KEGG   PATHWAY: oml04148
Entry
oml04148                    Pathway                                
Name
Efferocytosis - Oryzias melastigma (Indian medaka)
Class
Cellular Processes; Transport and catabolism
Pathway map
oml04148  Efferocytosis
oml04148

Organism
Oryzias melastigma (Indian medaka) [GN:oml]
Gene
112137236  casp3a; caspase-3a [KO:K02187] [EC:3.4.22.56]
112153020  caspase-3 [KO:K02187] [EC:3.4.22.56]
112154505  casp7; caspase-7 [KO:K04397] [EC:3.4.22.60]
112162928  casp17; caspase-3 [KO:K04397] [EC:3.4.22.60]
112140709  caspase-1 [KO:K01370] [EC:3.4.22.36]
112149501  caspase-1 [KO:K01370] [EC:3.4.22.36]
112149949  pannexin-1 [KO:K03443]
112137629  panx1b; pannexin-1b [KO:K03443]
112149233  p2ry2.1; P2Y purinoceptor 2 [KO:K04269]
112149249  P2Y purinoceptor 3 [KO:K04272]
112149240  p2ry12; P2Y purinoceptor 12 [KO:K04298]
112143277  sphk2; sphingosine kinase 2 [KO:K04718] [EC:2.7.1.91]
112157543  sphingosine kinase 1 [KO:K04718] [EC:2.7.1.91]
112146599  sphingosine kinase 1 [KO:K04718] [EC:2.7.1.91]
112136743  s1pr1; sphingosine 1-phosphate receptor 1 [KO:K04288]
112137092  pla2g6; 85/88 kDa calcium-independent phospholipase A2 isoform X1 [KO:K16343] [EC:3.1.1.4]
112140337  phospholipid-transporting ATPase ABCA1 isoform X1 [KO:K05641]
112156111  phospholipid-transporting ATPase ABCA1 [KO:K05641]
112150479  zgc:172302; phospholipid-transporting ATPase ABCA1 isoform X1 [KO:K05641]
112153262  abca1b; phospholipid-transporting ATPase ABCA1 isoform X1 [KO:K05641]
112155663  si:dkey-165a24.9; G-protein coupled receptor 4 [KO:K08426]
112158082  probable G-protein coupled receptor 132 [KO:K08426]
112149788  adam17a; disintegrin and metalloproteinase domain-containing protein 17a isoform X1 [KO:K06059] [EC:3.4.24.86]
112157702  adam17b; disintegrin and metalloproteinase domain-containing protein 17 isoform X1 [KO:K06059] [EC:3.4.24.86]
112160714  adam10a; disintegrin and metalloproteinase domain-containing protein 10 [KO:K06704] [EC:3.4.24.81]
112150653  si:ch1073-396h14.1; disintegrin and metalloproteinase domain-containing protein 10 [KO:K06704] [EC:3.4.24.81]
112152362  disintegrin and metalloproteinase domain-containing protein 10 [KO:K06704] [EC:3.4.24.81]
112144596  nuclear factor of activated T-cells, cytoplasmic 2 [KO:K17332]
112158691  nfatc2a; nuclear factor of activated T-cells, cytoplasmic 2 isoform X1 [KO:K17332]
112140481  nuclear factor of activated T-cells, cytoplasmic 1 [KO:K04446]
112138397  nuclear factor of activated T-cells, cytoplasmic 1 [KO:K04446]
112160932  nfatc3a; nuclear factor of activated T-cells, cytoplasmic 3 [KO:K17333]
112152364  nuclear factor of activated T-cells, cytoplasmic 3 [KO:K17333]
112152110  nfatc4; nuclear factor of activated T-cells, cytoplasmic 4 [KO:K17334]
112149211  hif1al; hypoxia inducible factor 1 subunit alpha, like isoform X1 [KO:K08268]
112157754  hif1aa; hypoxia inducible factor 1 subunit alpha a [KO:K08268]
112154224  epas1a; endothelial PAS domain-containing protein 1 isoform X2 [KO:K08268]
112143497  arnt; aryl hydrocarbon receptor nuclear translocator isoform X1 [KO:K09097]
112146323  epor; erythropoietin receptor isoform X1 [KO:K05079]
112148412  jak2b; tyrosine-protein kinase JAK2 [KO:K04447] [EC:2.7.10.2]
112163270  jak2a; tyrosine-protein kinase JAK2a [KO:K04447] [EC:2.7.10.2]
112136385  mapk1; mitogen-activated protein kinase 1 [KO:K04371] [EC:2.7.11.24]
112146278  mapk3; mitogen-activated protein kinase 3 [KO:K04371] [EC:2.7.11.24]
112158998  cebpb; CCAAT/enhancer-binding protein beta [KO:K10048]
112144662  pparg; peroxisome proliferator-activated receptor gamma [KO:K08530]
112162883  rxraa; retinoic acid receptor RXR-alpha-A isoform X2 [KO:K08524]
112143244  rxrbb; retinoic acid receptor RXR-beta-A isoform X1 [KO:K08524]
112160535  EGF-like repeat and discoidin I-like domain-containing protein 3 isoform X1 [KO:K17253]
112151945  mfge8b; milk fat globule EGF and factor V/VIII domain containing b isoform X1 [KO:K17253]
112160334  gas6; growth arrest-specific protein 6 [KO:K05464]
112161684  mertka; tyrosine-protein kinase Mer isoform X1 [KO:K05117] [EC:2.7.10.1]
112156612  cd36; platelet glycoprotein 4 [KO:K06259]
112147575  thrombospondin-1 [KO:K16857]
112158403  thrombospondin-1 [KO:K16857]
112152131  map2k1; dual specificity mitogen-activated protein kinase kinase 1 [KO:K04368] [EC:2.7.12.2]
112136869  map2k2a; dual specificity mitogen-activated protein kinase kinase 2a [KO:K04369] [EC:2.7.12.2]
112150839  ptgs2b; prostaglandin G/H synthase 2 [KO:K11987] [EC:1.14.99.1]
112160198  ptger2a; prostaglandin E receptor 2a (subtype EP2) [KO:K04259]
112147508  ptger4c; prostaglandin E receptor 4 (subtype EP4) c [KO:K04261]
112147980  ptger4a; prostaglandin E receptor 4 (subtype EP4) a [KO:K04261]
112163274  ptger4b; prostaglandin E receptor 4 (subtype EP4) b [KO:K04261]
112150516  prostaglandin E2 receptor EP4 subtype [KO:K04261]
112158493  dnmt3ab; DNA (cytosine-5)-methyltransferase 3A isoform X1 [KO:K17398] [EC:2.1.1.37]
112154837  cyclic AMP-responsive element-binding protein 1 [KO:K05870]
112155243  creb1b; cyclic AMP-responsive element-binding protein 1b [KO:K05870]
112156702  cyclic AMP-responsive element-binding protein 1 isoform X1 [KO:K05870]
112149754  tgfb1a; transforming growth factor, beta 1a [KO:K13375]
112154153  atp2a1l; ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1, like isoform X1 [KO:K05853] [EC:7.2.2.10]
112142370  atp2a3; sarcoplasmic/endoplasmic reticulum calcium ATPase 1 [KO:K05853] [EC:7.2.2.10]
112148869  atp2a2a; sarcoplasmic/endoplasmic reticulum calcium ATPase 2 [KO:K05853] [EC:7.2.2.10]
112163069  atp2a2b; sarcoplasmic/endoplasmic reticulum calcium ATPase 2b [KO:K05853] [EC:7.2.2.10]
112157083  si:dkey-28b4.8; sarcoplasmic/endoplasmic reticulum calcium ATPase 2 [KO:K05853] [EC:7.2.2.10]
112146608  atp2a1; sarcoplasmic/endoplasmic reticulum calcium ATPase 1 isoform X1 [KO:K05853] [EC:7.2.2.10]
112154180  calcium/calmodulin-dependent protein kinase type II subunit gamma isoform X1 [KO:K04515] [EC:2.7.11.17]
112156501  camk2d1; calcium/calmodulin-dependent protein kinase type II delta 1 chain isoform X1 [KO:K04515] [EC:2.7.11.17]
112156983  camk2d2; calcium/calmodulin-dependent protein kinase type II delta 2 chain isoform X1 [KO:K04515] [EC:2.7.11.17]
112163512  calcium/calmodulin-dependent protein kinase type II subunit beta isoform X1 [KO:K04515] [EC:2.7.11.17]
112136361  camk2b1; calcium/calmodulin-dependent protein kinase type II subunit beta [KO:K04515] [EC:2.7.11.17]
112136908  camk2a; calcium/calmodulin-dependent protein kinase type II subunit alpha isoform X2 [KO:K04515] [EC:2.7.11.17]
118599716  camk2g2; calcium/calmodulin-dependent protein kinase type II subunit gamma isoform X1 [KO:K04515] [EC:2.7.11.17]
112138354  calcium/calmodulin-dependent protein kinase type II subunit gamma [KO:K04515] [EC:2.7.11.17]
112158679  zgc:171775; STKc_p38 domain-containing protein [KO:K04441] [EC:2.7.11.24]
112152089  mapk12a; mitogen-activated protein kinase 12 isoform X1 [KO:K04441] [EC:2.7.11.24]
112158855  mapk14a; mitogen-activated protein kinase 14A isoform X2 [KO:K04441] [EC:2.7.11.24]
112159424  mapk13; mitogen-activated protein kinase 13 [KO:K04441] [EC:2.7.11.24]
112139315  mapk14b; mitogen-activated protein kinase 14B isoform X1 [KO:K04441] [EC:2.7.11.24]
112160268  mapk12b; mitogen-activated protein kinase 12b isoform X2 [KO:K04441] [EC:2.7.11.24]
112160269  mapk11; mitogen-activated protein kinase 11 isoform X1 [KO:K04441] [EC:2.7.11.24]
112145422  mapkapk2a; MAP kinase-activated protein kinase 2 isoform X1 [KO:K04443] [EC:2.7.11.1]
112162158  alox5a; polyunsaturated fatty acid 5-lipoxygenase [KO:K00461] [EC:1.13.11.34]
112147953  dusp2; dual specificity protein phosphatase 2 [KO:K04459] [EC:3.1.3.16 3.1.3.48]
112163157  dusp4; dual specificity protein phosphatase 4 [KO:K04459] [EC:3.1.3.16 3.1.3.48]
112157532  dusp16; dual specificity protein phosphatase 16 [KO:K04459] [EC:3.1.3.16 3.1.3.48]
112144717  dusp7; dual specificity protein phosphatase 7 [KO:K04459] [EC:3.1.3.16 3.1.3.48]
112137636  dusp5; dual specificity protein phosphatase 5 [KO:K04459] [EC:3.1.3.16 3.1.3.48]
112145839  si:ch211-195b15.8; dual specificity protein phosphatase 8 [KO:K04459] [EC:3.1.3.16 3.1.3.48]
112152072  dusp8a; dual specificity protein phosphatase 8a isoform X1 [KO:K04459] [EC:3.1.3.16 3.1.3.48]
112159710  dual specificity protein phosphatase 7 [KO:K04459] [EC:3.1.3.16 3.1.3.48]
112157999  ano6; anoctamin-6 [KO:K19500]
112152278  ano3; anoctamin-3 isoform X3 [KO:K19498]
112154274  anoctamin-4 isoform X1 [KO:K19499]
112161291  ano5b; anoctamin-5b isoform X1 [KO:K19480]
112152279  ano5a; anoctamin-5 isoform X1 [KO:K19480]
112149269  ano7; anoctamin-7 [KO:K19501]
112151781  ano11; anoctamin-7 isoform X1 [KO:K19501]
112160560  anoctamin-9 [KO:K19503]
112160557  anoctamin-9 [KO:K19503]
112152283  anoctamin-9 isoform X1 [KO:K19503]
112142128  bsg; basigin isoform X1 [KO:K06535]
112161616  XK-related protein 8 [KO:K26813]
112161607  xkr8.3; XK-related protein 8.3 isoform X1 [KO:K26813]
112151475  xkr9; XK-related protein 9 [KO:K26814]
112159450  xkr7; XK-related protein 7 [KO:K26811]
112159851  zgc:198371; XK-related protein 7 [KO:K26811]
112150681  xkr4; XK-related protein 4 [KO:K26811]
112157913  xkr6b; XK-related protein 6b [KO:K26811]
112159967  XK-related protein 6 isoform X1 [KO:K26811]
112151177  atp8a2; phospholipid-transporting ATPase IB isoform X1 [KO:K14802] [EC:7.6.2.1]
112153141  atp8a1; phospholipid-transporting ATPase IA isoform X1 [KO:K14802] [EC:7.6.2.1]
112155581  probable phospholipid-transporting ATPase IH isoform X1 [KO:K26934] [EC:7.6.2.1]
112153570  atp11c; phospholipid-transporting ATPase IG isoform X6 [KO:K26934] [EC:7.6.2.1]
112160076  atp11a; probable phospholipid-transporting ATPase IH isoform X1 [KO:K26934] [EC:7.6.2.1]
112150455  atp11b; probable phospholipid-transporting ATPase IF isoform X1 [KO:K26934] [EC:7.6.2.1]
112144866  tmem30aa; transmembrane protein 30Aa [KO:K26935]
112160333  pros1; vitamin K-dependent protein S isoform X2 [KO:K03908]
112154815  itgav; integrin alpha-V [KO:K06487]
112154448  integrin beta-3 [KO:K06493]
112146702  integrin beta-3 [KO:K06493]
112140932  itgb5; integrin beta-5 [KO:K06588]
112149720  tyrosine-protein kinase receptor UFO [KO:K05115] [EC:2.7.10.1]
112147371  tyro3; tyrosine-protein kinase receptor TYRO3 [KO:K05116] [EC:2.7.10.1]
112162522  adhesion G protein-coupled receptor B1 [KO:K04596]
112143830  adgrb1a; adhesion G protein-coupled receptor B1 [KO:K04596]
112144962  stab1; stabilin-1 isoform X1 [KO:K19020]
112154100  stab2; stabilin-2 [KO:K19013]
112138958  ptk2aa; protein tyrosine kinase 2aa isoform X1 [KO:K05725] [EC:2.7.10.2]
112143206  focal adhesion kinase 1 isoform X9 [KO:K05725] [EC:2.7.10.2]
112151935  bcar1; breast cancer anti-estrogen resistance protein 1 [KO:K05726]
112143053  adapter molecule crk [KO:K04438]
112149634  crk; adapter molecule crk [KO:K04438]
112163343  crkl; crk-like protein [KO:K04438]
112162771  elmo1; engulfment and cell motility protein 1 [KO:K12366]
112154096  dock1; dedicator of cytokinesis protein 1 [KO:K13708]
112154486  ras-related C3 botulinum toxin substrate 1 [KO:K04392]
112146454  ras-related C3 botulinum toxin substrate 1 [KO:K04392]
112146455  ras-related C3 botulinum toxin substrate 1 [KO:K04392]
112154110  zgc:174164; disintegrin and metalloproteinase domain-containing protein 9 [KO:K06834] [EC:3.4.24.-]
112138446  disintegrin and metalloproteinase domain-containing protein 9 [KO:K06834] [EC:3.4.24.-]
112147713  calr3b; calreticulin 3b [KO:K08057]
112150092  calr; calreticulin [KO:K08057]
112136810  calreticulin [KO:K08057]
112145095  complement C1q subcomponent subunit A isoform X1 [KO:K03986]
112144483  complement C1q subcomponent subunit B [KO:K03987]
112145159  complement C1q subcomponent subunit C [KO:K03988]
112145296  low-density lipoprotein receptor-related protein 1 isoform X1 [KO:K04550]
112159445  low-density lipoprotein receptor-related protein 1 [KO:K04550]
112152596  megf11; multiple epidermal growth factor-like domains protein 11 isoform X1 [KO:K24068]
112139232  megf10; multiple epidermal growth factor-like domains protein 10 isoform X1 [KO:K24068]
112140290  multiple epidermal growth factor-like domains protein 11 isoform X1 [KO:K24068]
112149532  scarf1; scavenger receptor class F member 1 [KO:K24318]
112155402  gulp1a; PTB domain-containing engulfment adapter protein 1 isoform X1 [KO:K23285]
112159579  PTB domain-containing engulfment adapter protein 1 [KO:K23285]
112162956  rab5aa; RAB5A, member RAS oncogene family, a [KO:K07887]
112136549  rab5ab; RAB5A, member RAS oncogene family, b [KO:K07887]
112137972  rab5b; ras-related protein Rab-5B isoform X1 [KO:K07888]
112146764  rab5c; ras-related protein Rab-5C [KO:K07889]
112160312  tgfbrap1; transforming growth factor-beta receptor-associated protein 1 homolog [KO:K20177]
112154339  vps8; vacuolar protein sorting-associated protein 8 homolog [KO:K20178]
112138996  vps11; vacuolar protein sorting-associated protein 11 homolog isoform X1 [KO:K20179]
112142209  vps16; vacuolar protein sorting-associated protein 16 homolog isoform X1 [KO:K20180]
112158425  vps18; vacuolar protein sorting-associated protein 18 homolog [KO:K20181]
112148820  vps33a; vacuolar protein sorting-associated protein 33A [KO:K20182]
112142073  ras-related protein Rab-14 [KO:K07881]
112162990  rab14l; RAB14, member RAS oncogene family, like [KO:K07881]
112144221  vps39; vam6/Vps39-like protein isoform X1 [KO:K20183]
112151299  vps41; vacuolar protein sorting-associated protein 41 homolog isoform X1 [KO:K20184]
112140944  ras-related protein Rab-7a-like [KO:K07897]
118598730  si:dkey-13a21.4; ras-related protein rab7 [KO:K07897]
112144682  ras-related protein Rab-7a [KO:K07897]
112158866  rab7a; ras-related protein Rab-7a [KO:K07897]
112159581  slc66a1; lysosomal amino acid transporter 1 homolog isoform X2 [KO:K23678]
112143364  arg2; arginase-2, mitochondrial [KO:K01476] [EC:3.5.3.1]
112138872  arg1; arginase-1 [KO:K01476] [EC:3.5.3.1]
112141431  odc1; ornithine decarboxylase [KO:K01581] [EC:4.1.1.17]
112147991  ch25hl3; cholesterol 25-hydroxylase-like protein [KO:K10223] [EC:1.14.99.38]
112141841  ch25h; cholesterol 25-hydroxylase-like protein [KO:K10223] [EC:1.14.99.38]
112162812  ch25hl2; cholesterol 25-hydroxylase-like protein 2 [KO:K10223] [EC:1.14.99.38]
112151827  ch25hl1.2; cholesterol 25-hydroxylase-like protein 1, member 2 [KO:K10223] [EC:1.14.99.38]
112152648  ch25hl1.1; cholesterol 25-hydroxylase-like protein 1, member 1 [KO:K10223] [EC:1.14.99.38]
112160647  nr1h3; oxysterols receptor LXR-alpha [KO:K08536]
112154614  carnitine O-palmitoyltransferase 1, liver isoform isoform X1 [KO:K08765] [EC:2.3.1.21]
112152272  cpt1ab; carnitine O-palmitoyltransferase 1, liver isoform isoform X1 [KO:K08765] [EC:2.3.1.21]
112152828  cpt1b; carnitine O-palmitoyltransferase 1, muscle isoform [KO:K08765] [EC:2.3.1.21]
112146686  cpt1cb; carnitine O-palmitoyltransferase 1, liver isoform [KO:K08765] [EC:2.3.1.21]
112141911  cytochrome b-c1 complex subunit Rieske, mitochondrial [KO:K00411] [EC:7.1.1.8]
112152356  cytochrome b-c1 complex subunit Rieske, mitochondrial [KO:K00411] [EC:7.1.1.8]
112161794  sirt1; NAD-dependent protein deacetylase sirtuin-1 [KO:K11411] [EC:2.3.1.286]
112147407  pbx1a; pre-B-cell leukemia homeobox 1a isoform X1 [KO:K09355]
112150672  pre-B-cell leukemia transcription factor 1 isoform X1 [KO:K09355]
112145307  il10; interleukin-10 [KO:K05443]
112141059  lysosomal acid lipase/cholesteryl ester hydrolase-like [KO:K01052] [EC:3.1.1.13]
112141836  lipf; gastric triacylglycerol lipase [KO:K01052] [EC:3.1.1.13]
112140631  phospholipase A2 group XV [KO:K06129] [EC:3.1.1.5]
112152629  pla2g15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
112159470  ppardb; peroxisome proliferator-activated receptor delta b [KO:K04504]
112140833  solute carrier family 2, facilitated glucose transporter member 1 [KO:K07299]
112150476  solute carrier family 2, facilitated glucose transporter member 1 isoform X2 [KO:K07299]
112145294  slc2a1b; solute carrier family 2, facilitated glucose transporter member 1 [KO:K07299]
112145805  slc16a1a; monocarboxylate transporter 1a [KO:K08179]
112159332  monocarboxylate transporter 1 [KO:K08179]
112161612  si:ch211-195b13.1; STKc_SGK domain-containing protein [KO:K13302] [EC:2.7.11.1]
112143993  sgk2b; serine/threonine-protein kinase Sgk2b [KO:K13302] [EC:2.7.11.1]
112157984  sgk1; serine/threonine-protein kinase Sgk1 isoform X1 [KO:K13302] [EC:2.7.11.1]
112157454  si:dkey-237i9.8; platelet endothelial cell adhesion molecule isoform X2 [KO:K06471]
112146635  pecam1; platelet endothelial cell adhesion molecule isoform X1 [KO:K06471]
112140556  sialic acid-binding Ig-like lectin 14 [KO:K06749]
112140561  hemicentin-1 [KO:K06749]
112144114  sialic acid-binding Ig-like lectin 11 [KO:K06749]
112143660  ptpn6; tyrosine-protein phosphatase non-receptor type 6 [KO:K05697] [EC:3.1.3.48]
112162955  ptpn11a; tyrosine-protein phosphatase non-receptor type 11 [KO:K07293] [EC:3.1.3.48]
112159720  ptpn11b; tyrosine-protein phosphatase non-receptor type 11b isoform X1 [KO:K07293] [EC:3.1.3.48]
Compound
C00002  ATP
C00003  NAD+
C00019  S-Adenosyl-L-methionine
C00031  D-Glucose
C00062  L-Arginine
C00073  L-Methionine
C00075  UTP
C00077  L-Ornithine
C00134  Putrescine
C00162  Fatty acid
C00186  (S)-Lactate
C00187  Cholesterol
C00584  Prostaglandin E2
C02530  Cholesterol ester
C02737  Phosphatidylserine
C04230  1-Acyl-sn-glycero-3-phosphocholine
C06124  Sphingosine 1-phosphate
C06314  Lipoxin A4
C15519  25-Hydroxycholesterol
C15610  Cholest-5-ene-3beta,26-diol
C18178  Resolvin D1
Reference
PMID:31822793
  Authors
Doran AC, Yurdagul A Jr, Tabas I
  Title
Efferocytosis in health and disease.
  Journal
Nat Rev Immunol 20:254-267 (2020)
DOI:10.1038/s41577-019-0240-6
Reference
PMID:36028471
  Authors
Zhang J, Ding W, Zhao M, Liu J, Xu Y, Wan J, Wang M
  Title
Mechanisms of efferocytosis in determining inflammation resolution: Therapeutic potential and the association with cardiovascular disease.
  Journal
Br J Pharmacol 179:5151-5171 (2022)
DOI:10.1111/bph.15939
Reference
PMID:30165442
  Authors
Kawano M, Nagata S
  Title
Efferocytosis and autoimmune disease.
  Journal
Int Immunol 30:551-558 (2018)
DOI:10.1093/intimm/dxy055
Reference
PMID:35650427
  Authors
Mehrotra P, Ravichandran KS
  Title
Drugging the efferocytosis process: concepts and opportunities.
  Journal
Nat Rev Drug Discov 21:601-620 (2022)
DOI:10.1038/s41573-022-00470-y
Reference
PMID:28496201
  Authors
Park SY, Kim IS
  Title
Engulfment signals and the phagocytic machinery for apoptotic cell clearance.
  Journal
Exp Mol Med 49:e331 (2017)
DOI:10.1038/emm.2017.52
Reference
PMID:28137963
  Authors
Kojima Y, Weissman IL, Leeper NJ
  Title
The Role of Efferocytosis in Atherosclerosis.
  Journal
Circulation 135:476-489 (2017)
DOI:10.1161/CIRCULATIONAHA.116.025684
Related
pathway
oml00010  Glycolysis / Gluconeogenesis
oml04140  Autophagy - animal
oml04145  Phagosome
KO pathway
ko04148   
LinkDB

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