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Table 3 Enriched Gene Ontology (GO) terms in male-bias and female-bias genes

From: Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata

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
  1. 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.
  2. * indicates that the same genes (except the italicized gene) were associated with both the cellular component and biological process GO terms.