Supplementary Table 3.
Functional annotations using Database for Annotation, Visualization and Integrated Discovery for proteins expressed from immature through spermatozoa maturation process (F1 through F4)
| Sample dataset | Key pathways | Key processes | Enriched functional categories | Cellular location | Functional categories that are associated with majority of proteins | Top TFBS | Key functions | Summary highlights of key processes/functions/pathways affected |
|---|---|---|---|---|---|---|---|---|
| F1 | Ribosome (21), protein export (3), SNARE interactions in vesicular transport (4), glutathione metabolism (4), influenza infection (27), UTR-mediated translational regulation (21), Met of proteins (27), GX (29), diabetes pathway (12), membrane trafficking (4) | Translational elongation (22), translation (27), intracellular transport (25), Golgi vesicle transport (10), cellular macromolecular complex assembly (15), protein localization (24), oxidation reduction (18), regulation of translation (8), cell death (19), regulation of apoptosis (17) | Translational elongation (22), ribosome (21), protein biosynthesis (21), RNA binding (28), structural molecule activity (26), ER (26), IC transport (925), Golgi vesicle transport (10), ER-Golgi transport (6), vesicle-mediated transport (15), macromolecular complex assembly (18), protein complex biogenesis (11), SRP (3), protein localization in organelle (8), NT binding (44), methylation (11), RasGTPase (6), lipoprotein (11), generation of precursor metabolites and energy (6) cell redox homeostasis (7), cell death (19), regulation of apoptosis (17), sexual reproduction (9), spermatogenesis (7), multicellular organism reproduction (8), spermatid development/differentiation (3) microtubule cytoskeleton (17), cytoskeletal part (21), mitochondrion (26) | Ribosomal subunit (20), ribonucleo protein complex (34), cytosol (53), nonmembrane bounded organelle (63), ER (33), organelle envelope (22), microtubule cytoskeleton (17), mitochondrion (26), Golgi apparatus (19), intracellular organelle lumen (33), nucleolus (15) | Acetylation (102), translational elongation (22), ribonucleo-protein (28), ribosome (21), protein biosynthesis (22); cytosol (53), translation (27), ER (26) | Pa×4 (143), AML1 (140), YY1 (129) | Structural constituent of ribosome (21), RNA binding (28), GTP binding (17), GTPase activity (12), nucleotide binding (44), HSP binding (5), purine ribonucleotide binding (35) | Translation elongation, protein transport, oxidoreductase activity, reproductive process, spermatid development/differentiation, regulation of apoptosis |
| F2 | Telomere maintenance (3), systemic lupus erythematosus (4), pyruvate metabolism (3), val-leu-ilu degradation (3) | Epidermis development (8), ectoderm development (8), oxidation–reduction (10), epithelial cell differentiation (5), protein transport (9), protein localization (9), intermediate filament organization (2), sexual reproduction (6) | Intermediate filament (8), keratin (8), protein transport (9), protein localization (9), membrane-bounded vesicle (8), sexual reproduction (6), reproductive process in a multicellular organism (6), EF-Hand2 domain (4), nucleosome assembly (3), chromatin (3), gonad development (3), sex differentiation (3), actin filament binding (3), ER membrane (3), proteolysis involved in cellular protein catabolic process (3), regulation of apoptosis (3) | Keratin filament (7), IF (8), mitochondrion (16), cytoskeletal part (13), membrane bounded vesicle (8), intracellular nonmembrane bounded organelle (21), ER (10) | Acetylation (23), intracellular nonmembrane bounded organelle (21), disease mutation (18), mitochondrion (16), cytoskeleton (15), coiled coil (15), structural molecular activity (12), transit peptide (10), oxidoreductase (10), ER (10), sexual reproduction (6) | SP1 (24), ROAZ (38) | Structural constituent of cytoskeleton (6), Structural molecular activity (12), coenzyme binding (5), actin filament binding (3), cofactor binding (5) | Epidermis and ectoderm development, cell differentiation, protein–protein interactions, protein transport and localization, oxidoreductase activity, gamete generation, gonad development, proteolysis |
| F3 | Huntington’s disease (6), pyrimidine metabolism (4), oxidative phosphorylation (4), ubiquitin-mediated proteolysis (4), metabolism of protein import into nucleus (2), metabolism of vitamins and cofactors (3), integration of energy metabolism (5), metabolism of nucleotides (3) | Nucleoside metabolic process (4), generation of precursor metabolites and energy (7), oxidation–reduction (9), vitamin metabolic process (3) | Mitochondrial inner membrane (9), oxidoreductase activity (3), oxidative phosphorylation (3), protein ubiquitination (3), protein modification by small protein conjugation (3), phospholipid metabolic process (3), spermatogenesis (4), male gamete generation (4), nucleotide biosynthetic process (3), lysosome (3), lytic vacuole (3), ubl conjugation pathway (5), proteolysis involved in cellular protein catabolic process (5), GTP binding (3), ER membrane (3), mitotic cell cycle (3) | Organelle inner membrane (10), organelle envelope (13), mitochondrion (12), respiratory chain (3), nuclear pore (3) | Alternative splicing (44), acetylation (22), cytoplasm (22), transport (15), secreted (14), organelle envelope (13), mitochondrion (12), oxidoreductase (9), generation of precursor metabolites and energy (7) | Cytochrome-c oxidase activity (3), transmembrane transporter activity (4), nucleotidyl transferase activity (4) | Generation of precursor metabolites and integration of energy metabolism, oxidative phosphorylation, protein catabolic process, protein ubiquitination | |
| F4 | Hedgehog signaling pathway (2), metabolism of amino acids (3), nuclear factor of activated T-cells, cytoplasmic, calcineurin dependent 2 (2) | Reproductive process in a multicellular organism (5), spermatogenesis (4), male gamete generation (4), sexual reproduction (4), phosphorus metabolic process (5), regulation of protein complex disassembly (2) heterocyclic biosynthetic process (2) | Multicellular organism reproduction (5), spermatogenesis (4), male gamete generation (4), sexual reproduction (4), transit peptide (5), mitochondrion (5), phosphate metabolic process (5), protein kinase activity (3), secreted (5), signal (8), cell surface (4), membrane (14), cation binding (8), cytoskeleton (3) | Cell surface (4) | Acetylation (11), hydrolase (8), multicellular organism reproduction (5), mitochondrion (5), phosphorus metabolic process (5), transit peptide (5), spermatogenesis (4), lipid catabolic process (3), hedgehog signaling pathway (2), regulation of protein complex | HAND1E47 (22), ATF (16), CDPCR3 (24); Domains-serine/threonine protein kinases active site signatures (3) | Oxidoreductase activity, acting on sulfur group of donors (2) | Multicellular organism reproduction |
| Increasing trend | Metabolism of amino acids (4), Huntington disease (3), valine-leucine-isoleucine degradation (4), propionate metabolism (3), aldosterone-regulated sodium reabsorption (3), beta-alanine metabolism (2) | Carboxylic acid catabolic process (5), oxidation–reduction (8), sexual reproduction (6), spermatogenesis (4), male gamete generation (4), integrin-mediated signaling pathway (3), generation of precursor metabolites and energy (5), amine catabolic process (4), sperm motility (2), cell motility (4) | Dynein (4), microtubule motor activity (4), purine nucleotide metabolic process (4), cilium axoneme (3), sodium/potassium transport (3), metallopeptidase activity (5), potassium ion binding (4), ion transport (4), cell motility (4), male gamete generation (4), spermatogenesis (4), multicellular organism reproduction (4), protein complex assembly (3) | Mitochondrion (17), dynein complex (4), cytoskeleton (12), cell projection (7), cilium axoneme (3), microtubule based flagellum (3) | Alternative splicing (34), cytoplasm (19), mitochondrion (17), acetylation (15), mitochondrion (15), nucleotide binding (15), coiled coil (13), cytoskeleton (12), transit peptide (10), sexual reproduction (6), generation of precursor metabolites and energy (5) | YY1 (51), CREBP1CJUN (13), CDPCR1 (30), AML1 (54), HSF1 (24) | Sodium: potassium exchanging ATPase activity (3), microtubule motor activity (4), nucleotide binding 915), purine nucleoside binding (11), metallo endopeptidase activity (3), purine nucleotide binding (12), coenzyme binding (5), potassium ion binding (4), magnesium ion binding (6) | Intracellular transport, oxidation reduction, cellular amino acid catabolic process, alternative splicing |
| Decreasing trend | Metabolism of proteins (38), UTR-mediated translational regulation (25), signaling by Wnt (13), apoptosis (13), integration of energy metabolism (16), cell cycle (19), metabolism of amino acids (12), diabetes pathways (22), regulation of activated PAK-2p34 by proteasome-mediated degradation (10), ubiquitin proteasome pathway (9), antigen processing and presentation (9), proteasome (9), ribosome (20), oxidative phosphorylation 99), role of Ran in mitotic spindle regulation (3), Prion pathway (3), mechanism of gene regulation by peroxisome proliferators via PPARa (4) | Protein folding (34), translational elongation (25), cell redox homeostasis (12), proteasomal protein catabolic process (13), protein transport (35), protein localization (36), regulation of ligase activity (11), proteolysis (28), regulation of apoptosis (27), homeostatic process (25), protein complex biogenesis (21), cell cycle (21), sexual reproduction (15) | Protein folding (34), translational elongation (25), protein biosynthesis (27), HSP70 (6), proteasome (10), stress response (12), response to unfolded protein (16), ER (38), mitochondrion (36), negative regulation of protein ubiquitination (10), regulation of ligase activity (11), oxidoreductase (17), intracellular protein transport (20), secreted (28), vesicle-mediated transport (15), cellular protein localization (20), EF-hand type domain (13), peroxidase activity (5), regulation of cell death (27), spermatogenesis (12), male gamete generation (12), sexual reproduction (15), spermatid development (3), spermatid differentiation (3), sperm cell development (3) | Cytosol (83), nonmembrane bounded organelle (65), mitochondrion (36), melanosome (19), ribosomal subunit (19), ER (46), ribonucleo protein complex (30), vesicle (33) | Phosphoprotein (151), acetylation (147), cytoplasm (97), cytosol (83), nonmembrane bounded organelle (65), signal (60), nucleotide binding (53), ER (46), unfolded protein binding (31), protein biosynthesis (29), proteolysis (28), regulation of apoptosis (27), translational elongation (25), homeostatic process (25), protein transport (24), mitochondrion (23), protein complex assembly (21), cell cycle (21), oxidoreductase (17) | NFY (123) | Unfolded protein binding (31), structural constituent of ribosome (20), structural molecule activity (26), nucleotide binding (60), calcium ion binding (24), peptidase activity (15), ATPase activity (12), protein transporter activity (9), GTPase activity (11), peptide binding (8), antioxidant activity (6) | Spermatogenesis, protein metabolism, cell cycle, integration of energy metabolism, regulation of apoptosis, cell redox homeostasis, translational elongation, response to protein folding |
The number of proteins is in the parenthesis. ER: endoplasmic reticulum; HSP: heat shock protein; TFBS: transcription factor binding sites