A Pathway Analysis Tool for Analyzing Microarray Data of Species with Low Physiological Information

Table 1

Pathways returned by searching the KEGG database. The list of gene names of the microarray was first updated for all synonyms using the Gene Ontology database before searching the KEGG database.

Pathways category	Number of
	pathways
A: total number of pathways returned by KEGG search	178
B: positive associated pathways (with links to other pathways)	57 (22)
C: no regulation^*	14
D: false positive^**	30
E: (too) limited information to conclude^***	35
F: uncertain^****	42

^*None of the genes in the pathways present on the microarray were regulated. These pathways were considered not related to the chicken line differences for Salmonella infection response.^**Plant or prokaryote-specific pathways—recognized due to gene name similarity. Almost always these pathways were recognized by a very limited number of genes on the microarray.^***The genes with microarray data on the pathway are too limited in number or their locations on the pathway are too scattered to conclude on the relevance of the pathway for the studied traits.^****The available microarray data of the genes on the pathway show either limited or confusing up- or downregulatory patterns.