Protein interaction network related to Helicobacter pylori infection response

Table 1 List of proteins extracted from the literary database showing significant change after H pylori infection

Protein/gene name	Uniprot ID	HPRD reference
ITGB2	P05107
LY96	Q9Y6Y9	X
TLR10	Q9BXR5
TLR2	O60903
TLR3	O15455	X
VCAM1	P19320
HCK	P08631
MAPK8	P45983
RAC2	P15153
SOCS2	O14508	X
STAT6	P42226
C2	P06681	X
C3	P01024
C4A	P0C0L4	X
CCL18	P55774	X
CCL19	Q99731	X
CCL3	P10147	X
CCL4	P13236	X
CRP	P02741
CXCL13	O43927
CXCL2	P19875	X
CXCL9	Q07325	X
HLA-DMA	P28067	X
HLA-DPB1	Q30154	X
HLA-DQB1	P03992	X
HLA-DRB5	Q30154	X
HSPH1	Q92598
C11TA	P33076
PLAT	P00750
IFITM1	P13164	X
IRF4	Q15306
MADCAM1	Q13477
ALOX5	P09917	X
TLR5	O60602	X
CD53	P19397	X
TLR6	Q9Y2C9	X
SLAMF1	Q13291
PTPRC	P08575
FAIM3	O60667	X
CD180	Q99467
TLR4	O00206
TLR1	Q15399
CXCL3	P19876	X
CD47	Q08722
IFNGR1	P15260
IL10RA	Q13651	X
IL18RAP	O95256	X
ITGAX	P20702	X
IL8	P10145

Nodes with no HPRD reference were marked with x. HPRD: Human protein reference database.

Table 2 List of proteins with a large degree value and their CC values

Protein	Degree	CC value
RELA/NF-κB3	105	0.047675522
MAPK8	68	0.046693511
NFKBIA	63	0.047164646
HCK	49	0.046599691
PTPRC	43	0.046388184
ITGB2	40	0.045643782
MAP2K1	36	0.045681818
PLAT	25	0.045451119
STAT6	24	0.046513422
HLA-DMA	24	0.04396646
TRAF4	24	0.044062843
TLR4	24	0.046527778
HLA-DRB5	23	0.04573032
TLR2	22	0.046083301
IL10RA	18	0.046206897
ALOX5	18	0.044056404

CC: Closeness centrality.

Table 3 List of proteins with both a large BC and degree, and their functions

Protein name	Function
RELA/NF-κB3	NF-κB is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis
MAPK8	Responds to activation by environmental stress and pro-inflammatory cytokines by phosphorylating a number of transcription factors, primarily components of AP-1 such as JUN, JDP2 and ATF2 and thus regulates AP-1 transcriptional activity
NFKBIA	Inhibits the activity of dimeric NF-κB/REL complexes by trapping REL dimers in the cytoplasm, masking their nuclear localization signals
HCK	May serve as part of a signaling pathway coupling the Fc receptor to activation of the respiratory burst. May also contribute to neutrophil migration and regulate the degranulation process of neutrophils
PTPRC	Required for T-cell activation through the antigen receptor
ITGB2	Receptor for ICAM1, ICAM2, ICAM3 and ICAM4
TLR4	Cooperates with LY96 and CD14 to mediate the innate immune response to bacterial lipopolysaccharide (LPS). Acts via MYD88, TIRAP and TRAF6, leading to NF-κB activation, cytokine secretion and the inflammatory response
PLAT	Converts the abundant, but inactive, zymogen plasminogen to plasmin by hydrolyzing a single Arg-Val bond in plasminogen. By controlling plasmin-mediated proteolysis, it plays an important role in tissue remodeling and degradation, in cell migration and many other physiopathological events
TRAF4	Adapter protein and signal transducer that links members of the tumor necrosis factor receptor family to different signaling pathways by association with the receptor cytoplasmic domain and kinases
MAP2K1	Catalyzes the concomitant phosphorylation of a threonine and a tyrosine residue in a Thr-Glu-Tyr sequence located in MAP kinases. Activates ERK1 and ERK2 MAP kinases
TLR2	Cooperates with LY96 to mediate the innate immune response to bacterial lipoproteins and other microbial cell wall components
STAT6	Carries out a dual function: signal transduction and activation of transcription. Involved in interleukin-4 signaling

Table 4 List of proteins with a large BC value and their CC values

Protein	BC	CC
RELA/NF-κB3	62240.75685	0.047675522
MAPK8	37123.82691	0.046693511
PTPRC	34614.23746	0.046388184
HCK	33484.99898	0.046599691
NFKBIA	28771.33132	0.047164646
ITGB2	27901.91607	0.045643782
TLR4	19587.75501	0.046527778
PLAT	19339.65216	0.045451119
CCL4	18441.86414	0.043654528
HMGB1	15263.85652	0.046466826
MAP2K1	14047.72141	0.045681818
STAT6	13376.61128	0.046513422
CXCR4	11471.71166	0.044769471
CSNK2A1	11279.76894	0.046574496
HLA-DRB5	11088.56681	0.045730320
BTK	11016.20767	0.046621308
TLR2	10824.15886	0.046083301
RAC2	10692.38019	0.044872749
TRAF4	10472.80579	0.044062843

BC: Betweenness centrality.

Table 5 List of proteins with only a large BC and their functions

Protein name	Function
HMGB1	Binds to preferentially single-stranded DNA and unwinds double-stranded DNA
BTK	Plays a crucial role in B-cell ontogeny
CSNK2A1	Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates
CXCR4	Transduces a signal by increasing the intracellular calcium ion level
CCL4	Monokine with inflammatory and chemokinetic properties
RAC2	Plasma membrane-associated small GTPase which cycles between an active GTP-bound and inactive GDP-bound state. In active state binds to a variety of effector proteins to regulate cellular responses, such as secretory processes, phagocytosis of apoptotic cells and epithelial cell polarization. Seems to be involved in the regulation of NADPH oxidase