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

From: HOMER: a human organ-specific molecular electronic repository

  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
  1. *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.
  2. ** 1494 of 6698 UniGene IDs were retired.
  3. *** 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.