA levels measured at every 7 minutes during 119 minutes (a total of 18 measurements). Matrix x is the chromatin immunoprecipitation on chip (ChIP-chip) data of Lee et al. (2002) and it contains the binding information for 106 transcription factors. See Chun and Keles (2010) for more details.

Source

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thomson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, and Young RA (2002), "Transcriptional regulatory networks in Saccharomyces cerevisiae", Science, Vol. 298, pp. 799–804.

Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, and Futcher B (1998), "Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hydrization", Molecular Biology of the Cell, Vol. 9, pp. 3273–3279.

References

Chun H and Keles S (2010), "Sparse partial least squares for simultaneous dimension reduction and variable selection", Journal of the Royal Statistical Society - Series B, Vol. 72, pp. 3–25.

Examples

data(yeast)
yeast$x[1:5,1:5]
yeast$y[1:5,1:5]

Example output

Sparse Partial Least Squares (SPLS) Regression and
Classification (version 2.2-1)

      ABF1_YPD    ACE2_YPD      ADR1_YPD  ARG80_YPD   ARG81_YPD
21  -0.2722730  0.21932294  0.9238359567 -0.4755756 -0.10389318
41   0.1691280  0.53831198  0.0097604993 -0.3219534 -0.19750606
71  -0.1388962  0.02636382  0.0877516229 -0.2234093  0.10307741
78  -0.2865169 -0.31409427 -0.0454998435  0.3262217  0.27757502
102 -0.4950561 -0.14827419  0.0002987512 -0.2179458 -0.02539585
  alpha0 alpha7 alpha14 alpha21 alpha28
1  -0.36  -0.42    0.29   -0.14   -0.19
2   1.04   0.19    0.47   -1.03   -0.63
5  -0.30  -0.45    0.75    0.37    0.27
8  -0.46   0.12   -0.06   -0.76   -0.70
9  -1.35  -0.86   -0.22   -0.38   -0.65

spls documentation built on May 6, 2019, 1:09 a.m.