Bioinformatics analysis of metastasis-related proteins in hepatocellular carcinoma

Table 1 Metastasis-related proteins in HCC

Protein name	IPI number	Ratio1	NO2	Coverage (%)3	Category
Filamin C	IPI00178352	2.49 ± 0.15	2	1.28	Cytoskeleton
Obscurin	IPI00549822	2.91 ± 0.18	2	1.16	Cytoskeleton
Keratin 8	IPI00554648	0.56 ± 0.15	4	25.1	Cytoskeleton
Titin	IPI00179357	1.73 ± 0.12	5	1.11	Cytoskeleton
Plectin 7	IPI00398776	2.49 ± 0.13	2	1.19	Cytoskeleton
MTA2	IPI00171798	0.24 ± 0.11	2	2.69	p53 regulation
Low density lipoprotein receptor-related protein 1 (LRP1)	IPI00020557	0.58 ± 0.15	2	2.27	Cell migration, proliferation, angiogenesis
Mos	IPI00018290	2.86 ± 0.2	2	6.36	Mitoses

¹Ratio calculated as MHCC97H/MHCC97L,

²number of quantified peptides,

³protein coverage calculated as the number of amino acid residues for protein identification divided by the total number of amino acid residues of the protein.

Table 2 KEGG pathway analysis of metastasis-related proteins

KEGG pathway	IPI accession	Protein description
Antigen processing and presentation	IPI00020984	Calnexin precusor
	IPI00025252	Protein disulfide-isomerase A3 precusor
	IPI00037070	Splice isoform 2 of heat shock cognate 71 kDa protein
	IPI00144014	MHC Cass I antigen
	IPI00514377	Heat shock 70 kDa protein
Regulation of actin cytoskeleton	IPI00001814	Serine/threonine- protein kinase PAK 7
	IPI00018290	Mos
	IPI00216691	Profiline-1
	IPI00384231	PAK4 protein
Renal cell carcinoma	IPI00001814	PAK 7
	IPI00384231	PAK4 protein
Thyroid cancer	IPI00022970	Translocated promoter region
Small cell lung cancer	IPI00217461	Splice isoform 3 of apoptotic protease activating factor 1
	IPI00377045	Laminin alpha 3 splice variant B1
Prostate cancer	IPI00219757	Glutahione S-transferase protein
p53 pathway	IPI00006160	Splice isoform alpha of tumor protein P73
	IPI00217461	Splice isoform 3 of apoptotic protease activating factor 1
MAPK pathway	IPI00018290	Mos
	IPI00037070	Splice isoform 2 of heat shock cognate 71 kDa protein (HSP70)
	IPI00155892	Voltage-dependent calcium channel gamma-5 subunit isoform B
	IPI00178352	Splice isoform 1 of filamin C
	IPI00382696	Splice isoform 1 of filamin B
	IPI00514377	Heat shock 70 kDa protein 1A
ErbB pathway	IPI00001814	PAK 7
	IPI00384231	PAK4

Table 3 Function classification of protein-protein interaction network

Cell function	Interactors	Percent (%)
Cell cycle	6	0.69
DNA repair	57	6.54
Stress response	14	1.61
Protein biosynthesis	9	1.03
Carbohydrate metabolism	26	2.99
DNA replication	3	0.34
Transcription	39	4.48
RNA processing	14	1.61
RNA localization	1	0.11
Signal transduction	120	13.78
Transport	41	4.71
Protein dephosphorylation	9	1.03
Cell organization and biogenesis	124	14.24
Metabolism	70	8.04
DNA damage response	3	0.34
Protein transport	59	6.77
Protein phosphorylation	60	6.89
Protein degradation	37	4.25
DNA repair	13	1.49
Unknown	166	19.06