Table 2 Transcripts with annotated functions (GO terms) related to immune recognition, signaling and regulation that were differentially expressed during M. mercenaria focal response against QPX. Additional information on these transcripts is given in Additional file 2. “Inf” designates an infinite fold change calculated for focal response as the expression of that transcript in non-nodule tissue was equal to 0
From: Clam focal and systemic immune responses to QPX infection revealed by RNA-seq technology
Transcripts ID | Annotation | Regul-ation | Fold change | Function/GOs |
|---|---|---|---|---|
Pathogen recognition receptors (PRRS) | ||||
Scavenger receptors | ||||
comp186077_c0_seq3 | somatomedin-b and thrombospondin type-1 domain-containing (RPE spondin) | Up | 71.3 | F:scavenger receptor activity; P:immune response; F:polysaccharide binding |
comp179365_c0_seq8 | insulin-related peptide receptor | Up | 11.5 | F:scavenger receptor activity; P:transmembrane receptor protein tyrosine kinase signaling pathway |
comp169098_c0_seq1 | hemicentin-1 | Up | 10.6 | F:scavenger receptor activity; P:cell adhesion |
comp169486_c0_seq1 | lysyl oxidase-like protein 2 | Up | 22.5 | F:scavenger receptor activity; F:copper ion binding |
comp192413_c0_seq18 | mam domain-containing glycosylphosphatidylinositol anchor protein 1 | Up | Inf | F:polysaccharide binding; F:scavenger receptor activity; P:immune response |
C-type lectin (CTL) | ||||
comp176879_c0_seq8 | c-type mannose receptor 2 | Up | 15.8 | F:binding; F:carbohydrate binding |
comp190222_c0_seq3 | perlucin-like protein | Up | 49.1 | F:binding; F:carbohydrate binding; |
Toll-like receptors (TLRs) | ||||
comp189381_c0_seq1 | toll-like receptor 1 | Up | 16.5 | F:protein binding |
comp190056_c0_seq8 | toll-like receptor e precursor | Down | Inf | P:signal transduction; F:protein binding |
comp188195_c0_seq7 | toll-like receptor g precursor | Up | Inf | F:protein binding; P:signal transduction |
comp189381_c1_seq2 | cell surface receptor tollo (toll 8) | Up | 10.9 | P:signal transduction; F:protein binding |
Integrin | ||||
comp189082_c0_seq13 | integrin alpha 4 | Up | Inf | P:cell-cell adhesion; C:integrin complex |
comp189082_c0_seq24 | integrin alpha 4 | Up | 16.2 | P:cell-cell adhesion; C:integrin complex |
comp185789_c0_seq4 | integrin alpha-ps | Up | 13.7 | P:cell adhesion; C:integrin complex |
comp184975_c0_seq10 | integrin beta-1-like | Up | 12.4 | F:protein binding; F:receptor activity; |
Low-density lipoprotein (LDL) | ||||
comp181432_c3_seq2 | LDL receptor-related protein 12 | Up | 12.1 | - |
comp187193_c1_seq4 | LDL receptor-related protein 12 | Up | Inf | F:protein binding |
G-protein coupled receptor | ||||
comp177186_c1_seq2 | G-protein coupled receptor partial | Up | 13.0 | P:cell surface receptor signaling pathway; F:transmembrane signaling receptor activity |
comp191316_c2_seq1 | G-protein coupled receptor 64-like | Up | 28.1 | - |
comp177657_c2_seq5 | guanine nucleotide-binding protein subunit | Up | Inf | P:G-protein coupled receptor signaling pathway; F:signal transducer activity |
comp187628_c0_seq44 | substance-k (neurokinin) receptor | Up | 9.1 | P:G-protein coupled receptor signaling pathway; F:G-protein coupled receptor activity; |
comp192446_c0_seq4 | orexin receptor type 2 | Up | 12.4 | P:G-protein coupled receptor signaling pathway; |
Immune signaling and cell communication | ||||
Phosphatase and kinases | ||||
comp192546_c5_seq4 | immunoglobulin i-set domain protein | Up | 13.2 | F:protein serine/threonine kinase activity |
comp165267_c0_seq3 | von willebrand factor type egf and pentraxin domain-containing protein | Up | 11.0 | F:protein tyrosine kinase activity |
comp191437_c1_seq4 | focal adhesion kinase 1 | Up | 19.7 | F:signal transducer activity; |
comp188649_c0_seq3 | calcium calmodulin-dependent protein kinase | Up | 9.3 | F:calmodulin-dependent protein kinase activity |
comp190317_c0_seq7 | neuronal cell adhesion | Down | −13.3 | F:rhodopsin kinase activity |
Rho signaling | ||||
comp189234_c1_seq21 | rho gtpase-activating protein 15-like isoform x3 | Up | 18.1 | P:signal transduction |
comp185122_c1_seq7 | rho gtpase-activating protein 24 | Up | 27.1 | P:signal transduction |
comp187736_c1_seq25 | rho-related protein raca | Up | Inf | F:protein binding |
comp188711_c0_seq2 | rho-associated protein kinase 2 | Up | Inf | P:intracellular signal transduction |
Ubiquitin pathway | ||||
comp190451_c2_seq9 | e3 ubiquitin-protein ligase hectd1 | Up | 164.9 | F:ubiquitin-protein ligase activity; F:metal ion binding |
comp184512_c0_seq2 | e3 ubiquitin-protein ligase march6 | Up | 15.0 | F:zinc ion binding |
comp192081_c0_seq1 | e3 ubiquitin-protein ligase ubr3 | Up | 8.7 | - |
comp179031_c0_seq4 | cop9 signalosome complex subunit 5 | Up | Inf | F:protein binding |
comp179031_c0_seq2 | cop9 signalosome complex subunit 5 | Up | Inf | F:protein binding |
Wnt and Notch pathway | ||||
comp185090_c0_seq10 | tyrosine-protein kinase ryk | Up | 26.3 | P:Wnt receptor signaling pathway |
comp187449_c0_seq2 | fizzy-like protein | Up | 13.0 | F:protein binding |
comp175460_c0_seq1 | neurogenic locus notch | Up | 11.7 | P:Notch signaling pathway; |
comp182793_c0_seq5 | neurogenic locus notch protein | Up | 9.6 | P:G-protein coupled receptor signaling pathway |
comp192565_c0_seq10 | nicastrin-like protein | Up | 12.6 | P:protein processing |
Calcium mediated signal transduction | ||||
comp183265_c0_seq1 | calmodulin 3b (phosphorylase delta) | Down | −11.6 | F:calcium ion binding |
comp191993_c0_seq4 | EF-hand Ca-binding domain-containing protein 5 | Down | −10.9 | - |
comp191855_c0_seq2 | EF-hand Ca-binding domain-containing protein 6 | Down | −15.9 | - |
Complement pathway | ||||
comp165285_c0_seq7 | macrophage-expressed gene 1 | Up | 11.5 | - |
Signal transducer | ||||
comp182953_c0_seq4 | signal recognition particle receptor subunit alpha | Up | 13.8 | F:signal recognition particle binding |
comp182953_c0_seq5 | signal recognition particle receptor subunit alpha | Up | 73.0 | F:signal recognition particle binding |
comp171563_c0_seq4 | gtp-binding nuclear protein | Up | Inf | P:small GTPase mediated signal transduction |
comp188686_c0_seq19 | neuralized pats1 | Down | −758.9 | P:small GTPase mediated signal transduction |
comp189853_c0_seq1 | unc5c-like protein | Down | −12.5 | P:signal transduction |
Cell death regulation | ||||
Apoptosis process | ||||
comp175357_c1_seq16 | solute carrier family 25 member 38-like isoform 1 | Down | −25.0 | P:transmembrane transport |
comp191590_c0_seq3 | p53-induced protein with a death domain isoform | Down | −39.1 | F:protein binding; P:signal transduction |
comp191147_c0_seq62 | inhibitor of apoptosis | Up | 24.6 | - |
comp191147_c0_seq70 | inhibitor of apoptosis | Up | Inf | F:metal ion binding; F:zinc ion binding; |
comp191055_c2_seq4 | programmed cell death protein 10 | Up | 367.1 | - |
comp190690_c2_seq9 | cell death abnormality protein 1-like | Up | Inf | F:binding; F:zinc ion binding |
comp186101_c3_seq4 | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | Down | −10.8 | P:positive regulation of apoptotic process; P:negative regulation of wound healing; P:oxidation-reduction process; |
Tumor necrosis factor (TNF) | ||||
comp182922_c0_seq5 | TNF ligand superfamily member 10-like | Up | 8.5 | - |
comp176786_c2_seq3 | TNF-like protein | Down | −26.3 | F:tumor necrosis factor receptor binding; P:immune response |
TNF ligand superfamily member 10-like | Up | 8.5 | - | |