Table 2

Association with GO annotation

System

Gene category

CS

LT

DC

(a) Upregulated genes

GO Biological Process

Defense response

x

x

x

GO Cellular Component

Extracellular space

x

x

GO Cellular Component

Extracellular

x

x

GO Biological Process

Response to biotic stimulus

x

x

x

GO Biological Process

Immune response

x

x

x

GO Biological Process

Response to external stimulus

x

x

x

GO Biological Process

Organismal physiological process

x

x

x

GO Biological Process

Antigen presentation

x

x

GO Biological Process

Response to stimulus

x

x

x

GO Biological Process

Antigen presentation\, endogenous antigen

x

GO Molecular Function

MHC class I receptor activity

x

GO Biological Process

Antigen processing

x

x

GO Biological Process

Complement activation

x

x

GO Biological Process

Antigen processing, endogenous antigen via MHC class I

x

GO Biological Process

Response to pest/pathogen/parasite

x

x

x

GO Biological Process

Humoral defense mechanism (sensu Vertebrata)

x

GO Molecular Function

Pheromone binding

x

x

GO Molecular Function

Oxidoreductase activity

x

GO Molecular Function

Oxidoreductase activity, acting on the aldehyde or oxo group of donors

x

GO Molecular Function

Odorant binding

x

x

GO Molecular Function

Transmembrane receptor activity

x

GO Biological Process

Humoral immune response

x

(b) Downregulated genes

GO Cellular Component

Mitochondrion

x

x

GO Biological Process

Main pathways of carbohydrate metabolism

x

x

GO Biological Process

Tricarboxylic acid cycle

x

x

GO Biological Process

Energy derivation by oxidation of organic compounds

x

x

GO Biological Process

Energy pathways

x

x

GO Cellular Component

Mitochondrial membrane

x

GO Biological Process

Carbohydrate metabolism

x

x

GO Cellular Component

Inner membrane

x

GO Biological Process

Blood vessel development

x

GO Cellular Component

Mitochondrial inner membrane

x

GO Cellular Component

Extracellular

x

Lists of differentially expressed genes derived from a hybrid ChipStat/Intersector approach (ChipStat: p_ps = 0.05, 6/16 probe pairs increasing AND Intersector: 7/9 increases + marginal increases), logit-T, and dChip were associated with GO terms using EASE [20]. Individual terms are annotated according to whether association with the given annotation group was statistically significant (P < 0.05 using within-system bootstrap to account for multiple testing) using lists derived from ChipStat/Intersector (CS), logit-T (LT), or dChip (DC). (a) Association with lists of upregulated genes. (b) Association with lists of downregulated genes.

Master et al. Genome Biology 2005 6:R20   doi:10.1186/gb-2005-6-2-r20