Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets

BMC Bioinformatics

Table 8 Comparison of the number of groups detected in the C2.KEGG category and of the number of common detections in three datasets

0.010	A2. fixed	Faeri. fixed.null	Faeri. fixed.perms	GSA. mean*	GSA. absmean*	GSA. maxmean*	Globaltest. asymptotic	Globaltest. gamma	Globaltest. permutations	Gsea. pval	Gsea. fdr	Samgs. pval	Samgs. qval
Emexp445	62	7	14	14	5	19	0	8	0	0	0	0	0
GSE-1056	36	9	51	5	0	8	1	15	0	0	0	0	0
GSE-4086	93	89	94	49	38	62	0	0	0	0	0	NA	NA
Emexp445-GSE-1056	5	0	6	1	0	0	0	1	0	0	0	0	0
Emexp445-GSE-4086	24	5	9	8	0	11	0	0	0	0	0	NA	NA
GSE-1056-GSE-4086	21	7	37	4	0	4	0	0	0	0	0	NA	NA
Emexp445-GSE-1056-GSE-4086	4	0	3	1	0	0	0	0	0	0	0	NA	NA
0.050	A2. fixed	Faeri. fixed.null	Faeri. fixed.perms	GSA. mean*	GSA. absmean*	GSA. maxmean*	Globaltest. asymptotic	Globaltest. gamma	Globaltest. permutations	Gsea. pval	Gsea. fdr	Samgs. pval	Samgs. qval
Emexp445	62	18	42	14	5	23	26	45	0	0	0	0	0
GSE-1056	51	27	80	8	2	12	33	70	40	11	0	15	69
GSE-4086	119	119	142	49	38	62	32	185	0	0	0	NA	NA
Emexp445-GSE-1056	15	6	34	1	0	0	4	20	0	0	0	0	0
Emexp445-GSE-4086	48	14	37	8	0	13	13	44	0	0	0	NA	NA
GSE-1056-GSE-4086	31	23	71	4	1	6	7	69	0	0	0	NA	NA
Emexp445-GSE-1056-GSE-4086	13	4	31	1	0	0	2	20	0	0	0	NA	NA

The results are shown for each method, for significance thresholds of 0.05 and 0.01. The three datasets analyzed are E-MEXP-445, GSE-1056 and GSE-4086, and concern the same condition (oxygen deprivation). The first column contains the datasets analyzed. The first 3 rows of each table contain the top list obtained by each geneset analysis method. When several datasets are mentioned at the beginning of the row, the number of genesets in the other columns is the intersection of the results from different datasets

ISSN: 1471-2105