Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs

Didier Gonze, Sylvie Pinloche, Olivier Gascuel and Jacques van Helden

Supplementary material

Flow chart

met_pho_flowchart.pdf

Position-specific scoring matrices

Binding sites

Transcription Factor Binding sites used for building PSSM [ps] [pdf]

Matrix scores

Upstream sequences were retrieved over 800bp for all the yeast ORFs. Sequences were scanned with patser to identify the 3 top-scoring matches for each one of the 5 PSSM used in the paper.
all_matrices_allup800_top3.tab

LDA results

Posterior probabilities and class assignment obtained with Linear Discriminant Analysis.

Data type	Training	Results
Matrix scores	PHO against CTL+MET	[all scores]
Matrix scores	MET against CTL+PHO	[all scores]
Matrix scores	3 groups (PHO, MET, CTL)	[all scores]

Comparisons

We summarized in a table the experimental result (ChIP-chip, expression) and predicitons (LDA posterior probabilities) about phosphate and methionine regulation, which were used to draw the comparative figures.
comparisons/comparison_expr_chip2_matrices.tab

Complete results, data and R scripts

complete_supmat.zip