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

Liu, Fang-Yu; Hsu, Te-Cheng; Choong, Patrick; Lin, Min-Hsuan; Chuang, Yung-Jen; Chen, Bor-Sen; Lin, Che

doi:10.1186/s12918-018-0544-3

Table 1 The top 10 hub proteins ranked by number of PPIs (edges) and corresponding GO biological process in the regenerative PPI networks for 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

Heart			Cerebellum			Fin			Retina
Symbol	PPIs	Biological process	Symbol	PPIs	Biological process	Symbol	PPIs	Biological process	Symbol	PPIs	Biological process
Ubc	458		Ubc	346		Tp53	56	Apoptosis	Mycb	58	Sequence-specific DNA-binding transcription factor activity
Sumo2	105	Embryo development	Ywhaqb	70	Oxidoreductase activity	Tat	44	Cellular amino acid metabolism	EUr1	35	DNA-templated regulation of transcription
Mycb	90	Sequence-specific DNA binding Transcription factor activity	Tat	59	Cellular amino acid metabolism	Hdac1	40	Inhibition of cell proliferation	Tat	33	Cellular amino acid metabolism
Tp53	68	Apoptosis	Hdac1	55	Inhibition of cell proliferation	Sp1	39	Regulation of transcription from the RNA polymerase II promoter	Hdac1	33	Inhibition of cell proliferation
Ywhaqb	60	Oxidoreductase activity	Tk1	53	DNA biosynthesis	Esr1	35	DNA-templated regulation of Transcription	Src	30	Cell cycle
Hdac1	52	Inhibition of cell proliferation	Ar	48	DNA-templated regulation of transcription	Rb1	31	Regulation of cell cycle	Pou5f1	29	Embryonic pattern specification
Sp1	52	Regulation of transcription from the RNA polymerase II promoter	Smn1	47	Peripheral nervous system neuron Axonogenesis	H2afx	31	Cell cycle	H2afx	25	Cell cycle
Tgfbr1a	49	Protein phosphorylation	Mepce	47		Ywhag1	31	Cerebellum development	Sp1	24	Regulation of transcription from the RNA polymerase II promoter
Tat	49	Cellular amino acid metabolism	Ywhae1	46	Oxidoreductase activity	Smarca4	30	Cardiac muscle cell proliferation	Mdm2	23	Inhibition of apoptosis process
Yhl	49	Regulation of angiogenesis	H2afx	46	Cell cycle	Ncor1	29	Anterior/posterior pattern specification	Ncor1	23	DNA-templated regulation of transcription

The zebrafish regenerative PPI networks for heart, cerebellum, fin, and retina capture the differentially expressed proteins and their corresponding PPIs. Hub proteins have numerous PPIs and act as the bridges of the network. Therefore, the functions of these hub proteins may represent the primary characteristics of the PPI network. The GO biological processes of the hub proteins for the four regenerative networks include metabolism, regulation of the cell cycle, cell proliferation, pattern specification, apoptosis, and transcription. Grey shading represents the gene ontology of proteins related to proliferation and cell cycle, including Hadac1, H2afx, and Rb1 for cell cycle regulation and Smarca4 for cardiac muscle cell proliferation. It was observed that the regenerative PPI networks are closely related to cell cycle in the regeneration of all four organs

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ISSN: 1752-0509

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