Table 5 Number of preferentially expressed genes in testis located in clusters within tandem duplicate-free mouse genome Out of the 19 684 known genes (LocusLink) mapped on mouse genome assembly (NCBI, build32), 16 858 genes remained in tandem duplicate-free genome, including 1 300 and 1 050 preferentially expressed genes in total testis and testicular somatic cells, respectively. Chromosome search found clusters containing at least three adjacent preferentially expressed genes (tight clusters) or at least three preferentially expressed genes among the six adjacent genes (loose clusters). The tight clusters therefore form a subset of the loose clusters. Observed gene counts were evaluated using permutations (100000 random shufflings of the expression status of genes while keeping the gene positions constant) and the average number of genes located in clusters in the randomized genomes was computed.
Total testis (TT 1+2) | Adult testis somatic cells (ATSC) | |||
|---|---|---|---|---|
1 300 | 1 050 | |||
in tight clusters | in loose clusters | in tight clusters | in loose clusters | |
Observed gene counts | 44 | 230 | 36 | 120 |
Proportion of preferentially expressed genes | 3.4 % | 17.7 % | 3.4 % | 11.4 % |
Gene counts in randomized genomes (mean ± std. dev.) | 21.9 ± 8.1 | 168.4 ± 20.1 | 11.7 ± 5.9 | 94.2 ± 15.6 |
Ratio observed/mean in randomized genomes | 2.0 | 1.4 | 3.1 | 1.3 |
Permutations yielding > = observed gene counts | 741 | 180 | 52 | 5 722 |
p-value (one tailed) | 0.0074 | 0.0018 | 0.0005 | 0.0572 |