Table 5. Selection of transcripts with highest correlation to transcript co-expression module eigengene (module membership, MM) in the darkgreen consensus module identified in Aplysia californica sensory neurons by WGCNA.
| Refseq ID | MM | MM p value | TAS | TAS P value | Human Ortholog | Ortholog Name | Ortholog Function |
|---|---|---|---|---|---|---|---|
| XM_013082889.1 | 0.96 | 9.81E-41 | 0.39 | 6.56E-04 | RPA2 | Replication protein A 32 kDa subunit | DNA replication [158], DNA damage repair [159,160] |
| XM_005094195.2 | 0.95 | 3.60E-37 | 0.51 | 4.61E-06 | TRIM3 | Tripartite motif-containing protein 3 | E3 ubiquitin-protein ligase, negative regulator of inflammation [161–163], inhibits synaptic plasticity [164] |
| XM_013086128.1 | 0.94 | 2.71E-34 | 0.47 | 2.42E-05 | TIPARP | Poly [ADP-ribose] polymerase | Inhibitor of AHR-dependent transcription [165], suppressor of INF due to AHR activation [166], activator of INF due to ROS [167] |
| XM_005113357.2! | 0.93 | 7.35E-33 | 0.53 | 1.71E-06 | SOCS2 | Suppressor of cytokine signaling 2[160] | Inhibits JAK/STAT signaling, promotes neurite outgrowth [168], regulates cytokine signaling [169,170] |
| XM_005092855.1! | 0.91 | 3.77E-28 | 0.46 | 3.57E-05 | |||
| XM_005108083.2! | 0.85 | 4.32E-21 | 0.42 | 2.17E-04 | |||
| XM_005092772.2 | 0.93 | 1.77E-32 | 0.29 | 1.39E-02 | ENDOG | Endonuclease G, mitochondrial | mitochondrial biogenenesis and homeostasis [171,172], apoptosis [173,174] |
| XM_005107816.2* | 0.93 | 3.24E-32 | 0.52 | 2.29E-06 | HENMT1 | Small RNA 2’-O-methyltransferase | piRNA biogenesis [175] |
| XM_005095515.2* | 0.93 | 3.35E-32 | 0.60 | 2.12E-08 | ICE2 | Little elongation complex subunit 2 | snRNA transcription [176] |
| XM_005101982.2 | 0.93 | 1.01E-31 | 0.38 | 8.51E-04 | LGALS4 | Galectin-4 | Reduced pro-inflammatory cytokine secretion [177], inhibits myelination [178] |
| XM_013087261.1* | 0.92 | 3.26E-31 | 0.48 | 1.80E-05 | GALC | Galactocerebrosidase | Lysosomal degradation of galactocerebrosides [179] |
| XM_013084530.1 | 0.92 | 1.26E-30 | 0.43 | 1.36E-04 | SMARCD1 | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 | Transcription activation and repression via chromatin remodeling as part of SWI/SNF complex [180], immune regulation [181] |
| XM_005102729.2 | 0.92 | 5.39E-30 | 0.28 | 1.59E-02 | WDR53 | WD repeat-containing protein 53 | unknown |
| XM_005105962.2 | 0.92 | 8.43E-30 | 0.46 | 4.99E-05 | EPSTI1 | Epithelial-stromal interaction protein 1 | Macrophage differentiation [182] |
| XM_005111022.2 | 0.92 | 1.03E-29 | 0.52 | 2.03E-06 | RBBP9 | Putative hydrolase RBBP9 | Inhibits TGF-beta growth-inhibition [183] |
| XM_005101042.1 | 0.91 | 1.34E-29 | 0.44 | 9.85E-05 | RPA3 | Replication protein A 14 kDa subunit | DNA damage repair [184] |
| XM_005108381.2 | 0.91 | 1.78E-29 | 0.43 | 1.39E-04 | MOV10L1 | RNA helicase Mov10l1 | piRNA biogenesis [185] |
| XM_013088805.1 | 0.91 | 2.10E-29 | 0.47 | 3.26E-05 | SLC16A14 | Monocarboxylate transporter 14 | Neuronal aromatic-amino-acid transporter [186] |
| XM_005100427.2* | 0.91 | 3.91E-29 | 0.50 | 6.50E-06 | NSMCE1 | Non-structural maintenance of chromosomes element 1 homolog | E3 ubiquitin-protein ligase, DNA damage response, and iron homeostasis [187] |
| XM_013084495.1 | 0.91 | 5.14E-29 | 0.42 | 1.84E-04 | DDX58 | Probable ATP-dependent RNA helicase DDX58 | RIG 1, antiviral immune receptor [188] |
| XM_005091253.2* | 0.91 | 9.96E-29 | 0.56 | 2.70E-07 | TENT4A | Terminal nucleotidyltransferase 4A | mRNA stability and quality control [189,190] |
| XM_013090188.1! | 0.91 | 1.24E-28 | 0.56 | 2.35E-07 | MPEG1 | Macrophage-expressed gene 1 protein | Antibacterial protein, pore-forming protein, innate immunity [191] |
| XM_005088804.2 | 0.91 | 1.75E-28 | 0.44 | 1.00E-04 | PLA2G16 | HRAS-like suppressor 3 | Phospholipid metabolism [192], sensor for sites of viral entry [193] |
| XM_013082099.1 | 0.90 | 1.24E-27 | 0.42 | 1.97E-04 | NUP214 | Nuclear pore complex protein Nup214 | Nuclear pore formation and protein import into nucleus [194,195] |
| XM_013088902.1! | 0.89 | 1.45E-26 | 0.50 | 8.27E-06 | DIS3L2 | DIS3-like exonuclease 2 | Mediates degradation of polyuridylated RNAs [196], mRNA metabolism [197] |
| XM_005089228.2 | 0.89 | 2.04E-26 | 0.48 | 2.03E-05 | SSUH2 | Protein SSUH2 homolog | Odontogenesis, upstream of several transcriptional regulators [163] |
| XM_005107110.2 | 0.89 | 2.47E-26 | 0.43 | 1.52E-04 | PARP14 | Protein mono-ADP-ribosyltransferase PARP14 | Suppresses IFN-gamma response, induces IL-4 response, counteracts PARP9 [198] |
| XM_013081916.1 | 0.89 | 6.38E-26 | 0.53 | 1.16E-06 | NUP98 | Nuclear pore complex protein Nup98-Nup96 | Nuclear pore formation, gene expression regulation [199] |
| XM_005106449.2*! | 0.89 | 1.87E-25 | 0.57 | 1.31E-07 | ZRANB3 | DNA annealing helicase and endonuclease ZRANB3 | Rewinds DNA and maintains genome stability, replication stress response [200,201] |
| XM_005106672.2! | 0.88 | 3.94E-25 | 0.44 | 1.18E-04 | JAK2 | Tyrosine-protein kinase JAK2 | JAK/STAT signaling, interferon gamma response [202] |
| XM_005106450.2 | 0.88 | 5.72E-25 | 0.46 | 3.81E-05 | BANF1 | Barrier-to-autointegration factor | Chromatin organization and gene expression [203], blocks viral DNA replication [204] |
| XM_013085923.1 | 0.87 | 7.99E-24 | 0.42 | 2.17E-04 | TREX2 | Three prime repair exonuclease 2 | DNA repair, mRNA export, transcription [205–207] |
| XM_013080704.1* | 0.87 | 8.51E-24 | 0.52 | 2.95E-06 | VRK1 | Serine/threonine-protein kinase VRK1 | Regulates BANF1 [208], activates ATF2 [209] |
| XM_005107122.2! | 0.87 | 4.34E-23 | 0.35 | 2.44E-03 | GLE1 | Nucleoporin GLE1 | Export of mRNA from nucleus [210] |
| XM_005110865.2 | 0.86 | 5.48E-22 | 0.41 | 2.70E-04 | DXO | Decapping and exoribonuclease protein | Pre-mRNA quality control [211] |
| XM_005113277.2! | 0.85 | 6.73E-22 | 0.28 | 1.77E-02 | NUP88 | Nuclear pore complex protein Nup88 | Nuclear pore formation [212] |
| XM_005099732.2 | 0.85 | 9.14E-22 | 0.35 | 2.59E-03 | MTPAP | Poly(A) RNA polymerase, mitochondrial | mtDNA stabilization [213,214], histone mRNA degradation [215] |
| XM_013087644.1 | 0.77 | 3.02E-15 | 0.39 | 7.51E-04 | RPUSD3 | Mitochondrial mRNA pseudouridine synthase RPUSD3 | mtRNA translation, mitochondrial ribosome biogenesis via pseudouridylation [216,217] |
| XM_005104572.2 | 0.74 | 1.10E-13 | 0.41 | 2.66E-04 | GIMAP1 | GTPase IMAP family member 1 | Immune cell development [218] |
| XM_005109614.2! | 0.73 | 1.84E-13 | 0.30 | 9.16E-03 | XIAP | E3 ubiquitin-protein ligase XIAP | E3 protein-ubiquitin ligase, apoptosis inhibitor [219], NFkB activation [220] |
| XM_005109011.2 | 0.72 | 5.24E-13 | 0.25 | 2.98E-02 | STRA6 | Receptor for retinol uptake STRA6 | Retinol importer [221] |
See Table 2 for description of organization. Common functions include nuclear pore formation, DNA damage repair, immune and inflammation signaling. The expression trend of this module increased linearly until age 10 months after which it stabilized, suggesting increasing activity of these in early age and stable, heightened activity in old age.