Table 4 Distribution of testis-specific genes on autosomes and the X chromosome The total of 14 222 LocusLink genes were identified in total testis, adult testis somatic cells and non-testis tissue SAGE libraries (see Additional file 4) using RNA evidence mapping (tags matching multiple LocusLink genes were discarded). The genes identified by total tag count = 1 were then excluded from analysis. The genes expressed only in one tissue type (total testis, adult testis somatic cells, brain, eye, heart, liver, kidney, limbs and adipose tissue) were considered to be tissue-specific genes. Chromosomal distribution of genes specific for total testis (a) and testis somatic cells (b) in comparison to the non-testis tissue-specific genes was evaluated. The significance was tested by permutations (100 000 random shufflings of the chromosomes while keeping the sum of genes on autosomes and the X chromosome fixed) and confirmed by Fisher's exact test. Abbreviations: total t. = total testis; t. somatic = testicular somatic cells; other = non-testis tissues; ChrA = autosomes; ChrX = X chromosome.
a) Total testis: 395 genes specific for the combined total testis SAGE library (TT 1+2) Other tissues: 877 genes specific for one tissue type in the pool of other SAGE libraries | |||||||
|---|---|---|---|---|---|---|---|
Chrom | Observed gene counts | Gene counts in randomized genome | % observed gene counts | Ratio of observed proportions | |||
total t. | other | total t. | other | total t. | other | total t./other | |
ChrA | 381 | 836 | 378 | 839 | 96.5 | 95.3 | 1.0 |
ChrX | 14 | 41 | 17 | 38 | 3.5 | 4.7 | 0.7 |
Permutations yielding < = observed gene counts in total t. on ChrX | 22 395 | ||||||
Permutations, p-value (two tailed) | 0.4479 | ||||||
Fisher's exact, p-value (two tailed) | 0.4563 | ||||||
Confidence interval (0.95) | 0.70 – 2.68 | ||||||
b) Testis somatic cells: 81 genes specific for the adult testis somatic cells SAGE library (ATSC) Other tissues: 924 genes specific for one tissue type in the pool of other SAGE libraries | |||||||
Chrom | Observed gene counts | Gene counts in randomized genome | % observed gene counts | Ratio of observed proportions | |||
t.somatic | other | t.somatic | other | t.somatic | other | t. somatic/other | |
ChrA | 70 | 885 | 77 | 878 | 86.4 | 95.8 | 0.9 |
ChrX | 11 | 39 | 4 | 46 | 13.6 | 4.2 | 3.2 |
Permutations yielding > = observed gene counts in t. somatic on ChrX | 121 | ||||||
Permutations, p-value (two tailed) | 0.0024 | ||||||
Fisher's exact, p-value (two tailed) | 0.0013 | ||||||
Confidence interval (0.95) | 0.13 – 0.64 | ||||||