Table 1. The X chromosome is enriched for genes induced before and after MSCI and for testis-biased genes.
| % Expresseda | % Inducedb | % Testis-biasedc | Functional annotation | ||||
|---|---|---|---|---|---|---|---|
| Auto | X | Auto | X | Auto | X | Auto and X | |
| By cell | |||||||
| Spermatogonia | 54.3 | 50.5 | 19.1 | 40.3*** | 5.6 | 11.3*** | Cell, intracellular, anatomical structure development, biosynthetic process, nucleic acid binding transcription factor activityd |
| Leptotene/zygotene spermatocytes | 52.7 | 45.6 | 15.3 | 34.0*** | 5.2 | 7.5 | Organelle, intracellular, cell, cellular nitrogen metabolic process, nucleusd |
| Diplotene spermatocytese | 48.0 | 13.2 | 16.2 | — | 48.4 | — | Cilium, reproduction, microtubule organizing center |
| Round spermatids | 50.3 | 35.6 | 22.8 | 23.0 | 42.5 | 44.9 | Cilium, reproduction |
| By stage | |||||||
| Early | NA | NA | 10.6 | 33.9*** | 3.1 | 7.5*** | Anatomical structure development, immune system process, plasma membrane, signal transduction, cell differentiationd |
| Early and late | NA | NA | 2.3 | 9.3 | 14.3 | 19.5 | Anatomical structure development, cytoskeletal organization, cytoskeletal protein binding, cell differentiation, cytoskeletond |
| Late | NA | NA | 7.9 | 19.1*** | 35.6 | 49.4*** | Reproduction, signal transducer activity, extracellular region, cell wall organization or biogenesis, neurological system process |
Values represent the percentage of genes that meet a given expression threshold in each cell type and stage of spermatogenesis. Enrichment of X-linked genes are based on chromosome-wise hypergeometric tests, FDR-corrected P-values: *** P ≤ 0.001.
Expressed, genes with FPKM > 1 in a minimum of four individuals for a given cell type out of the total genes detected (14,223 genes).
Induced, by cell: genes with a median FPKM > 2× the median FPKM of all other cell types combined out of the total genes expressed. By stage: genes with a maximum FPKM > 4× the maximum FPKM of all other stages combined of the total genes expressed. (Note: a gene can be induced in more than one cell type, but can only be induced at a single stage).
Testis-biased, genes with higher expression in the testes compared 96 other tissues from the Mouse MOE430 Gene Atlas out of the total genes induced.
Only the top five gene enrichment categories are listed.
Due to MSCI there are too few genes expressed in diplotene spermatocytes to report X-linked induced genes.