Novel definition files for human GeneChips based on GeneAnnot

BMC Bioinformatics

Table 1 Differentially expressed genes selected using different CDFs.

CDF type	Number of DEG	DEG found by all CDFs		DEG shared in the pair-wise comparisons of lists generated using different CDFs
		Number	%
q-value < 1%
Bio	42	17	40.5		Entrez8	RefSeq8	AceView	GA6	GA11
Entrez8	28		60.7	Bio	25	29	22	33	33
RefSeq8	34		50	Entrez8		25	20	28	28
AceView	35		48.6	RefSeq8			22	29	29
GA6	46		37	AceView				23	23
GA11	42		40.5	GA6					42
q-value < 5%
Bio	76	42	55.3		Entrez8	RefSeq8	AceView	GA6	GA11
Entrez8	99		42.4	Bio	51	54	52	56	54
RefSeq8	88		47.7	Entrez8		82	64	92	86
AceView	92		45.7	RefSeq8			63	82	77
GA6	109		38.5	AceView				66	63
GA11	99		42.4	GA6					99
q-value < 10%
Bio	140	73	52.1		Entrez8	RefSeq8	AceView	GA6	GA11
Entrez8	125		58.4	Bio	89	94	97	100	96
RefSeq8	125		58.4	Entrez8		112	90	111	106
AceView	129		56.6	RefSeq8			94	109	103
GA6	139		52.5	AceView				93	89
GA11	130		56.2	GA6					129

Results from samr analysis of GSE974 dataset using six different CDFs under different q-value cut-offs in terms of number of total identified differentially expressed genes (DEG), of number and percentage of DEG in common by all lists generated using the various CDFs, and of number of DEG present in the pair-wise comparison of lists generated using different CDFs. EntrezGene IDs were used as reference identifiers to verify overlap of lists.

ISSN: 1471-2105