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Table 2 Association with GO annotation

From: Genomic analysis of early murine mammary gland development using novel probe-level algorithms

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  
  1. Lists of differentially expressed genes derived from a hybrid ChipStat/Intersector approach (ChipStat: pps = 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.