Table 3.
Enriched Gene Ontology (GO) terms in male-bias and female-bias genes
| GO term | SB (All) | p-value | Representative genes |
|---|---|---|---|
| (A) Brain tissue | |||
| Male: differentially expressed: 702; best Blastx hits in NR database: 420; genes with GO terms: 237 | |||
| Ionotropic glutamate receptor signaling (GO:0035235: BP) | 13 (46) | < 0.0001 | GRIK5 (2of2); GRIK4; GRIN2A (1 of 2); Glutamate [NMDA] receptor subunit zeta-1 |
| Ion transmembrane transport (GO:0034220: BP) | 29 (529) | < 0.0001 | Potassium channels: KCNJ3; KCNJ11 (1of2); KCNH1; KCNA1 (2 of2), Calcium channels: CACNA1I (4of4); Ryanodine receptor (RYR2 (1 of 3)), Sodium channel: SCN8A(2of2) |
| Regulation of cell development (GO:0060284: BP) | 9 (203) | 0.00699 | Lens calpain-3 (CAPN3); distal-less homeobox gene-1a (DLX1a); protein tyrosine phosphatase receptor-d (PTPRD); retinal cadherin-4 (CDH4 (1 of 2)) |
| Cerebellar Purkinje cell differentiation (GO:0021702: BP) | 3 (11) | 0.00068 | LIM/homeobox protein (LHX1); voltage-dependent P/Q-type calcium channel subunit alpha-1A (CACNA1A) ; LIM domain binding-1 (LDB1(2 of 2)) |
| Integral to membrane (GO:0016021: CC) | 84 (2448) | < 0.0001 | Hypocretin (orexin) receptor-1 (HCRTR1); multidrug resistance-associated protein 9; coiled-coil domain containing 149 CCDC149 (2 of 2); protocadherin 15b; gamma-aminobutyric acid A receptor, alpha-3 (GABRA3) |
| Female: differentially expressed: 1764; best Blastx hits in NR database: 1596; genes with GO terms: 955 | |||
| Endothelial cell migration (GO:0043542: BP) | 10 (44) | < 0.00036 | Sushi-repeat containing protein, X-linked2 (SRPX2); angiopoietin1 (ANGPT1); myosin heavy chain 9,non-muscle (MYH9(2 of 2)) |
| Gonad development (GO:0008406: BP) | 8 (37) | 0.00194 | WNT10A; WNT5A; secreted frizzled related proteins (SFRP1, SFRP5) ; TGFB2; Phospholipase A2 groupIVa (PLAG4A); |
| Immune response (GO:0006955: BP) | 23 (135) | < 0.0001 | WNT5A; TGFB2; kelch-like protein 6 (KLHL6); MHC classI-E (HLA-E); complement component (C6); MHC class II invariant chain (CD74(1of2)); chemokine(C-X-C motif) ligand12 (CXCL12(2of2)) |
| Integrin-mediated signaling pathway (GO:0007229: BP) | 8 (35) | 0.00132 | Integrin b1 binding protein1 (ITGB1BP1); Integrin, alpha10 (ITGA10);Integrin beta (ITGBL1, ITGB3a); nicotinamide riboside kinase-2 (NMRK2(2of2)) |
| DNA-dependent DNA replication initiation (GO:0006270: BP) | 5 (10) | 0.0002 | Minichromosome maintenance complex components (MCM2,MCM3,MCM4,MCM5,MCM6) |
| proteinaceous extracellular matrix (GO:0005578: CC) | 61 (151) | < 0.0001 | ADAM metallopeptidase with thrombospondin family members (ADAMTS12, ADAMTS15); NID1 (1of2); FBN3; MFAP2; CYR61 (2of2); COL4A1; COL10A1; COL11A1; WNT11; matrix metalloproteinases (MMP12, MMP14,MMP2 ) |
| (B) Tail tissue | |||
| Male: differentially expressed: 755; best Blastx hits in NR database: 635; genes with GO terms: 404 | |||
| Neuropeptide signaling pathway (GO:0007218: BP) | 5 (15) | < 0.00016 | Tachykinin, precursor 1 (TAC1); prepronociceptin PNOC (1 of 2); secretogranin V (7B2like) (SCG5); brain-specific angiogenesis inhibitor-3 (BAI3) |
| Neurotransmitter transport (GO:0006836: BP) | 11 (46) | 0.00057 | Syntaxin1B (STX1B); solute carrier family (SLC6A2, SLC6A5); syntaxin binding protein 1 STXBP1 (1 of 2) |
| Locomotory behavior (GO:0007626: BP) | 9 (42) | 0.00072 | Glycine receptor subunit beta (GLR-b2); choline O-acetyltransferase CHAT (2 of 2); astrotactin 1 (ASTN1) |
| *melanosome (GO:0042470:CC) | 4 (15) | 0.00241 0.01329 | 5,6-dihydroxyindole-2-carboxylic acid oxidase TYRP1 (1 of 2, 2 of 2); Tyrosinase TYR (2 of 2); synaptotagmin-like-2 (SYTL2); adenosine deaminase CECR1 |
| *Pigment biosynthetic process (GO:0046148: BP) | 4 (25) | ||
| Insulin receptor binding (GO:0005158: MF) | 4 (14) | 0.00156 | Sorbin and SH3 domain containing 1 SORBS1; DOK7 (1 of 2); growth factor receptor-bound protein 10 (GRB10) |
| Female: differentially expressed: 705; best Blastx hits in NR database: 616; genes with GO terms: 387 | |||
| Glycolysis (GO:0006096: BP) | 12 (43) | < 0.0001 | lactate dehydrogenase A (LDHA); phosphoglycerate kinase 1 (PGK1); pyruvate kinase, muscle (PKM (1 of 2)); glucose-6-phosphate isomerase (GPI (2 of 2)); 2,3-bisphosphoglycerate mutase (BPGM) |
| DNA-dependent DNA replication (GO:0006261: BP) | 10 (29) | < 0.0001 | Topoisomerase2a (TOP2a); primase, DNA, polypeptide 1 (PRIM1); tonsoku-like, DNA repair protein (TONSL); minichromosome maintenance complex components (MCM2, MCM4, MCM5, MCM6); polymerase (DNA directed), epsilon2 (POLE2) |
| Mitosis (GO:0007067: BP) | 13 (91) | 0.00105 | Aurora kinase C AURKC; cyclin-dependent kinase 1 CDK1 ; spindle apparatus coiled-coil protein 1 SPDL1; cyclin B1 CCNB1; non-SMC condensin I complex, subunitH, subunitD2 (NCAPH, NCAPD2); checkpoint kinase-1 (CHEK1) |
| Proteinaceous extracellular matrix (GO:0005578: CC) | 26 (125) | 0.00106 | Secreted protein, acidic, cysteine-rich (osteonectin) (SPARC); versican VCAN VCAN (2 of 2); tenascin(TNC (1 of 2)); collagens (COL11A1a, COL11A1b, COL27A1 (2 of 2)) |
| (C) Gonad Tissue | |||
| Male: Differentially expressed: 4891; Best Blastx hits in NR database: 3879; Genes with GO terms: 2033 | |||
| Cilium assembly (GO:0042384: BP) | 32 (46) | < 0.0001 | Radial spoke head 9 homolog (RSPH9); ARPC4-TTLL3 readthrough; forkhead box J1 (FOXJ1); Transmembrane proteins (TMEM237, TMEM17, TMEM231); B9 protein domain 1 (B9D1); coiled-coil and C2 domain containing-2A (CC2D2A) |
| Spermatogenesis (GO:0007283: BP) | 25 (58) | < 0.0001 | Kelch-like family member 10 KLHL10 (3 of 3); rhophilin associated tail protein 1-like (ROPN1L); phosphate cytidylyltransferase 1, choline-b ( PCYT1B (1 of 2)); Outer dense fiber protein 2/Cenexin (ODF2) |
| Meiosis I (GO:0007127: BP) | 12 (25) | 0.00025 | MutS homolog 5 (E. coli) MSH5; DMC1 dosage suppressor of mck1 homolog, meiosis-specific homologous recombination (DMC1); HORMA domain containing 1 HORMAD1; cyclin B1 interacting protein 1, E3 ubiquitin protein ligase CCNB1IP1 |
| Fertilization (GO:0009566: BP) | 8 (14) | 0.00064 | KLHL10 (3 of 3); spectrin, beta, non-erythrocytic 4 SPTBN4 (1 of 2); glycine receptor, beta GLRB (1 of 2); polypyrimidine tract-binding protein-1 (PTPB1) |
| Female: Differentially expressed: 5163; Best Blastx hits in NR database: 4577; Genes with GO terms: 2847 | |||
| Regulation of BMP signaling pathway (GO:0030510: BP) | 15 (27) | < 0.00028 | Forkhead box H1 (FOXH1); Noggin (NOG); WNT5a; activin A receptor, type I (ACVR1); follistatin-like 1 (FSTL1); bone morphogenetic protein 15 (BMP15); growth differentiation factor 9 (Gdf9) |
| Fibroblast growth factor receptor signaling (GO:0008543: BP) | 21 (47) | < 0.00094 | Kinesin family member-16Bb (KIF16bb); sal-like-4 (SALL4); serine threonine-protein phosphatase 2a (PP2a); sal-like 1 (SALL1); catenin, beta 1 (CTNNB1); fibroblast growth factor receptor-1(FGFR1 (2 of 2)); sprouty homolog 1, antagonist of FGF signaling (SPRY1); FGF20, FGF13, FGF 10 |
| Focal adhesion (GO:0005925: CC) | 26 (50) | < 0.0001 | Filamin A alpha FLNA (2 of 2); ezrin EZR (1 of 2); Rho guanine nucleotide exchange factor-7 (ARHGEF7 (al 3 paralogs)); syndecan-4 (SDC4); PDZ and LIM domain 2 (PDLIM2); talin 2 TLN2 (2 of 2) |
| Blood vessel development (GO:0001568: BP) | 90 (234) | < 0.0001 | Forkhead box H1 (FOXH1); lysophosphatidic acid receptor-2(LPAR2 (2 of 2)); angiopoietin-2 (ANGPT2); Rho guanine nucleotide exchange factor-7(ARHGEF7(3 of 3)); melanoma cell adhesion molecule (MCAM1 of 2); angiopoietin-like-1(ANGPTL1 (2 of 2)); activin A receptor, typeI (ACVR1); activin A receptor type II-like-1(ACVRL1) |
| Proteinaceous extracellular matrix (GO:0005578: CC) | 50 (111) | < 0.0001 | Netrin-4 (NTN4 (2 of 2)); sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) (SPOCK2 (2 of 2)); collagens (COL9A2, COL5A2, COL11A1a, COL11A1b, COL27A1 (2 of 2)); ADAMTS8 |
For each tissue we show GO terms enriched in both male-biased and female-biased genes. We report the total number of genes that have sex-biased (SB) expression and the number of sex-biased genes that were annotated with Blastx against NR and with GO terms. For each enriched GO term we report the GO term, its ID, and ontology (BP, Biological Process; MF, Molecular Function, and CC, Cellular Component), the number of sex-biased sequences, number of expressed sequences (in brackets) and the p-value. Statistical significance values were calculated with the Fisher’s test using the elim algorithm for reducing comparisons. We also list representative genes associated with the enriched GO term ordered by fold change expression.
* indicates that the same genes (except the italicized gene) were associated with both the cellular component and biological process GO terms.