HOMER: a human organ-specific molecular electronic repository

BMC Bioinformatics

Table 2 A comparison of human organ-specific genes/proteins in HOMER against several common human tissue/organ-specific data sources

	TissueDistributionDBs[3]	TiGER[10]	TiSGeD[11]	HPA[12]	HOMER
Organ coverage	40	30	18	24	52
Gene coverage	1359*	4283**	957***	74	5703
Last Updated	2010	March 2008	July 2010	Jan 2011	June 2011
Criteria for organ-specific genes	TissueSpecificityIndex	p-value<1e-3.5 EE>5	SPM	Exclusively detected in a single cell	p-value ≤ 1e-5 RZ ≥ 4 AE ≥ 10 RE ≥ 4
Expression Value	Relative expression	Yes	No	No	Relative Expression
Plasma Detectability	No	No	No	No	Yes
Disease Association	No	No	No	No	Yes

*1359 gene IDs were filtered out from 54, 576 human UniGene IDs with TissueSpecificityIndex = 1. We used TissueSpecificityIndex = 1 as the website didn’t recommend any criteria for us to derive organ-specific genes.
** 1494 of 6698 UniGene IDs were retired.
*** 957 gene IDs were filtered out from 2423 gene IDs with SPM ≥ 0.9. We used SPM ≥ 0.9 as the website didn’t recommend any criteria for us to derive organ-specific genes.

ISSN: 1471-2105