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Blood, Vol. 104, Issue 13, 3918-3926, December 15, 2004
Molecular characterization of early human T/NK and B-lymphoid progenitor cells in umbilical cord blood
Blood Haddad et al.
104: 3918
Supplemental materials for: Haddad et al, Vol 104, Issue 13, 3918-3926
Detailed analysis of functional annotations of genes differentially expressed between CD45RAhiCD7+, CD45RAintCD7- and CD45RAhiLin-CD10+ HPCs. Genes were selected using the LPE (Local Pooled Error) test1 based on the following criteria: a fold change (FC) of at least 1.3, a raw P value of no more than 0.05 according to the LPE test, an adjusted P value of no more than 0.10 (false discovery rate < 10%) according to the Benjamini and Hochberg procedure for multiple comparison adjustment2, and a minimum average signal intensity for each considered probe set above 70 in at least one of the 2 compared groups. According the selection criteria, 95 probe sets representing 52 genes and 42 consensus sequences were identified as being enriched in CD45RAintCD7- versus CD45RAhiCD7+ HPCs (Table S1), whereas 71 probe sets representing 49 genes and 20 consensus sequences were overexpressed in CD45RAhiCD7+ versus CD45RAintCD7- HPCs (Table S2). Among the 857 common probe sets differentially expressed in CD45RAhiLin-CD10+ versus CD45RAintCD7- HPCs and CD45RAhiLin-CD10+ versus CD45RAhiCD7+ HPCs, 401 probe sets representing 270 genes and 149 consensus sequences were enriched in CD45RAhiLin-CD10+ HPCs (Table S3). Functional annotation are based on NetAffx U133A annotation file (release Sept. 19.2003), OMIM (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM), PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed), and Conserved Domains (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=cdd).
References
1. Jain N, Thatte J, Braciale T, Ley K, O'Connell M, Lee J. Local pooled error test for identifying differentially expressed genes with a smaller number of replicated microarrays. Bioinformatics. 2003;19:1-7
2. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B. 1995;57:289-300
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