High-Throughput GoMiner Paper Supplementary Material

GO categories with at least one instance of FDR <= 0.100 for total changed genes are displayed, sorted in ascending order by the FDR for the first column of 1000 resamplings. These results indicate that 100 resamplings provide a stable and reliable estimate of the 'true' (ie., 1000 resamplings) FDR. This table applies only to the specific example used here and is not intended to represent a more generalized conclusion. (Zeeberg and Qin, in preparation).

A version of this data are available in Excel format as well.

HYPERLINKED GO CATEGORY	10 Resamplings			100 Resamplings			1000 Resamplings
GO:0006952 defense response	0	0	0	0	0	0	0	0	0
GO:0006955 immune response	0	0	0	0	0	0	0	0	0
GO:0050874 organismal physiological process	0	0	0	0	0	0	0	0	0
GO:0009613 response to pest pathogen parasite	0	0	0	0	0	0	0	0	0
GO:0009607 response to biotic stimulus	0	0	0	0.002	0	0	0	0	0
GO:0009605 response to external stimulus	0	0	0	0.003	0.008	0	0.003	0.004	0.003
GO:0042221 response to chemical substance	0	0	0.014	0.003	0.014	0.001	0.007	0.007	0.008
GO:0006950 response to stress	0	0.05	0.025	0.013	0.031	0.023	0.02	0.019	0.025
GO:0050896 response to stimulus	0.009	0.036	0.045	0.021	0.045	0.042	0.026	0.027	0.032
GO:0007186 G-protein coupled receptor protein signaling pathway	0.01	0.04	0.05	0.023	0.049	0.046	0.028	0.029	0.035
GO:0009611 response to wounding	0.011	0.044	0.056	0.026	0.048	0.043	0.029	0.03	0.038
GO:0006968 cellular defense response	0.014	0.071	0.043	0.033	0.055	0.05	0.035	0.037	0.041
GO:0006959 humoral immune response	0.015	0.069	0.038	0.035	0.056	0.054	0.036	0.037	0.042
GO:0006935 chemotaxis	0.012	0.059	0.047	0.043	0.054	0.052	0.037	0.038	0.04
GO:0042330 taxis	0.012	0.059	0.047	0.043	0.054	0.052	0.037	0.038	0.04
GO:0006874 calcium ion homeostasis	0.017	0.075	0.042	0.038	0.061	0.058	0.038	0.04	0.045
GO:0009628 response to abiotic stimulus	0.013	0.067	0.053	0.047	0.059	0.057	0.041	0.043	0.044
GO:0006805 xenobiotic metabolism	0.022	0.061	0.044	0.047	0.059	0.058	0.042	0.042	0.045
GO:0009410 response to xenobiotic stimulus	0.032	0.079	0.058	0.062	0.08	0.078	0.054	0.055	0.055
GO:0016064 humoral defense mechanism (sensu Vertebrata)	0.035	0.095	0.055	0.063	0.08	0.082	0.055	0.056	0.057
GO:0045087 innate immune response	0.033	0.095	0.052	0.07	0.083	0.09	0.06	0.061	0.062
GO:0006875 metal ion homeostasis	0.043	0.126	0.07	0.087	0.093	0.108	0.075	0.077	0.079
GO:0030005 di- tri-valent inorganic cation homeostasis	0.043	0.126	0.07	0.087	0.093	0.108	0.075	0.077	0.079
GO:0007166 cell surface receptor linked signal transduction	0.046	0.133	0.075	0.089	0.093	0.109	0.077	0.077	0.08
GO:0006873 cell ion homeostasis	0.037	0.123	0.073	0.092	0.09	0.105	0.078	0.076	0.079
GO:0007178 transmembrane receptor protein serine threonine kinase signaling pathway	0.037	0.123	0.073	0.092	0.09	0.105	0.078	0.076	0.079
GO:0019884 antigen presentation exogenous antigen	0.037	0.123	0.073	0.092	0.09	0.105	0.078	0.076	0.079
GO:0019886 antigen processing exogenous antigen via MHC class II	0.037	0.123	0.073	0.092	0.09	0.105	0.078	0.076	0.079
GO:0030003 cation homeostasis	0.037	0.123	0.073	0.092	0.09	0.105	0.078	0.076	0.079
GO:0050801 ion homeostasis	0.037	0.123	0.073	0.092	0.09	0.105	0.078	0.076	0.079
GO:0009617 response to bacteria	0.038	0.156	0.078	0.098	0.098	0.107	0.083	0.084	0.085
GO:0019935 cyclic-nucleotide-mediated signaling	0.038	0.156	0.078	0.098	0.098	0.107	0.083	0.084	0.085
GO:0007218 neuropeptide signaling pathway	0.052	0.185	0.118	0.115	0.112	0.116	0.095	0.095	0.096

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GoMiner was originally developed jointly by the Genomics and Bioinformatics Group (GBG) of LMP, NCI, NIH and the Medical Informatics and Bioimaging group of BME, Georgia Tech/Emory University. It is now maintained and under continuing development by GBG.

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