Kim KK, Kim HB. Protein interaction network related to Helicobacter pylori infection response. World J Gastroenterol 2009; 15(36): 4518-4528 [PMID: 19777610 DOI: 10.3748/wjg.15.4518]
Corresponding Author of This Article
Dr. Han Bok Kim, Professor, Department of Biotechnology, The Research Institute for Basic Sciences, Hoseo University, Asan 336-795, South Korea. hbkim@hoseo.edu
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World J Gastroenterol. Sep 28, 2009; 15(36): 4518-4528 Published online Sep 28, 2009. doi: 10.3748/wjg.15.4518
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
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
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
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
Citation: Kim KK, Kim HB. Protein interaction network related to Helicobacter pylori infection response. World J Gastroenterol 2009; 15(36): 4518-4528