Background
Methods
Mice testis preparation
Gene expression microarrays
Enrichment score
Cluster analysis
Association of transcript clusters to specific testis cells
Gene set enrichment analysis
Immunohistochemistry (IHC)
In silicoquantification of Leydig cells
Results
Clusters of transcripts affected by low dose irradiation
Assignment of transcript clusters to specific testicular cells
Gene symbol | Gene name | Associated cell | Identified cluster # |
---|---|---|---|
Dazl | Deleted in azoospermia-like | Spermatogonia | 1 |
1500011H22Rik | RIKEN cDNA 1500011H22 gene | Spermatocytes | 2 |
1700029G01Rik | RIKEN cDNA 1700029G01 gene | Spermatocytes | 3 |
2410022L05Rik | RIKEN cDNA 2410022 L05 gene | Spermatocytes | 2 |
Akap12 | A kinase (PRKA) anchor protein (gravin) 12 | Spermatocytes | 5 |
Aldoa-ps1 | Aldolase 1, A isoform, retrogene 2 | Spermatocytes | 4 |
Atl3 | Atlastin GTPase 3 | Spermatocytes | 4 |
Cypt3 | Cysteine-rich perinuclear theca 3 | Spermatocytes | 3 |
D030056L22Rik | RIKEN cDNA D030056L22 gene | Spermatocytes | 1 |
Gsg2 | Germ cell-specific gene 2 | Spermatocytes | 3 |
H3f3b | H3 histone, family 3B | Spermatocytes | 1 |
Hnrpa2b1 | Heterogeneous nuclear ribonucleoprotein A2/B1 | Spermatocytes | 1 |
Lyar | Ly1 antibody reactive clone | Spermatocytes | 2 |
Nt5c1b | 5′-nucleotidase, cytosolic IB | Spermatocytes | 4 |
Pgk2 | Phosphoglycerate kinase 2 | Spermatocytes | 4 |
Slc2a3 | Solute carrier family 2 (facilitated glucose transporter), member 3 | Spermatocytes | 2 |
Spert | Spermatid associated | Spermatocytes | 4 |
Stard10 | START domain containing 10 | Spermatocytes | 4 |
Stmn1 | Stathmin 1 | Spermatocytes | 1 |
Vkorc1 | Vitamin K epoxide reductase complex, subunit 1 | Spermatocytes | 5 |
Acrv1 | Acrosomal vesicle protein 1 | Spermatids | 3 |
Actl7a | Actin-like 7a | Spermatids | 4 |
Akap4 | A kinase (PRKA) anchor protein 4 | Spermatids | 4 |
Marcksl1 | MARCKS-like 1 | Spermatids | 5 |
Pdpk1 | 3-phosphoinositide dependent protein kinase-1 | Spermatids | 4 |
Pdzk1 | PDZ domain containing 1 | Spermatids | 4 |
Prm1 | Protamine 1 | Spermatids | 2 |
Spag4l | Sperm associated antigen 4-like | Spermatids | 3 |
Tctex1d1 | Tctex1 domain containing 1 | Spermatids | 4 |
Tnp2 | Transition protein 2 | Spermatids | 3 |
Zpbp | Zona pellucida binding protein | Spermatids | 3 |
Hsd17b3 | Hydroxysteroid (17-beta) dehydrogenase 3 | Leydig cells | 5 |
Hsd3b1 | Hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 | Leydig cells | 5 |
Cyp17a1 | Cytochrome P450, family 17, subfamily a, polypeptide 1 | Leydig cells | 5 |
Acta2 | Actin, alpha 2, smooth muscle, aorta | PTM cells | 5 |
Cldn11 | Claudin 11 | Sertoli cells | 5 |
Clu | Clusterin | Sertoli cells | 5 |
Ctsl | Cathepsin L | Sertoli cells | 5 |
Vim | Vimentin | Sertoli cells | 5 |
Gene set enrichment analysis
Cluster | Category | Term | Count | % | p-value | Fold enrichment | Bonferroni p-value |
---|---|---|---|---|---|---|---|
1: Spermatogonia | BP | mRNA processing | 11 | 11.83 | 6.12E-07 | 8.22 | 3.11E-04 |
mRNA metabolic process | 11 | 11.83 | 2.46E-06 | 7.05 | 0.001 | ||
RNA splicing | 9 | 9.68 | 6.05E-06 | 8,87 | 0.003 | ||
CC | Ribonucleoprotein complex | 19 | 20.43 | 4.15E-12 | 8.28 | 6.56E-10 | |
Macromolecular complex | 34 | 36.56 | 5.83E-09 | 2.75 | 9.21E-07 | ||
Intracellular organelle | 60 | 64.52 | 2.24E-08 | 1.54 | 3.54E-06 | ||
Organelle | 60 | 64.52 | 2.32E-08 | 1.54 | 3.67E-06 | ||
Intracellular part | 64 | 68.82 | 4.10E-08 | 1.41 | 6.48E-06 | ||
Intracellular | 64 | 68.82 | 2.70E-07 | 1.36 | 4.26E-05 | ||
Intracellular organelle part | 35 | 37.63 | 5.02E-07 | 2.25 | 7.93E-05 | ||
Organelle part | 35 | 37.63 | 5.95E-07 | 2.24 | 9.40E-05 | ||
Spliceosome | 8 | 8.60 | 2.23E-06 | 12.97 | 3.53E-04 | ||
Nucleus | 38 | 40.86 | 1.60E-05 | 1.85 | 0.003 | ||
Intracellular membrane-bounded organelle | 51 | 54.84 | 4.71E-05 | 1.47 | 0.007 | ||
Membrane-bounded organelle | 51 | 54.84 | 4.90E-05 | 1.47 | 0.008 | ||
MF | RNA binding | 21 | 22.58 | 2.81E-12 | 7.11 | 4.35E-10 | |
Nucleic acid binding | 31 | 33.33 | 1.36E-06 | 2.36 | 2.11E-04 | ||
2: Spermatocytes | BP | Sexual reproduction | 18 | 12.41 | 1.02E-09 | 6.70 | 7.80E-07 |
Gamete generation | 16 | 11.03 | 7.42E-09 | 6.94 | 5.67E-06 | ||
Male gamete generation | 14 | 9.66 | 2.03E-08 | 7.89 | 1.55E-05 | ||
Spermatogenesis | 14 | 9.66 | 2.03E-08 | 7.89 | 1.55E-05 | ||
Multicellular organism reproduction | 16 | 11.03 | 1.22E-07 | 5.62 | 9.34E-05 | ||
Reproductive process in a multicellular organism | 16 | 11.03 | 1.22E-07 | 5.62 | 9.34E-05 | ||
Reproductive process | 18 | 12.41 | 1.01E-06 | 4.17 | 7.72E-04 | ||
Reproduction | 18 | 12.41 | 1.11E-06 | 4.14 | 8.44E-04 | ||
Cell cycle process | 14 | 9.66 | 2.88E-06 | 5.12 | 0.002 | ||
CC | Intracellular organelle part | 45 | 31.03 | 1.01E-06 | 2.03 | 2.04E-04 | |
Macromolecular complex | 39 | 26.90 | 1.16E-06 | 2.21 | 2.36E-04 | ||
Organelle part | 45 | 31.03 | 1.22E-06 | 2.02 | 2.48E-04 | ||
Intracellular part | 90 | 62.09 | 1.67E-06 | 1.35 | 3.39E-04 | ||
Intracellular membrane-bounded organelle | 74 | 51.03 | 6.04E-06 | 1.47 | 0.001 | ||
Membrane-bounded organelle | 74 | 51.03 | 6.04E-06 | 1.47 | 0.001 | ||
Intracellular organelle | 80 | 55.17 | 6.71E-06 | 1.41 | 0.001 | ||
Organelle | 80 | 55.17 | 6.87E-06 | 1.41 | 0.001 | ||
3: Early spermatids | BP | Sexual reproduction | 19 | 9.60 | 2.17E-10 | 6.69 | 1.19E-07 |
Male gamete generation | 13 | 6.57 | 2.33E-07 | 7.03 | 1.28E-04 | ||
Spermatogenesis | 13 | 6.57 | 2.33E-07 | 7.03 | 1.28E-04 | ||
Reproductive process | 19 | 9.60 | 3.10E-07 | 4.21 | 1.70E-04 | ||
Reproduction | 19 | 9.60 | 3.51E-07 | 4.17 | 1.93E-04 | ||
Gamete generation | 14 | 7.07 | 5.99E-07 | 5.81 | 3.29E-04 | ||
Multicellular organism reproduction | 14 | 7.07 | 6.43E-06 | 4.69 | 0.004 | ||
Reproductive process in a multicellular organism | 14 | 7.07 | 6.43E-06 | 4.69 | 0.004 | ||
CC | Acrosomal vesicle | 10 | 5.05 | 1.06E-10 | 25.52 | 1.76E-08 | |
Secretory granule | 10 | 5.05 | 1.11E-06 | 9.26 | 1.84E-04 | ||
4: Late spermatids | BP | Sexual reproduction | 16 | 7.24 | 4.98E-08 | 6.01 | 2.95E-05 |
Spermatogenesis | 12 | 5.43 | 1.27E-06 | 6.83 | 7.51E-04 | ||
Male gamete generation | 12 | 5.43 | 1.27E-06 | 6.83 | 7.51E-04 | ||
Gamete generation | 13 | 5.88 | 2.51E-06 | 5.70 | 0.001 | ||
Reproductive process in a multicellular organism | 14 | 6.33 | 3.97E-06 | 4.97 | 0.002 | ||
Multicellular organism reproduction | 14 | 6.33 | 3.97E-06 | 4.97 | 0.002 | ||
CC | Cytoplasm | 73 | 33.03 | 1.65E-05 | 1.49 | 0.002 | |
5: Somatic cells | BP | Oxidation reduction | 28 | 15.56 | 2.32E-09 | 3.87 | 3.34E-06 |
Lipid metabolic process | 28 | 15.56 | 4.93E-09 | 3.74 | 7.10E-06 | ||
Response to oxidative stress | 10 | 5.56 | 3.62E-07 | 10.68 | 5.22E-04 | ||
Lipid biosynthetic process | 16 | 8.89 | 4.00E-07 | 5.21 | 5.76E-04 | ||
Cellular ketone metabolic process | 20 | 11.11 | 1.23E-06 | 3.79 | 0.002 | ||
Oxoacid metabolic process | 19 | 10.56 | 3.61E-06 | 3.69 | 0.005 | ||
Carboxylic acid metabolic process | 19 | 10.56 | 3.61E-06 | 3.69 | 0.005 | ||
Organic acid metabolic process | 19 | 10.56 | 3.71E-06 | 3.68 | 0.005 | ||
Cellular lipid metabolic process | 19 | 10.56 | 3.93E-06 | 3.66 | 0.006 | ||
Response to hydrogen peroxide | 6 | 3.33 | 4.71E-06 | 23.23 | 0.007 | ||
CC | Cytoplasm | 114 | 63.33 | 4.81E-13 | 1.68 | 1.11E-10 | |
Cytoplasmic part | 85 | 47.22 | 1.37E-11 | 1.94 | 3.14E-09 | ||
Mitochondrion | 37 | 20.56 | 6.64E-08 | 2.67 | 1.53E-05 | ||
Intracellular part | 128 | 71.11 | 5.25E-06 | 1.27 | 0.001 | ||
Intracellular | 130 | 72.22 | 2.52E-05 | 1.23 | 0.006 | ||
MF | Oxidoreductase activity | 29 | 16.11 | 2.67E-10 | 4.12 | 1.02E-07 | |
Oxidoreductase activity, acting on CH-OH group of donors | 13 | 7.22 | 2.96E-09 | 10.68 | 1.13E-06 | ||
Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 6.67 | 6.67 | 1.19E-08 | 10.91 | 4.56E-06 |