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Table 2 Pathway distribution for core proteins and organ-specific proteins in the regeneration networks of the heart, cerebellum, fin, and retina

From: Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration

 

Pathway

Proteins

Core proteins

TGF-β signaling pathway

Smad7, Jun, Mapk1, Mapk3, Map3k7, Smurf2, Smad3a, Skib, Smad2,Spaw

Gonadotropin releasing hormone receptor pathway

Jun, Mapk1, Napk3, Cdc42, Map3k7, Pou2f1b, Smad3a, Map2k1,Smad2

Angiogenesis

Crk, Jun, Mapk1, Mapk3, Pak2a, Pak1, Tcf7l2, Map2k1

Heart specific proteins

Gonadotropin releasing hormone receptor pathway

Fstb, Srf, Gata2b, Map2k2a, Pparaa, Prkcz, Bmpr2a, Slc2a1a, Fosb, 1hx2b, Pparg, Sos1, Tcf7, Sdf4

Integrin signaling pathway

Parvaa, Rras, Map2k2a, Kras, Lamb1a, Rac3a, Tln1, Arl1, Mapk10, Vasp, Lama5, Sos1, Bcar1

FGF signaling pathway

Ptpn11a, Map2k2a, Akt3a, Kras, Ppp2r2bb, Prkcz, Rac3a, Mapk10, Sos1, Fgf13b, Fgfr1b

PDGF signaling pathway

Ehf, Mor, Arhgap1, Kras, Map2k2a, Shc2, Sos1, Rps6ka3b, Elf2b

Cerebellum specific proteins

Wnt signaling pathway

Csnk1g1, Ntla, Gnb3b, Ppardb, Sagb, Siah1, Wnt16, Wnt3, Wnt11, Ppp2ca, Prkchb, Wnt3a, Aes, Gng12a, Ppp2r5eb, Ppp3r1b, Prkcbb, Fzd6

Gonadotropin releasing hormone receptor pathway

Nab1a, Gnb3b, Vcl, Cga, Jund, Bmpr1aa, Gnao1b, Gnb5b, Per1a, Prkcbb, Rela

Inflammation mediated by chemokine and cytokine signaling pathways

Gnb3b, Jund, Arpc4, Arpc2, Gnao1b, Myh9a, Gng12a, Pdpk1b, Prkcbb, Rela, Arpc5la

Fin specific proteins

Angiogenesis

Mapk14a, Axin2, Pdgfaa, Hspb1

Wnt signaling pathway

Mycl1b, Axin2, Wnt11r, Fzd10

TGF-β signaling pathway

Mapk14a, Ndr1, Acvrl1

Retina specific proteins

Huntington disease pathway

Dync1li2, Dync1li1, Rhoq, Bdnf

Alzheimer disease-presenilin pathway

Aph1b, Wnt4b, Furina

Cytoskeletal regulation by Rho GTPase

Cfl1, Rock2a, Myo3a

  1. The primary pathways for core proteins and organ-specific proteins were analyzed using PANTHER, whereby core proteins were identified by taking the intersection sets between each regenerative PPI network, while organ-specific proteins were identified through taking the relative complement set of each regenerative PPI network with respect to the other three PPI networks. The primary pathways for core proteins and organ-specific proteins were different from each other. The primary pathway for core proteins was TGF-β signaling pathway while the primary pathway was different for each organ; consisting of integrin signaling for the heart, Wnt signaling for the cerebellum, angiogenesis for the fin, and the Huntington disease pathway for the retina