Table 2.

Summary of PROMPT's generic comparison methods and the corresponding examples presented. The symbol x in the data column means corresponding data values for the same protein, whereas a comma simply states that two sets of values are utilized.

Example	Type of data used	PROMPT methoda:	Applied statistical methods d
Fold comparison of GroEL substrates with the whole proteome	{ Nominal }, { Nominal }	Categorical feature comparison b	• Chi-Square test
Fold enrichment of GroEL substrates	{ Nominal }, subset of { Nominal }	Categorical feature enrichment c	• Sampling from hypergeometric distribution with correction
Abundance distribution of essential vs. all proteins	{ Numeric }, { Numeric }	Numeric distribution comparison	• Mann-Whitney (MW) and Kolmogorov-Smirnov (KS) of the whole distribution • MW and Chi-Square test of each bin separately
Protein abundance vs. mRNA expression	{ Numeric × Numeric }	Numeric feature correlation	• Pearson correlation coefficient and • Pearson correlation test

^a Extensive description of each method can be found in the context sensitive help integrated in the PROMPT GUI, or in the manual supplied with PROMPT.

^b Both groups with categorical data can be independent from each other.

^c One group must be drawn from the other group.

^d As described in the Methods section