Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics

Table 1 Pairs of pathways selected as examples

EcoCyc Pathway	KEGG Pathway	Pathway Size
		EcoCyc	KEGG	Table
L-cysteine biosynthesis CYSTSYN-PWY	Cysteine and Methionine metabolism map00270	3	34	2
Arginine biosynthesis ARGSYN-PWY	Arginine biosynthesis map00220	12	18	3
L-selenocysteine biosynthesis I PWY0-901	Selenocompound metabolism map00450	4	17	4
L-valine biosynthesis VALSYN-PWY	Valine, leucine, and isoleucine biosynthesis map00290	9	16	5
Guanosine deoxyribosenucleotides de novo biosynthesis II PWY-7222	Purine Metabolism map00230	10	78	6
Pyrimidine deoxyribonucleotides de novo biosynthesis PWY-7184	Pyrimidine Metabolism map00240	13	51	7

The first four pairs are amino acid synthesis pathways. The remaining pairs are two large KEGG pathways covering purine and pyrimidine metabolism and one of several EcoCyc pathways that correspond to a part of the pathway. Each row contains corresponding EcoCyc and KEGG pathways identified by their name and EcoCyc or KEGG pathway identifier, and the pathway size expressed as number of associated genes

ISSN: 1471-2164