© kamla-raj 2018 int j hum genet, 18(2): 137-151 (2018...
TRANSCRIPT
Screening Hub Genes in Microbial Keratitis Based on GibbsSampling Analysis
Qiao-Ling Wang1, Meng-Hui Zhang2 and Xi Chen3*
1Department of Ophthalmology, The Second People’s Hospital of Jinan, Jinan 250012,Shandong, P.R. China
2Department of General Surgery, The Fourth People’s Hospital of Jinan, Jinan 250031,Shandong, P.R. China
3Department of Ophthalmology, The Ninth People’s Hospital of Chongqing,Chongqing 400700, P.R. China
KEYWORDS Gibbs Sampling. Hub Gene. Key Differential Pathway. Markov Chain. Microbial Keratitis. Probability
ABSTRACT This study aimed to identify potential key pathways and hub genes. The enrichment pathways werechosen through merging the gene expression data from microarray data with KEGG pathways. Gibbs sampling wasperformed to screen out significant pathways and the pathway gene set was determined. Finally, hub genes wereidentified using Gibbs sampling and statistics. A total of 278 pathways were chosen according to gene overlap greaterthan 5. Markov chain (MC) was established based on the enrichment of the gene expression profile in each pathwayusing Gibbs sampling and then 26 significant pathways were determined judging by adj_ápi greater than 0.8. Additionally,1167 pathway gene sets were found out. Finally, 26 pathways were chosen as key pathways and 5 hub genes wereidentified on basis of their importance, which will contribute to elucidating potential molecular mechanism ofmicrobial keratitis. We identified potential key pathways and hub genes in microbial keratitis.
Address for correspondence:Xi ChenDepartment of Ophthalmology,The Ninth People’s Hospital of Chongqing,Chongqing 400700, P.R. ChinaE-mail: [email protected]
INTRODUCTION
Microbial keratitis is an infective ophthalmicdisease, caused by spectrums of pathogenicmicroorganisms including bacteria, viruses, fun-gi, Acanthamoeba and other prokaryote patho-gens. In spite of recent advances in antimicrobi-al measures, due to ensuing excessive inflamma-tory response and ocular tissue damage, largenumbers of patients’ conditions fail to achieveeffective controls or continue to deteriorate, andeventually patients have to undergo cornealtransplantation or even enucleation. According-ly, it is imperative to have a bearing on relevantphysiopathologic mechanisms, which inevitablywill be a breakthrough for diagnosing, treatingor monitoring microbial keratitis.
Microbial keratitis initiation and progressionrelate to intricate biological process that involvesvarious genes alterations and diverse molecularmechanisms underlying the pathophysiology.With the aid of bioinformatics analyses, a pow-
erful approach emerging of proteome analysisin tear protein profile has indicated that glutare-doxin-related protein, lipocalin, prolactin induc-ible protein, serum albumin precursor, apolipo-protein, lacritin precursor (Ananthi et al. 2008;Ananthi et al. 2013; Kandhavelu et al. 2017). Sev-eral molecular pathways were reported to involvein the development of microbial keratitis, name-ly, p38 mitogen-activated protein kinases(MAPK) pathway (Hua et al. 2017), Toll-like re-ceptor-3 (TLR3)/ TIR domain-containing adap-tor inducing IFN-β (TRIF) pathway (Park et al.2015), spleen-tyrosine kinase (Syk) signaling(Liu et al. 2015). With the increasingly biologi-cal importance of highly connective hub genesthat play a pivotal role in maintaining interac-tion network, hub genes or key pathways iden-tified were particularly crucial for uncoveringthe pathogenesis of microbial keratitis. In thewake of rapidly diverse bioinformatics method-ologies, the understanding of underlying phys-iopathologic molecular mechanisms of disordershas been greatly improved. Here, in this work,coupled with microarray data, Kyoto Encyclo-pedia of Genes and Genomes (KEGG) enrich-ment, Gibbs sampling, the researchers identi-fied key pathways and hub genes associatedwith microbial keratitis.
© Kamla-Raj 2018 Int J Hum Genet, 18(2): 137-151 (2018)DOI: 10.31901/24566330.2018/18.2.697
138 QIAO-LING WANG, MENG-HUI ZHANG AND XI CHEN
Objective
In the present study, the researchersachieved 278 enrichment pathways based ongenes intersection greater than 5 from microar-ray data performed on samples with 15 keratitit-ides and 12 normal. Moreover, Gibbs samplingwas implemented to identify 26 key differentialpathways. Then, the researchers applied Gibbssampling to acquire 5 hub genes through differ-ential pathway gene sets. Overall, hub genes anal-ysis improved comprehending of microbial kerati-tis through providing relevant gene changes thatoccur during microbial keratitis progression anddiscovered the key biomarkers with potential util-ity for clinical diagnosis, therapy, and surveillanceof microbial keratitis progression.
METHODOLOGY
Microarray Data Acquisition andPreprocessing
The gene expression profile, with the acces-sion number of E-GEOD-58291 (Chidambaram etal. 2017), was downloaded from ArrayExpress(http://www.ebi.ac.uk/arrayexpress/). In the mi-croarray data of E-GEOD-58291, there were 15keratitis samples and 12 normal samples. Theprobe annotation data were downloaded andthen each probe was mapped to matched genesymbols. Amongst which the probe was discard-ed if it can’t match any one gene, or the averageexpression value was computed if there weremultiple probes match one gene. After data pre-processing, the researchers eventually acquiredthe gene expression matrix containing 14,832genes.
EGG Pathway Enrichment
Pathway enrichment analysis of gene expres-sion matrix was conducted based on the KEGGpathway database. The researchers merged thegene expression data with KEGG regulatory path-ways and chose 278 pathways judging by geneoverlap greater than 5.
Gibbs Sampling
In order to obtain the pivotal pathways andkey genes, Gibbs sampling was introduced.Gibbs sampling is a Markov chain (MC) Monte
Carlo (MCMC) algorithm extensively applied instatistical inference that generates samples froma sequence of different conditional probabilitydistributions. To executing Gibbs sampling, theabove 278 pathways were converted into MC.
According to the enrichment of the geneexpression profile in each pathway, the mean val-ue of gene expression in each pathway was com-puted in normal and keratitis states. The normalstate served as the initial state and the keratitisstate served as prior state, then the third statewas inferred by the prior state, in turn the state nwas gained according to this model extrapolated.
An empty Gibbs sampling set comprising ak-dimensional (k = 278) random vector was de-fined. Following, n samples MC data set con-taining the initial value and prior value were de-posited into the empty Gibbs sampling set. Then,a k-dimensional vector was initialized, k-1 ele-ments of this vector were fixed, the remainingelement was extracted, like this cycled k timeswhich was equal to updating the whole vectorsand also generate a novel sample. The third statewas obtained. Ultimately, through n cycles ofGibbs sampling, a MC was established.
Differential Pathways Analysis
On basis on the posterior value of pathwaysgenerated by the MC and utilizing the probabil-ity formula αpi, the probability of each pathwaywas acquired. Then, by statistical analysis (stu-dent’s t-test) of the pathways expression in kerati-tis and normal states, the P values were calcu-lated and according to it, the pathways wereranked (ranki). Combining αpi and P value, cor-rection coefficient (Rvalue) was calculated andthen adj-αpi (multiplying αpi by Rvalue) was calcu-lated. Key differential pathways were selectedjudging by adj_αpi greater than 0.8. Related com-putational formulas were as follows.
Hub Genes Identification
The genes in the differential pathways wereanalyzed to find the pathway gene set and theirfrequencies in differential pathways were count-
α = ∑1000−20001000 − 2000 + 1 R = 1 − adj_α = × pi
HUB GENES IN MICROBIAL KERATITIS 139
ed. Subsequently, pathway gene set were con-verted into MC and then Gibbs sampling wasperformed. Finally, differential pathway genesof which alfa-adj were greater than 0.8 were cho-sen as hub genes.
RESULTS
KEGG Pathway Enrichment Analysis
By data preprocessing, a total of 14832 geneswere obtained and these genes were enrichedinto the KEGG pathway with 287 pathways con-taining 6,894 genes. The enrichment analysissuggested that 278 pathways were determinedbased on the gene overlap greater than 5.
Differential Pathways Identification
To further determine key pathways, the re-searchers used the Gibbs sampling via comput-ing adj_pi to gain the probabilities distributionof enriched pathways shown in Figure 1, in theimage, a total of 26 key pathways were identifiedaccording to the adj-pi > 0.8, including NF-kap-pa B signaling, TNF signaling, Cytokine-cytok-ine receptor interaction, Phagosome, Hemato-
poietic cell lineage, Toll-like receptor signalinget al. As shown in Table 1, the expression valuesof these pathways in normal and keratitis statessuggested that these pathways were upregulat-ed significantly in keratitis groups compared tonormal group (P < 0.05), correspondingly, theheat map of pathways expression levels werepresented in Figure 2. Compared with normalgroup, these 26 significant pathways in keratitisgroup were higher expressed.
Pathway Gene Set Selection
In an effort to find out the hub genes are ofimportance in gene expression network, 1167genes in significant pathways were needed tobe analyzed. Gene set in 26 significant pathwayscomprised 82 genes in Rheumatoid arthritis sig-naling pathway, 195 genes in Cytokine-cytokinereceptor interaction signaling pathway, 150genes in Tuberculosis signaling, 158 genes inChemokine signaling pathway, 115 genes in Os-teoclast differentiation signaling pathway, 49genes in Staphylococcus aureus infection path-way et al. Several genes may appear in multi-pathways and a total of 1167 genes were con-tained in 26 key differential pathways and the
A Probabilities of differential pathways B Density of probabilities of differential pathways
Differential pathways Differential pathways
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Fig. 1. The probabilities distribution of 278 pathways. The X axis denoted the pathways, and the Y axisrepresented the posterior value of the pathways. A. The adjusted posterior value distribution of 278pathways. B. The density of 278 differential pathways posterior value distribution. Pathway was con-sidered as the key differential pathway judging by adj_pi > 0.8.Source: Author
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NG
;IFN
GR
1; I
FNG
R2;
STA
T1;
IL
1A;I
L1B
;IL
1R1;
T
NF;
TN
FRSF
1A;T
GFB
2 ;T
GFB
R1;
TG
FBR
2;
TN
FRSF
11A
;TN
FRSF
11B
;T
RA
F2;T
RA
F6;L
CK
;FY
N;M
AP3
K 1
4;C
HU
K;R
EL
B;N
FKB
2; M
AP3
K7;
TAB
1;TA
B2;
IKB
KG
;IK
BK
B;N
FKB
IA;R
EL
A;N
F K
B1;
NFA
TC
1;
MA
P2K
1;M
APK
11;M
APK
12;
MA
PK13
;MA
PK14
;M
AP2
K7;
MA
PK8;
MA
PK10
;MA
PK9;
FO
S;FO
SB;F
OSL
2;FO
SL1;
JUN
;JU
ND
;JU
N B
;RA
C1;
CY
BB
;CY
BA
;NC
F2;N
CF1
; N
CF4
;BT
K;T
EC
;OSC
AR
;L
ILR
B2;
LIL
RB
1;L
IL
RB
5;L
ILR
B4;
LIL
RB
3;L
ILR
A3;
LIL
RA
2; L
ILR
A4;
LIL
RA
6;L
ILR
A5;
FC
GR
1A;F
CG
R2A
;FC
GR
2B;F
CG
R3B
;TR
EM
2;SI
RPA
;S
IRPB
1;T
YR
OB
P;SY
K;L
CP2
;PLC
G2;
PPP
3CA
;PPP
3CB
;PPP
3CC
;PPP
3R1
;CR
EB1;
SPI1
;MIT
F;C
TSK
; AC
P5;
ITG
B3;
PPA
RG
;IFN
AR
1; I
FNA
R2;
JAK
1;TY
K2;
STA
T2;IR
F9;S
OC
S1;
SOC
S3;G
AB
2;FH
L2;
CY
LD;S
QST
M1
Stap
hylo
cocc
us a
ureu
s in
fect
ion
49FG
G;C
3;C
FB;C
FD;
CFH
;MA
SP1;
C1Q
A;C
1QB
;C1Q
C;C
1R;C
1S;C
2;C
4A;C
5;C
3A R
1;C
5AR
1;FC
GR
1A;F
CG
R2A
; FC
GR
2B;F
CG
R3B
;FC
AR
; FP
R3;
FPR
2;FP
R1;
CFI
;SE
LPL
G;S
EL
P;IC
AM
1;IT
GA
L;IT
GA
M;I
TGB
2;D
SG1;
HLA
-DM
A;H
LA-D
MB
;HLA
-DO
A;H
LA-D
OB
;HLA
-D
PA1;
HL
A-D
PB1;
HL
A-D
QA
1;H
LA
-DQ
A2;
HL
A-D
QB
1;H
LA
-DR
A;H
LA
-DR
B1;
HL
A-
DR
B3;
HL
A-D
RB
4;H
LA
-DR
B5;
PTA
FR;I
L10
;KR
T10
Pha
goso
me
132
VAM
P3;
STX
12;
STX
7; A
CT
B;A
CT
G1;
CO
RO
1A;S
TX
18;S
EC
22B
;HL
A-A
;HL
A-B
;HL
A-C
;HL
A-F
; H
LA
-G
;HL
A-E
; H
LA
-DM
A;H
LA
-DM
B;H
LA
-DO
A;H
LA
-DO
B;H
LA
-DPA
1;H
LA
-DPB
1; H
LA
-D
QA
1; H
LA
-DQ
A2;
HL
A-D
QB
1;H
LA
-DR
A;H
LA
-DR
B1;
HL
A-D
RB
3;H
LA
-DR
B4;
HL
A-
DR
B5;
RA
B5A
;RA
B5B
;RA
B5C
; E
EA
1;PI
K3C
3;T
FRC
; H
GS;
AT
P6V
1A;
AT
P6V
1B1;
AT
P6V
1B2;
AT
P6
V1C
1;A
TP6
V1D
;AT
P6V
1E2;
A
TP6
V1E
1;A
TP6
V1F
; A
TP6
V1G
1;A
TP6
V1G
2;A
TP6
V0E
1;A
TP6
V0E
2;T
CIR
G1;
AT
P6
V0A
2;A
TP6
V0A
4;A
T
P6V
0A1;
AT
P6V
0D1;
AT
P6V
1H;A
TP6
V0C
;AT
P6V
0B;A
TP6
AP1
;RA
B7A
;R
AB
7B;D
YN
C1H
1;D
YN
C2H
1;D
YN
C1I
1;D
YN
C1I
2;D
YN
C1L
I2;T
UB
A1B
;TU
BA
4A;T
UB
A1
A;T
UB
A1C
;T
UB
A3
D;T
UB
AL
3;T
UB
B6
;TU
BB
;TU
BB
2A
;TU
BB
3;T
UB
B8
;TU
BB
2B
;TU
BB4B
;LA
MP1
;LA
MP2
;M6P
R;M
PO;C
TSL;
CTSS
;SEC
61A
1;SE
C61A
2;SE
C61B
;SEC
61G
;TA
P1;T
A
142 QIAO-LING WANG, MENG-HUI ZHANG AND XI CHENTa
ble
1: C
ontd
...
Pat
hway
Num
ber
Mem
ber
P2;C
ALR
;CA
NX
;FC
AR
;FC
GR
1A;F
CG
R2A
;FC
GR
2B;F
CG
R3B
;C1R
;ITG
AM
;ITG
B2
;C
3;C
OL
EC
11;C
OL
EC
12
;SF
TP
D;I
TG
AV
;IT
GA
2;I
TG
A5
;IT
GB
1;I
TG
B3;
ITG
B5;
THB
S1;C
OM
P;TH
BS2
;TH
BS3
;TH
BS4
;TL
R2;
TLR
6;TL
R4;
CD
14;P
LA2R
1;M
RC1;C
D209
;CLE
C7A;
MSR
1;MAR
CO;O
LR1;S
CARB
1;CD3
6;CYB
A;CY
BB;R
AC1;N
CF1;N
CF2;N
CF4
Gra
ft-v
ersu
s-ho
st d
isea
se35
IL6;
IL1A
;IL1
B;T
NF;
HLA
-DM
A;H
LA-D
MB
;HLA
-DO
A;H
LA-D
OB
;HLA
-DPA
1;H
LA-
DP
B1;
HL
A-D
QA
1;H
LA
-DQ
A2;
HL
A-D
QB
1;H
LA
-DR
A;H
LA
-DR
B1;
HL
A-
DR
B3;
HL
A-D
RB
4;H
LA
-DR
B5;
CD
80;C
D86
;CD
28;H
LA
-A;H
LA
-B;H
LA
-C;H
LA
-F;
HLA
-G;H
LA-E
;FA
S;PR
F1;G
ZMB
;IFN
G;K
LRD
1;K
IR2D
L3;K
IR3D
L1;K
LRC
1Ty
pe I
dia
bete
s m
ellit
us37
GA
D1;
PT
PR
N;P
TP
RN
2;C
PE
;HS
PD
1;H
LA
-DM
A;H
LA
-DM
B;H
LA
-DO
A;H
LA
-D
OB
;HLA
-DPA
1;H
LA-D
PB1;
HLA
-DQ
A1;
HLA
-DQ
A2;
HLA
-DQ
B1;
HLA
-DR
A;H
LA-
DR
B1;
HLA
-DR
B3;
HLA
-DR
B4;
HLA
-DR
B5;
CD
80;C
D86
;CD
28;I
FNG
;HLA
-A;H
LA-
B;H
LA-C
;HLA
-F;H
LA-G
;HLA
-E;F
AS;
PRF1
;GZM
B;L
TA;T
NF;
IL1A
;IL1
B;I
CA
1H
emat
opoi
etic
cel
l lin
eage
74K
ITL
G;I
L7;
CSF
2;FL
T3L
G;C
SF3;
IL6;
IL11
;IL
1A;I
L1B
;TN
F ;C
SF1;
CD
34;F
LT3;
CD
44;K
IT;IL
2RA
;IL7R
;TFR
C;C
D7;
CD
2;C
D5;
CD
1A;C
D1B
;CD
1C;C
D1D
;CD
1E;C
D4;
CD
8A;C
D3D
;CD
3E;C
D3G
;MM
E; C
D9;
CD
19;
CD
22;
CD
24;M
S4A
1;C
R2;
CD
37;F
CER
2;C
R1;
CSF
2RA
;IL3
RA
;CD
3 3;
IL4R
; IL
6R;F
CG
R1A
; C
SF1R
;AN
PEP;
ITG
AM
;CD
14;
IL1R
1;IL
1R2;
CSF
3R;I
L5
RA
;EPO
R;
CD
36;C
D55
;CD
59;I
L11
RA
;IT
GB
3;G
P1B
A;I
TGA
1; I
TGA
2; I
TGA
3; I
TGA
4;IT
GA
5;IT
GA
6;H
LA-D
RA
;HLA
-DR
B1;
HLA
-D
RB
3;H
LA-D
RB
4;H
LA-D
RB
5;C
D38
Infl
amm
atio
ry b
owel
dis
ease
(IB
D)
51T
LR
2;T
LR
4;T
LR
5;N
FKB
1;R
EL
A;N
OD
2;H
LA
-DM
A;H
LA
-DM
B;H
LA
-DO
A;H
LA
-D
OB
;HLA
-DPA
1;H
LA-D
PB1;
HLA
-DQ
A1;
HLA
-DQ
A2;
HLA
-DQ
B1;
HLA
-DR
A;H
LA-
DR
B1;
HL
A-D
RB
3;H
LA
-DR
B4;
HL
A-D
RB
5;IF
NG
;IF
NG
R1;
IFN
GR
2;S
TAT
1;T
BX
21;I
L12
RB
1;ST
AT
4;IL
18;I
L 18
R1;
IL18
RA
P;JU
N;T
NF;
IL6
;IL
1A;
IL1B
;TG
FB2;
TG
FB3;
S M
AD
2;SM
AD
3;ST
AT
3 ;I
L21
R;I
L23
A;
RO
RC
;RO
RA
;IL
17F;
IL4R
;IL2
RG
;STA
T6;I
L10;
MA
F;N
FATC
1In
test
inal
im
mun
e ne
twor
k fo
r Ig
A p
rodu
ctio
n38
CD
80;C
D86
; H
LA
-DM
A;H
LA
-DM
B;H
LA
-DO
A;H
LA
-DO
B;
HL
A-D
PA1;
HL
A-
DPB
1;H
LA
-DQ
A1;
HL
A-D
QA
2;H
LA
-DQ
B1;
HL
A-D
RA
; H
LA
-DR
B1;
H
LA
-D
RB
3;H
LA
-DR
B4
;HL
A-D
RB
5;C
D2
8;I
L6
;IL
10
;TN
FS
F1
3;
TNFS
F13B
;TN
FRSF
13B
;TN
FRSF
17;C
D40
;C D
40LG
;IC
OS;
ICO
SLG
;ITG
A4;
ITG
B7;
CX
CL1
2; C
XC
R4;
CC
L28;
CC
R10
; LT
BR
; M
AP3
K14
; IL
15;
IL15
RA
;PIG
RLe
ishm
ania
sis
66T
LR
2;T
LR
4;M
YD
88;I
RA
K1;
IRA
K4;
TR
AF6
;MA
P3K
7;
TAB
1;TA
B2;
NFK
BIB
;N
FKB
IA;N
FKB
1;R
EL
A;I
L1A
;IL
1B;T
NF;
NO
S2;I
L10
;TG
FB2;
TG
FB3;
C3;
CR
1;I
TG
AM
;IT
GB
2;
FCG
R1A
;FC
GR
2A;F
CG
R3B
;IT
GA
4;IT
G
B1;
PTG
S2;N
CF1
;N
CF2
;NC
F4;
CY
BA
; M
APK
1;M
APK
3;EL
K1;
FOS;
JUN
;MA
PK11
; M
APK
12;M
APK
13;
MA
PK14
; IF
NG
;IFN
GR
1; I
FNG
R2;
JAK
1;JA
K2;
STAT
1;H
LA-D
MA
;HLA
-DM
B;H
LA-
DO
A;H
LA
-DO
B;
HL
A-D
PA1;
HL
A-D
PB1;
HL
A-D
QA
1;H
LA
-DQ
A2;
HL
A-
DQ
B1;
HL
A-D
RA
;HL
A-D
RB
1;
HL
A-D
RB
3;H
LA
-DR
B4;
HL
A-
DR
B5;
MA
RC
KSL
1;PT
PN6;
PRK
CB
Nat
ural
kill
er c
ell
med
iate
d cy
toto
xici
ty98
HLA
-A;H
LA-B
;HLA
-C;H
LA-F
;HLA
-G;H
LA-E
;KIR
3DL1
; K
IR2D
L3 ;
KIR
2DL4
; K
LRC
1;K
LR
D1;
PTPN
6;PT
PN11
;IC
AM
1;IC
A M
2;IT
GA
L;
ITG
B2;
PTK
2B;
VAV
3; V
AV
1;VA
V2;
RA
C1;
RA
C2;
RA
C3;
PAK
1;M
AP2
K1;
MA
P 2K
2; M
APK
1; M
APK
3;TN
F;C
SF2;
IFN
G;K
IR2D
S3;T
YR
OB
P;LC
K;F
CG
R3B
;FC
ER1G
;CD
247;
ZAP
HUB GENES IN MICROBIAL KERATITIS 143
70;S
YK
;LC
P2;L
AT;
PLC
G1;
PL
CG
2;PI
K3C
A;
PIK
3CD
;PIK
3CB
;PI
K3C
G;P
IK3R
1;PI
K3R
5; P
IK3R
2;PI
K3R
3;FY
N;S
HC
1;SH
C2;
SHC
3;
SH C
4;G
RB
2;SO
S1;
SOS2
; H
RA
S;K
RA
S;N
RA
S; A
RA
F;B
RA
F;R
AF1
; M
ICB
; M
IC A
; U
LBP1
; U
LBP2
; R
AET
1G;
RA
ET1L
;R
AE
T1E
; H
CST
;CD
48;P
P P3
CA
; PP
P3C
B;
PPP3
CC
; PP
P3R
1;N
FAT
C1;
PR
K C
A;
PRK
CB
;SH
2D1B
;SH
2D1A
;IFN
GR
1;IF
N G
R2;
IFN
AR
1; I
FNA
R2;
TNFS
F10;
TN
FRSF
10A
;TN
FRSF
10B
; TN
FRSF
10C
; TN
FRSF
10D
; FA
S; G
ZMB
;PR
F1;C
ASP
3;B
IDIn
flue
nza
A14
6PR
SS3;
PRSS
2; T
MPR
SS2;
TM
PRSS
4;O
AS1
;OA
S2;
OA
S3;R
NA
SEL;
DN
AJB
1;D
NA
JC3;
HSP
A8;
H
SPA
1A
;HSP
A2;
HSP
A1L
;H
SPA
1B;E
IF2A
K1;
E
IF2A
K2;
EIF
2AK
3;E
IF2A
K4;
EIF
2S1;
M
AP2
K3;
M
APK
11;M
APK
12;M
APK
13;M
APK
14;M
A
P2K
4;M
AP2
K7;
MA
PK8
;MA
PK10
;MA
PK9;
JUN
; ATF
2;D
DX
58;I
FIH
1; M
AVS;
NLR
X1;
IKB
KB
;N
FKB
IB;
NFK
BIA
; N
FKB
1;R
EL
A;T
RIM
25;T
LR
3;T
ICA
M1;
TB
K1;
IKB
KE
;IR
F3;
CR
EBB
P; E
P300
; PI
K3R
1;PI
K3R
5;PI
K3R
2;PI
K3R
3;PI
K3C
A;P
IK3C
D ;
PIK
3CB
; PI
K3C
G;
AK
T1;A
KT3
; TL
R4;
TLR
7;M
YD
88;
IRA
K4;
IRF7
;IL1
A;I
L1B
; IL
6;TN
F;C
XC
L8;C
CL2
;C
CL5
; C
XC
L10;
ICA
M1;
IFN
A R
1;IF
NA
R2;
JAK
1; T
YK
2;ST
A T
1;ST
AT2
;IR
F9;
SOC
S3;
MX
1; A
DA
R;
PML;
IFN
G;I
FNG
R1;
IFN
GR
2;JA
K2;
CII
TA;H
LA-D
MA
;HLA
-DM
B;H
LA-
DO
A;
HLA
-DO
B;H
LA-D
PA1;
HLA
-DPB
1;H
LA-D
QA
1;H
LA-D
QA
2;H
LA-D
QB
1; H
LA-
DR
A;
HLA
-DR
B1;
HLA
-DR
B3;
HLA
-DR
B4;
HLA
-DR
B5;
NLR
P3;P
YC
AR
D;
CA
SP1;
IL1
8;IL
33;T
NFS
F 10
;TN
FRSF
10A
;TN
FRSF
10B
;TN
FRSF
10C
;T N
FRSF
10D
; FA
S; T
NFR
SF1A
;V
DA
C1;
CY
CS;
C A
SP9;
GSK
3B;K
PNA
1;K
PNA
2;X
PO1;
A G
FG1;
RA
F1; M
AP2
K1;
M A
P2K
2;M
APK
1;M
APK
3;R
SAD
2;FD
PS;A
CTB
;AC
TG1;
IV N
S1A
BP;
CPS
F4;
NX
F1;
NX
F3;
NX
T1;
NX
T2;R
AE1
;HN
RN
PUL1
; N
UP9
8;FU
RIN
;TM
PRSS
13;
SLC
25A
6; P
RK
CA
; PR
KC
BA
ntig
en p
roce
ssin
g an
d pr
esen
tatio
n62
IFN
G;T
NF;
PSM
E1;P
S M
E2;P
SME3
;HSP
A8;
HSP
A1A
;HSP
A2;
HSP
A1L
; H
SPA
1B;
HSP
A4;
HS
P9
0A
A1
;HS
P9
0A
B1
;HL
A-A
;HL
A-B
;HL
A-C
;HL
A-F
;HL
A-G
;HL
A-E
;C
AN
X;B
2M;C
ALR
;TA
PBP;
TAP1
;T A
P2;C
D8A
; K
IR3D
L1;
KIR
2DL3
; K
IR2D
L4;
KLR
C1;
KL
RD
1;K
IR2D
S3;I
FI30
;LG
MN
;CT
SB;H
LA
-DM
A;
HL
A-D
MB
;HL
A-D
OA
;HL
A-
DO
B;H
LA
-DPA
1;H
LA
-DPB
1;H
LA
-DQ
A1;
HL
A-D
QA
2;H
LA
-DQ
B1;
HL
A-D
RA
;HL
A-
DR
B1;
HL
A-D
RB
3;H
LA
-DR
B4;
HL
A-D
RB
5; C
D74
; C
TSL
;CT
SS;
CD
4;C
IITA
; R
FX5;
RFX
AN
K;
RFX
AP;
CR
EB1;
NFY
A;N
FYB
;NFY
C;H
SPA
5N
F-ka
ppa
B s
igna
ling
path
way
84L
CK
;ZA
P70;
LA
T;PL
CG
1;
PRK
CQ
;SY
K;L
YN
; B
TK
;PL
CG
2;C
AR
D11
; B
CL
10;
MA
LT1;
IL1B
;IL1
R1;
MY
D88
;IR
AK
1; I
RA
K4;
TRA
F6;T
NF;
TN
FRSF
1A;R
IPK
1; T
RA
DD
;T
RA
F2;
TR
AF5
; B
IRC
2;B
IRC
3; D
DX
58;T
RIM
25;L
B P
;CD
14;
TL
R4;
LY96
;TIR
AP;
TIC
AM
1; C
D40
LG;
CD
40;
TRA
F3;
TNFR
SF11
A;
LTA
; LT
B;T
NFS
F14;
LTB
R;M
AP3
K14
;M
AP3
K7;
TA
B1;
TA
B2;
TN
FSF1
3B;
IK
BK
G;C
HU
K;IK
BK
B;P
IAS4
;UB
E2I;A
TM ;P
IDD
1;E
RC
1; N
FKB
IA;
NFK
B1;
RE
LA
;CFL
AR
;XIA
P;B
CL
2L
1;B
CL
2; T
RA
F1;
BC
L2A
1;N
FKB
2;C
XC
L8;
TNFA
IP3;
PTG
S2;C
CL4
;VC
AM
1 ;P
LAU
;CSN
K2A
1; C
SNK
2A2;
CSN
K2B
;R
ELB
;CC
L13;
CC
L19;
CC
L21;
CX
CL1
2;IC
AM
1; P
AR
P1;
CX
CL2
; G
AD
D45
B;
PRK
CB
Pert
ussi
s67
ITG
A5;
ITG
B1;
ITG
AM
;IT
GB
2;C
AL
ML
3 ;C
AL
M2;
CA
LM
3;
CA
LM
1;C
AL
ML
5;R
HO
A;C
FL1;
CFL
2;C
ASP
3; C
ASP
7;C
ASP
1;PY
CA
RD
;NLR
P3;I
L1B
;C1Q
A;
C1Q
B;C
1QC
;C
1R;C
1S;C
2;C
4A
;C3;
C5;
SER
PIN
G1;
C4B
PA ;
LY96
;TLR
4; C
D14
;TIR
AP;
MY
D88
;I R
AK
4;IR
AK
1;TR
AF6
;NFK
B1;
REL
A;T
ICA
M1;
IRF3
;M A
PK11
; M
APK
12;
MA
PK13
; M
APK
14;
MA
PK8;
MA
PK10
; M
APK
9;M
APK
1;
MA
PK3;
FO
S;JU
N;
IL6;
IL23
A;T
NF;
IL10
;IR
F1;I
RF8
;GN
AI1
;GN
AI3
;GN
AI2
;C
XC
L8;C
XC
L5;
CX
CL6
;NO
D1;
IL1A
;NO
S2
Tabl
e 1:
Con
td...
Pat
hway
Num
ber
Mem
ber
144 QIAO-LING WANG, MENG-HUI ZHANG AND XI CHEN
Allo
graf
t re
ject
ion
31H
LA-A
; HLA
-B;H
LA-C
;HLA
-F;H
LA-G
;HLA
-E;C
D80
;CD
86; C
D28
; FA
S; P
RF1
; GZM
B; H
LA-
DM
A;H
LA
-DM
B;H
LA
-DO
A;H
LA
-DO
B;H
LA
-DPA
1;H
LA
-DPB
1; H
LA
-DQ
A1;
HL
A-
DQ
A2
;HL
A-D
QB
1;H
LA
-DR
A;H
LA
-DR
B1
;HL
A-D
RB
3;H
LA
-DR
B4
;HL
A-
DR
B5;
CD
40LG
;CD
40;I
FNG
;TN
F;IL
10To
ll-lik
e re
cept
or s
igna
ling
path
way
84T
LR
1;T
LR
2;T
LR
6;L
BP;
CD
14;L
Y96
; T
LR
3;T
LR
4;T
LR
5;T
LR
7;
TL
R8;
CT
SK;R
AC
1;PI
K3C
A;P
IK3C
D;P
IK3C
B;P
IK3C
G;P
IK3R
1;PI
K3R
5;PI
K3R
2;
PIK
3R3;
AK
T1;
AK
T3;T
OLL
IP;M
YD
88;T
IRA
P;FA
DD
;CA
SP8;
IRA
K4;
IRA
K1;
TRA
F6;T
AB1
;TA
B2;M
AP3
K7;
IKBK
G;C
HU
K;I
KB
KB
;NFK
BIA
;NFK
B1;
REL
A;M
AP3
K8;
MA
P2K
1;M
AP2
K2;
MA
PK1;
MA
PK3;
MA
P2
K3
;MA
P2
K4
;MA
P2
K7
;MA
PK
11
;MA
PK
12
;MA
PK
13
;MA
PK
14
;MA
PK
8;M
AP
K1
0;M
AP
K9
;JU
N;F
OS
;TN
F;I
L1
B;I
L6
;CX
CL
8;C
CL
5;C
CL
3;C
CL
3L1;
CC
L3L
3;C
CL
4;T
ICA
M1;
R I
PK1;
IRF5
;IR
F7;S
PP1;
IKB
KE
;TB
K1;
TRA
F3;I
RF3
;CD
40;C
D80
;CD
86;I
FNA
R1;
IFN
AR
2;ST
AT1
;CX
CL1
0;C
XC
L9;C
XC
L11
TNF
sign
alin
g pa
thw
ay10
4TN
F; T
NFR
SF1A
;BA
G4;
TRA
DD
;T R
AF2
;TR
AF5
;RIP
K1;
B I
RC
2; B
IRC
3; M
AP3
K7;
TAB
1;TA
B2;
MA
P2K
4;M
AP2
K7;
MA
PK 8
;MA
PK10
; M
APK
9;JU
N;
ITC
H;
CFL
AR
;MA
P2K
3;M
APK
11;M
APK
12;
MA
PK13
; M
APK
14;C
EBP
B;
MA
P3K
5; M
AP3
K14
; IK
BK
G;I
KB
KB
;C
HU
K;
NFK
BIA
; R
EL
A;N
FKB
1;M
AP3
K8;
MA
P2K
1;M
APK
1;M
APK
3; R
PS6K
A5;
RPS
6KA
4; C
RE
B1;
CR
EB
3;C
RE
B3L
2;C
RE
B3L
4;A
TF2
;AT
F4;C
RE
B5;
AT
F 6B
;RIP
K3;
MLK
L; P
GA
M5;
DN
M1L
; FA
DD
;CA
SP8;
CA
SP10
; C
ASP
7;C
ASP
3; C
CL2
;CC
L5;
CC
L20;
CX
CL
1;C
XC
L2;
CX
CL
10;
CX
3CL
1;C
SF1;
CSF
2;FA
S;IL
18R
1;I
L1B
;IL
6; I
L15
;LIF
;LT
A;B
CL
3;SO
CS3
;TN
FA I
P3;
TR
AF1
; FO
S;JU
NB
;MM
P3;M
MP9
; M
MP1
4;E
DN
1;N
OD
2;IC
AM
1;SE
LE;V
CA
M1;
PTG
S2;
TNFR
SF1B
;TR
AF3
;PIK
3CA
;PI
K3C
D;P
IK3C
B;P
IK3
CG
; PI
K3R
1;PI
K3R
5; P
IK3R
2;PI
K3R
3; A
KT1
;AK
T3 M
AG
I2;J
AG
1; C
XC
L5;V
EGFC
Aut
oim
mun
e th
yroi
d di
seas
e31
CT
LA
4;T
PO;H
LA
-DM
A;H
LA
-DM
B;H
LA
-DO
A;H
LA
-DO
B;H
LA
-DPA
1;H
LA
-DPB
1;H
LA
-D
QA
1;H
LA
-DQ
A2;
HL
A-D
QB
1;H
LA
-DR
A;H
LA
-DR
B1;
HL
A-D
RB
3;H
LA
-DR
B4;
HL
A-
DR
B5
;CD
80
;CD
86
;CD
28
;HL
A-A
;HL
A-B
;HL
A-C
;HL
A-F
;HL
A-G
;HL
A-
E;FA
S;PR
F1;G
ZMB
;CD
40LG
;CD
40;I
L10
Syst
emic
lup
us e
ryth
emat
osus
78C
1QA
;C1Q
B;C
1QC
;C2;
C4A
; H
2AFX
;HIS
T2H
2AC
; H
IST
3H2A
;HIS
T1H
2AE
;H
2AFY
2;H
2AFY
;H2A
FJ;
HIS
T2H
2AB
;H2A
FV
;H2A
FZ;
HIS
T1H
2AC
; H
IST
1H2B
H;
HIS
T2H
2BF;
HIS
T1H
2BG
;HIS
T1H
2BC
;HIS
T1H
2B
D;
HIS
T1H
2BE
; H
IST
2H2B
E;
HIS
T1H
2BK
; H
2BFM
;H3F
3 C
;H3F
3B;
HIS
T1H
3D;
HIS
T2H
3D;H
IST1
H3E
;HI
ST1H
3G;
HIS
T1H
3F;H
IST1
H4C
;HIS
T1H
4H;H
IST1
H4E
; H
IST1
H4A
; S
NR
PB;
SNR
PD1;
SNR
PD3;
GR
IN2A
; T
RIM
21;T
RO
VE
2;SS
B;
AC
TN
1;A
CT
N4;
HL
A-D
MA
;HL
A-D
MB
;HL
A-D
OA
;H
LA-D
OB
;HLA
-DPA
1;H
LA-D
PB1;
HLA
-DQ
A1;
HLA
-DQ
A2;
HLA
-DQ
B1;
HLA
-DR
A;H
LA-
DR
B1;
HL
A-D
RB
3;H
LA
-DR
B4;
HL
A-D
RB
5;C
D80
; C
D86
;CD
28;
CD
40L
G;C
D40
;TN
F;IF
NG
;IL10
;C1R
;C1S
;C3;
C5;
C7;
C8A
;CTS
G;E
LAN
E ;F
CG
R1A
;FC
GR
2A;
FCG
R3B
Vir
al m
yoca
rditi
s57
CX
AD
R;C
D55
;FY
N;C
AV1;
AB
L1;A
BL2
;RA
C1;
RA
C2;
RA
C3;
S G
CD
;SG
CA
;SG
CB
;DA
G1;
DM
D;A
CT
B;
AC
TG
1;E
IF4G
3;E
IF4G
1;
EIF
4G2;
CC
ND
1;
CA
SP8;
BID
;CY
CS;
C
ASP
9;C
ASP
3;M
YH
7;M
YH
6;C
D40
LG;C
D40
;HLA
-DM
A;H
LA-D
MB
; H
LA-D
OA
; H
LA-D
OB
;HLA
-D
PA1;
HL
A-D
PB1;
HL
A-D
QA
1;H
LA
-DQ
A2;
HL
A-D
QB
1;H
LA
-DR
A;H
LA
-DR
B1;
HL
A-
DR
B3;
HL
A-D
RB
4;H
LA
-DR
B5;
HL
A-A
;HL
A-B
;HL
A-C
;HL
A-F
;HL
A-G
;HL
A-
E;C
D80
;CD
86;C
D28
;PR
F1;I
TGA
L;IT
GB
2;IC
AM
1;LA
MA
2
Tabl
e 1:
Con
td...
Pat
hway
Num
ber
Mem
ber
HUB GENES IN MICROBIAL KERATITIS 145
concrete results are presented in SupplementTable 1.
Hub Genes Identification
Finally, to acquire the potential hub genesinvolved in keratitis, Gibbs sampling was reuti-lized to calculate probabilities of pathway geneset. As presented in Figure 3, there were 5 hubgenes identified based on adj_αpi > 0.8, includ-ing CXCL5, MARCO, FCER1G, RAC2, HCK.Their expression values in normal and keratitisstates suggested that they were enhanced mark-edly in keratitis group when compared with nor-mal group (Fig. 4, P < 0.05), accordingly, the heatmap of hub genes expression levels in twogroups were exhibited in Figure 5. These hubgenes were shown to be higher expressed inkeratitis group on comparing normal group.
DISCUSSION
In the current study, the gene expressionmatrix with 14832 genes was gained through datapreprocessing and then 278 pathways were ob-tained via KEGG enrichment analysis. Moreover,26 significant pathways were chose by Gibbssampling. Furthermore, 5 hub genes werescreened by analyzing pathway gene set usingGibbs sampling. These results demonstrated thatidentified key pathways and hub genes wouldprovide valuable information on the progress ofmicrobial keratitis and offer new insights for in-vestigating molecule mechanisms potentiallyinvolved in the microbial keratitis.
Microbial keratitis is recognized as the lead-ing eye-threatening disease of keratitis, charac-terised by the presence of white/yellowish infil-trates in the corneal stroma, with/without anoverlaying corneal epithelial defect, and relatedwith strong signs of inflammation (Upadhyay etal. 2015), which caused considerable inconve-nience to patients. In an effort to uncover theunderlying molecular mechanisms that drive themicrobial keratitis development, more and moreresearchers have spared no efforts to carry outexperiments. It was suggested that activity ofToll-like receptors (TLRs) signaling resulting inthe activation of nuclear factor-kB (NF-kB) andproduction of proinflammatory cytokines likeTNF-α, enable to trigger the earliest immune re-sponses that lead to inflammation in ocular im-munology (Pandey et al. 2013). Beyond that,A
sthm
a23
HL
A-D
MA
;HL
A-D
MB
;HL
A-D
OA
;HL
A-D
OB
;HL
A-D
PA1;
HL
A-D
PB1;
HL
A-D
QA
1;H
LA
-D
QA
2;H
LA
-DQ
B1
;HL
A-D
RA
;HL
A-D
RB
1;H
LA
-DR
B3
;HL
A-D
RB
4;H
LA
-D
RB
5;C
D40
LG;C
D40
;FC
ER1A
;MS4
A2;
FCER
1G;I
L10;
CC
L11;
TNF;
PRG
2A
moe
bias
is92
IL1B
;IL1
R1;
IL1R
2;N
FKB
1;R
ELA
;HSP
B1;
CO
L1A
1;C
OL1
A2;
CO
L3A
1;C
OL5
A1;
CO
L5A
2;C
OL1
1A 1
;CO
L11A
2; C
OL5
A3;
CO
L24A
1; C
OL4
A2;
CO
L4A
4; C
OL4
A6;
CO
L4A
1; C
OL4
A5;
CO
L4A
3; F
N1;
LAM
A1;
LAM
A2;
LA
MA
3;LA
MA
5;
LAM
A4
;LA
MB
1 ;L
AM
B2
;LA
MB
3;L
AM
B4;
LA
MC
1;L
AM
C2;
LA
MC
3;C
ASP
3; G
NA
Q;G
NA
11;
GN
A14
; G
NA
15;P
LC
B1;
PLC
B2;
PLC
B4;
PR K
CA
; PR
KC
B;G
NA
S; G
NA
L;PR
KA
CB
; PR
KX
;RA
B5A
; R
AB
5B;R
AB
5C;
RA
B7A
;R A
B7B
; TL
R2;
TLR
4; C
D14
; IL
6;C
SF2;
CX
CL8
;TN
F;IF
NG
;PTK
2;V
CL;
AC
TN 1
;A
CT
N4;
A
RG
2;A
RG
1;
NO
S2;I
TG
B2;
ITG
AM
;PIK
3R1;
P IK
3R5;
PI
K3R
2;PI
K3R
3;P
IK3C
A;P
IK3C
D;P
IK
3CB
; PI
K3C
G;S
ERPI
NB
1; S
ER P
INB
2; S
ERPI
NB
3; S
ERPI
NB
4;SE
RPI
NB
6;
SER
PIN
B9;
SER
PIN
B13
; C
TSG
;IL10
;TG
FB2;
TG
FB3;
C8A
;CX
CL1
; C
D1D
Tabl
e 1:
Con
td...
Pat
hway
Num
ber
Mem
ber
146 QIAO-LING WANG, MENG-HUI ZHANG AND XI CHEN
Fig.
2.
Hea
t m
ap o
f th
e to
p 26
sig
nifi
cant
pat
hway
s. R
ed:
high
exp
ress
ion
leve
l; G
reee
n: l
ower
exp
ress
ion
leve
l.So
urce
: A
utho
r
hsa0
5330
: A
llogr
aft
reje
hsa0
5320
: A
utoi
mm
une
hsa0
5150
: St
aphy
loco
ccus
has0
5310
: Ast
hma
hsa0
5332
: G
raft-
vers
ushs
a049
40: T
ype
I di
abet
hsa0
5140
: Le
ishm
atio
rhs
a053
21:
Infla
mm
afor
hsa0
5416
: V
iral
myo
car
hsa0
5164
: Inf
luen
za A
hsa
0515
2: T
uber
culo
sis
hsa0
4380
: Ost
eocl
ast d
ihs
a046
12: A
ntig
en p
roc
hsa0
5133
: Per
tuss
ishs
a053
23: R
heum
atoi
dhs
a041
45:
Phag
osm
ome
hsa0
4064
: N
F-ka
ppa
Bhs
a046
20: T
oll-l
ike
rece
hsa0
4668
: TN
F si
gnal
inhs
a051
46: A
moe
bias
ishs
a046
50: N
atur
al k
iller
hsa0
4062
: Che
mok
ine
hsa0
5322
: Sys
tem
ic lu
phs
a046
72: I
ntes
tinal
imr
hsa0
4640
: H
emat
opoi
eths
a040
60: C
ytok
ine-
cyk
HUB GENES IN MICROBIAL KERATITIS 147
Fig.
3. T
he p
roba
bilit
ies
dist
ribu
tion
of 1
167
diff
eren
tial
path
way
gen
e se
t. T
he X
axi
s de
note
d th
e di
ffer
entia
l pa
thw
ay g
ene
set,
and
the
Y a
xis
dent
edth
e po
ster
ior
valu
e of
the
dif
fere
ntia
l pa
thw
ay g
enes
. A.
The
adj
uste
d po
ster
ior
valu
e di
stri
buti
on o
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148 QIAO-LING WANG, MENG-HUI ZHANG AND XI CHEN
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HUB GENES IN MICROBIAL KERATITIS 149
activation of TLR2 and TLR4 through NF-kap-paB could contribute to pathogenesis of kerato-mycosis (Jie et al. 2009). In addition, Toll-likereceptor 4 signalling pathway was activated in arat model of Acanthamoeba keratitis (Ren andWu 2011). TNF-α and IL-6 was reported to facil-itate corneal lymphangiogenesis during acuteHSV-1 infection (Bryant-Hudson et al. 2014). Con-
sistent with this. This study demonstrated that aseries of inflammation signaling pathways, suchas NF-kappa B signaling, TNF signaling path-way, Toll-like receptor signaling pathway wereidentified using bioinformatics measurement.
Previous research demonstrated that kerati-tis was associated with longstanding rheuma-toid arthritis, besides, morbidity and mortality
Fig. 5. Heat map of the top 5 hub genes. Red: high expression level; Greeen: lower expression level.Source: Author
150 QIAO-LING WANG, MENG-HUI ZHANG AND XI CHEN
of which were increasingly improved (Domnga-ng Noche et al. 2016; Lee et al. 2016; Petrushkinet al. 2016). HLA-DR expression was reported tobe considered as a biomarker of inflammationfor multicenter clinical trials of ocular surfacedisease (Epstein et al. 2013). Accumulating evi-dence showed that peripheral ulcerative kerati-tis was associated with tuberculosis in a child(Al-Mendalawi 2016), mycobacterium tubercu-losis may lead to formation of interstitial kerati-tis (Gupta et al. 2015). Cytokines and chemok-ines served as small proteins played an impor-tant proinflammatory or anti-inflammatory rolein modulating the herpes simplex keratitis (Azheret al. 2017). It is reported that chemokine CXCL10inhibition of hem- and lymph-angiogenesisemerged in inflamed corneas (Gao et al. 2017). Ithas also reported that IL-8, IL-6 and IL-1â ex-pressions were increased in tears samples ofpatients with microbial keratitis compared withnegative normal (Santacruz et al. 2015). The im-portance of long-lasting Ag presentation in in-ducing peripheral T cell tolerance was also de-termined in the model of herpes stromal keratitisautoimmune disease (Raimondi et al. 2006). Thus,in line with above evidence, results of this studydetermined that Rheumatoid arthritis pathway,Tuberculosis pathway, chemokine signalingpathway, Staphylococcus aureus infection sig-naling pathway were selected.
Based on Gibbs sampling, several hub geneslike RAC2, MARCO, CXCL5, HCK, FCER1Gwere identified and these key genes may con-tribute to predict, monitor and even treat micro-bial keratitis. Lin et al demonstrated that CXCL5/lipopolysaccharide (LPS)-induced chemokinemediated neutrophil recruitment into the corneaduring LPS keratitis (Lin et al. 2007). A previousinvestigation determined that CXCL5 as a pro-inflammatory chemokine was downregulated inmice corneal with alkali burns after treated withtofacitinib (Sakimoto and Ishimori 2016). Sweetet al demonstrated that the presence of FcR com-mon γ-chain (Fcer1g) or/and MyD88 were re-sponsible for proinflammatory responses to ex-ogenous antigens while the absence of themreduced extrafollicular plasmablast response(Sweet and Nickerson 2017). It is suggested thatLck/Hck/Fgr triple knockout enhanced antiviralsensing and resistance substantially while ec-topic expression of them dampened cells antivi-ral defense (Liu et al. 2017). Nonetheless, thisstudy is only a bioinformatics screening for biom-
arkers in microbial keratitis preliminarily and fur-ther in-depth investigations in molecular patho-genesis and validations with several experimentsare still demanded.
CONCLUSION
Collectively, this study found out several keypathways associated with microbial keratitisbased on bioinformatics method, accordingly,monitoring these signaling pathways might aidprediction or treatment of microbial keratitis oc-currence and development. Importantly, hubgenes in microbial keratitis, namely, RAC2, MAR-CO, CXCL5, HCK, FCER1G were identified onthe basis of pathway gene set using Gibbs sam-pling, which were likely to be prognostic anddiagnostic implications of microbial keratitis.
RECOMMENDATIONS
Findings from the present study will providethe molecular basis for the understanding ofmicrobial keratitis pathogenesis, implying a novelstrategy for relieving the burden of microbialkeratitis.
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Paper received for publication on March 2018Paper accepted for publication on May 2018