Table 3

Clusters of differentially expressed genes

Clusters

Differential expression VS CD34+ cells

Total number of differentially expressed genes

Number of clusters

Total number of differentially expressed genes in clusters

Total number of data matrix genes in clusters

Total number of EntrezGenes in clusters

p-value

Erythroblasts up-regulated genes

269

7

26

151

360

7.94E-05

Erythroblasts down-regulated genes

223

4

14

54

127

0.0088

Megakaryoblasts up-regulated genes

214

7

25

138

379

0.0035

Megakaryoblasts down-regulated genes

136

1

3

7

18

0.0033

Monoblasts up-regulated genes

277

7

24

166

439

0.0101

Monoblasts down-regulated genes

126

0

0

0

0

nd

Myeloblasts up-regulated genes

32

0

0

0

0

nd

Myeloblasts down-regulated genes

15

0

0

0

0

nd

REEF software was used to analyse the genomic distribution of differentially expressed genes and to find significant positional enrichments (q-value < 0.05). Columns 2 and 3 indicate the total number of differentially expressed genes in the human genome and the number of clusters identified by REEF. In the following three columns, the numbers of differentially expressed genes, genes represented in the myelopoiesis data matrix and EntrezGenes falling in identified clusters are reported. The numbers of genes represented in the myelopoiesis data matrix showing up- or down-regulation, respectively for clusters of significantly up- or down-regulated genes, results to be higher than expected by chance, accordingly with hypergeometric distribution (p < = 0.01). Calculated p-values are reported in the last column. Further details concerning each cluster are reported in Additional file 7.

Ferrari et al. BMC Genomics 2007 8:264   doi:10.1186/1471-2164-8-264