Comparison of gene expression profiling between
lung fibrotic and emphysematous tissues sampled
from patients with combined pulmonary fibrosis
and emphysema
Masayuki Hanaoka*, Michiko Ito, Yunden Droma, Atsuhito Ushiki, Yoshiaki
Kitaguchi, Masanori Yasuo, Keishi Kubo
First Department of Medicine, Shinshu University School of Medicine, 3-1-1 Asahi,
Matsumoto, Japan
*Corresponding author
E-mail addresses: masayuki@shinshu-u.ac.jp
Data deposition: The data reported in this paper have been deposited in the Gene
Expression Omnibus database:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38934
Additional file 1:
Table S1. One hundred and forty genes with signal log ratio over 1 were overexpressed
in lung tissues with fibrotic lesions versus tissues with emphysematous lesions
Table S1. One hundred and forty genes with signal log ratio over 1 were overexpressed in lung tissues with fibrotic lesions versus
tissues with emphysematous lesions
Probe Name*
SLR†
P-value‡
Gene Title
Gene
Symbol
Chromosomal
Location
Gene Ontology Molecular
Function
structural constituent of
201820_at
2.7
2.0.E-05 keratin 5
KRT5
chr12q12-q13
204136_at
1.7
8.4.E-05 collagen, type VII, alpha 1
COL7A1
chr3p21.1
204259_at
2.5
MMP7
chr11q21-q22
204268_at
3.3
S100A2
chr1q21
calcium ion binding
204269_at
1.4
4.9.E-05 matrix metallopeptidase 7
S100 calcium binding
2.0.E-05
protein A2
9.4.E-05 pim-2 oncogene
cytoskeleton
G-protein-coupled receptor
binding
metalloendopeptidase activity
PIM2
chrXp11.23
nucleotide binding
204455_at
1.9
DST
chr6p12.1
204469_at
1.9
PTPRZ1
chr7q31.3
204475_at
4.1
MMP1
chr11q22.3
actin binding
phosphoprotein phosphatase
activity
metalloendopeptidase activity
204532_x_at
2.3
7.5.E-05 dystonin
protein tyrosine
4.7.E-04
phosphatase,
2.0.E-05 matrix metallopeptidase 1
UDP
6.6.E-04 glucuronosyltransferase 1
family, polypeptide A1
UGT1A1
chr2q37
204734_at
2.9
2.9.E-05 keratin 15
KRT15
chr17q21.2
204855_at
2.8
4.4.E-05
SERPINB5
chr18q21.3
serpin peptidase inhibitor,
clade B (ovalbumin),
glucuronosyltransferase
activity
structural constituent of
cytoskeleton
serine-type endopeptidase
inhibitor activity
member 5
205157_s_at
1.7
2.0.E-05 keratin 17
205267_at
2.2
2.6.E-05
205513_at
2.2
205901_at
1.4
205903_s_at
1.5
205997_at
1.8
206032_at
206033_s_at
2.1
2.2
206094_x_at
2.4
206121_at
1.7
206150_at
206165_s_at
1.3
2.4
POU class 2 associating
factor 1
transcobalamin I (vitamin
2.3.E-05 B12 binding protein, R
binder family)
6.7.E-04 prepronociceptin
potassium intermediate
4.4.E-04 calcium-activated channel,
subfamily N, member 3
ADAM metallopeptidase
3.1.E-05
domain 28
2.1.E-04 desmocollin 3
6.0.E-05 desmocollin 3
UDP
9.4.E-05 glucuronosyltransferase 1
family, polypeptide A1
adenosine monophosphate
7.6.E-05
deaminase 1 (isoform M)
3.8.E-05 CD27 molecule
8.8.E-05 chloride channel accessory 2
KRT17
chr17q12-q21
structural constituent of
cytoskeleton
POU2AF1
chr11q23.1
DNA binding
cobalt ion transmembrane
TCN1
chr11q11-q12
PNOC
chr8p21
transporter activityinferred
from electronic annotation
opioid peptide activity
KCNN3
chr1q21.3
ion channel activity
ADAM28
chr8p21.2
metalloendopeptidase activity
DSC3
DSC3
chr18q12.1
chr18q12.2
calcium ion binding
calcium ion binding
UGT1A1
chr2q37
UDP-glycosyltransferase
activity
AMPD1
chr1p13
AMP deaminase activity
CD27
CLCA2
chr12p13
chr1p31-p22
receptor activity
chloride channel activity
206276_at
3.8
206478_at
206513_at
2.3
1.2
206641_at
2.0
lymphocyte antigen 6
complex, locus D
4.3.E-05 KIAA0125
3.7.E-04 absent in melanoma 2
tumor necrosis factor
3.6.E-05 receptor superfamily,
6.5.E-05
206686_at
1.4
207126_x_at
2.9
207734_at
1.3
208153_s_at
1.8
208269_s_at
1.4
208596_s_at
2.7
member 17
pyruvate dehydrogenase
1.2.E-03
kinase, isozyme 1
UDP
2.3.E-04 glucuronosyltransferase 1
family, polypeptide A1
lymphocyte transmembrane
8.2.E-05
adaptor 1
FAT tumor suppressor
2.4.E-04
homolog 2 (Drosophila)
ADAM metallopeptidase
7.6.E-04
domain 28
UDP
1.4.E-04 glucuronosyltransferase 1
2.6
1.3
family, polypeptide A1
3.9.E-05 keratin 6A
3.9.E-05 immunoglobulin heavy
209125_at
209374_s_at
LY6D
chr8q24-qter
protein binding
KIAA0125
AIM2
chr14q32.33
chr1q22
--protein binding
TNFRSF17
chr16p13.1
receptor activity
PDK1
chr2q31.1
two-component sensor activity
UGT1A1
chr2q37
glucuronosyltransferase
activity
LAX1
chr1q32.1
FAT2
chr5q32-q33
calcium ion binding
ADAM28
chr8p21.2
metalloendopeptidase activity
UGT1A1
chr2q37
KRT6A
IGHM
chr12q12-q13
chr14q32.33
protein binding
UDP-glycosyltransferase
activity
structural molecule activity
antigen binding
209863_s_at
209875_s_at
1.6
2.3
constant mu
5.6.E-05 tumor protein p63
2.0.E-05 secreted phosphoprotein 1
210387_at
1.7
1.2.E-04 histone cluster 1, H2bg
TP63
SPP1
HIST1H2B
G
chr3q28
chr4q21-q25
DNA binding
cytokine activity
chr6p21.3
DNA binding
IGHG1
chr14q32.33
antigen binding
IGHM
chr14q32.33
antigen binding
chr14q32.33
antigen binding
GHA0
chr14q32.33
antigen binding
GHA1
chr14q32.33
antigen binding
IGHG1
chr14q32.33
antigen binding
IGHA1
chr14q32.33
antigen binding
IGHA2
chr2p11.2
antigen binding
Immunoglobulin heavy
211633_x_at
1.8
211634_x_at
2.2
211635_x_at
2.3
211637_x_at
2.0
211639_x_at
1.7
211640_x_at
2.4
211641_x_at
1.6
211643_x_at
1.9
5.6.E-05 constant gamma 1 (G1m
marker)
immunoglobulin heavy
3.0.E-05
constant
immunoglobulin heavy
1.7.E-04
locus
immunoglobulin heavy
2.6.E-04
locus
immunoglobulin heavy
1.4.E-04
locus
immunoglobulin heavy
1.5.E-04 constant gamma 1 (G1m
marker)
immunoglobulin heavy
9.2.E-05
locus
immunoglobulin kappa
2.0.E-05
locus
IGHA1
211644_x_at
1.9
211645_x_at
1.8
211650_x_at
1.8
211798_x_at
1.8
211868_x_at
1.5
211881_x_at
2.0
211908_x_at
1.9
immunoglobulin kappa
locus
2.0.E-05 --immunoglobulin heavy
4.9.E-05
constant alpha 1
immunoglobulin lambda
5.5.E-05
joining 3
immunoglobulin heavy
5.2.E-04
locus
immunoglobulin lambda
5.2.E-05
joining 3
Immunoglobulin heavy
4.3.E-04 constant gamma 1 (G1m
2.0.E-05
212236_x_at
214580_x_at
1.4
3.5
2.4.E-05
6.0.E-04
214768_x_at
1.9
2.1.E-05
214777_at
1.4
2.0.E-05
214916_x_at
1.6
2.4.E-05
214973_x_at
1.8
marker)
keratin 17
keratin 6A
Family with sequence
similarity 20, member B
immunoglobulin kappa
variable 4-1
immunoglobulin heavy
locus
2.0.E-05 immunoglobulin heavy
IGHA2
chr2p11.2
antigen binding
---
---
---
IGHA1
chr14q32.33
IGLJ3
chr22q11.1-q11.
2
antigen binding
---
IGHA1
chr14q32.33
antigen binding
IGLJ3
chr22q11.1-q11.
2
---
IGHG1
chr14q32.33
antigen binding
KRT17
KRT6A
chr17q12-q21
chr12q12-q13
structural molecule activity
structural molecule activity
FAM20B
chr1q25
---
IGKV4-1
chr2p12
antigen binding
chr14q32.33
antigen binding
chr14q32.33
antigen binding
IGHA1
IGHD
215035_at
2.7
215118_s_at
1.5
constant delta
immunoglobulin lambda
5.9.E-04
variable 6-57
Immunoglobulin heavy
5.7.E-04 constant gamma 1 (G1m
marker)
215125_s_at
3.5
UDP
3.7.E-04 glucuronosyltransferase 1
family, polypeptide A1
215176_x_at
1.4
2.0.E-05 similar to hCG26659
215214_at
2.2
2.0.E-05
215565_at
2.0
1.9.E-04
215777_at
1.4
215949_x_at
1.5
216207_x_at
1.5
216365_x_at
2.3
Immunoglobulin lambda
locus
hypothetical protein
LOC100289053
immunoglobulin lambda
8.9.E-05
variable 4-60
immunoglobulin heavy
6.1.E-05
constant
immunoglobulin kappa
3.0.E-05
constant
immunoglobulin lambda
2.0.E-05
locus
IGLV6-57
chr22q11.2
---
IGHG1
chr14q32.33
antigen binding
UGT1A1
chr2q37
UDP-glycosyltransferase
activity
LOC100291
--464
chr22q11.1-q11.
IGL@
2
antigen binding
---
LOC100289
chr2p23.3
053
calcium ion binding
IGLV4-60
chr22q11.2
---
IGHM 4
chr14q32.33
antigen binding
IGKC
chr2p12
antigen binding
IGL@
chr22q11.1-q11.
2
---
216401_x_at
1.8
216412_x_at
2.5
216430_x_at
2.2
216491_x_at
2.1
216510_x_at
1.9
216541_x_at
2.3
216542_x_at
1.8
216557_x_at
1.8
216560_x_at
2.3
216576_x_at
1.8
216853_x_at
2.1
similar to Ig kappa chain
LOC652493 --V-I region HK102 precursor
immunoglobulin lambda
chr22q11.1-q11.
2.5.E-05
IGL@
locus
2
immunoglobulin lambda
chr22q11.1-q11.
1.9.E-04
IGL@
locus
2
3.1.E-05
immunoglobulin heavy
constant
immunoglobulin heavy
2.0.E-04
constant alpha 1
immunoglobulin heavy
3.9.E-04 constant gamma 1 (G1m
marker)
2.5.E-04
immunoglobulin heavy
constant alpha 1
immunoglobulin heavy
6.0.E-05
constant alpha 1
immunoglobulin lambda
2.7.E-05
locus
immunoglobulin kappa
4.1.E-05
locus
immunoglobulin lambda
3.1.E-05
variable 3-19
2.1.E-04
antigen binding
-----
IGHM
chr14q32.33
antigen binding
IGHA1
chr14q32.33
antigen binding
IGHG1
chr14q32.33
antigen binding
IGHA1
chr14q32.33
antigen binding
IGHA1
chr14q32.33
antigen binding
IGL@
chr22q11.1-q11.
2
---
IGK@
chr2p12
antigen binding
IGLV3-19
chr22q11.2
---
immunoglobulin lambda
locus
immunoglobulin heavy
6.5.E-04
constant alpha 1
216984_x_at
1.7
7.6.E-05
217084_at
2.1
217148_x_at
1.9
2.0.E-05 similar to Ig lambda chain
217157_x_at
1.6
3.5.E-05
217179_x_at
2.0
217198_x_at
1.7
217227_x_at
1.9
217235_x_at
1.9
217258_x_at
2.4
217281_x_at
1.9
217378_x_at
1.7
6.0.E-05 similar to hCG26659
217384_x_at
2.3
4.4.E-04
immunoglobulin kappa
locus
2.8.E-05 --immunoglobulin heavy
3.4.E-04
locus
immunoglobulin lambda
2.0.E-05
locus
immunoglobulin lambda
locus
immunoglobulin lambda
2.0.E-05
locus
immunoglobulin heavy
2.3.E-05
locus
2.5.E-05
immunoglobulin heavy
variable 3-23
IGL@
chr22q11.1-q11.
2
---
IGHA1
chr14q32.33
antigen binding
LOC100293
--440
---
IGK@
chr2p12
antigen binding
---
---
antigen binding
IGH@
chr14q32.33
antigen binding
IGL@
chr22q11.1-q11.
2/
---
IGL@
IGL@
IGH@
LOC100130
100
IGHV3-23
chr22q11.1-q11.
2
chr22q11.1-q11.
2
-----
chr14q32.33
antigen binding
chr2q13
---
chr14q32.33
antigen binding
LOC100287
chr10q11.21
723
chloride channel accessory 2 CLCA2
chr1p31-p22
chemokine (C-X-C motif)
CXCL14
chr5q31
ligand 14
gremlin 1, cysteine knot
GREM1
chr15q13-q15
superfamily, homolog
gremlin 1, cysteine knot
GREM1
chr15q13-q15
superfamily, homolog
transmembrane protease,
TMPRSS4
chr11q23.3
serine 4
FK506 binding protein 11,
FKBP11
chr12q13.12
19 kDa
217480_x_at
1.7
3.5.E-05 similar to Ig kappa chain
---
217528_at
3.6
1.5.E-04
chloride channel activity
218002_s_at
2.2
3.6.E-05
218468_s_at
1.7
2.0.E-05
218469_at
1.6
2.0.E-05
218960_at
2.8
2.9.E-04
219118_at
1.4
2.0.E-05
219159_s_at
1.7
219936_s_at
2.5
220306_at
1.5
220338_at
1.3
4.0.E-04 SLAM family member 7
G protein-coupled receptor
1.4.E-04
87
family with sequence
6.2.E-05
similarity 46, member C
Ral GEF with PH domain
3.4.E-04
and SH3 binding motif 2
221286_s_at
2.1
222068_s_at
2.6
hypothetical protein
MGC29506
3.6.E-05 leucine rich repeat
3.4.E-05
cytokine activity
cytokine activity
cytokine activity
catalytic activity
peptidyl-prolyl cis-trans
isomerase activity
SLAMF7
chr1q23.1-q24.1
receptor activity
GPR87
chr3q24
signal transducer activity
FAM46C
chr1p12
---
RALGPS2
chr1q25.2
guanyl-nucleotide exchange
factor activity
MGC29506
chr5q23-q31
---
LRRC50
chr16q23.3-q24.
protein binding
222484_s_at
2.3
222549_at
222838_at
1.2
1.6
223565_at
2.1
224342_x_at
1.9
224404_s_at
224406_s_at
2.0
1.5
226150_at
1.1
226452_at
1.5
227224_at
1.4
229147_at
1.7
229656_s_at
1.5
229721_x_at
1.8
containing 50
chemokine (C-X-C motif)
2.0.E-05
ligand 14
2.2.E-05 claudin 1
2.0.E-05 SLAM family member 7
hypothetical protein
2.1.E-05
MGC29506
immunoglobulin lambda
2.0.E-05
locus
2.0.E-05 Fc receptor-like 5
7.1.E-04 Fc receptor-like 5
phosphatidic acid
2.8.E-05 phosphatase type 2 domain
containing 1B
pyruvate dehydrogenase
2.4.E-05
kinase, isozyme 1
Ral GEF with PH domain
2.7.E-05
and SH3 binding motif 2
1.3.E-04 --echinoderm microtubule
1.9.E-04
associated protein like 6
Der1-like domain family,
2.0.E-05
member 3
1
CXCL14
chr5q31
cytokine activity
CLDN1
SLAMF7
chr3q28-q29
chr1q23.1-q24.1
structural molecule activity
receptor activity
MGC29506
chr5q23-q31
---
IGL@
FCRL5
FCRL5
chr22q11.1-q11.
2
chr1q21
chr1q21
antigen binding
receptor activity
receptor activity
PPAPDC1B chr8p11.23
catalytic activity
PDK1
chr2q31.1
two-component sensor activity
RALGPS2
chr1q25.2
---
---
guanyl-nucleotide exchange
factor activity
---
EML6
chr2p16.2-p16.1
---
DERL3
chr22q11.23
protein binding
230030_at
1.7
230128_at
3.2
231145_at
231647_s_at
2.2
2.4
233413_at
3.4
233463_at
2.4
234366_x_at
1.7
234390_x_at
3.1
234419_x_at
2.3
234477_at
3.1
234764_x_at
2.0
234792_x_at
2.8
heparan sulfate
6-O-sulfotransferase 2
Immunoglobulin lambda
2.3.E-04
locus
3.5.E-04 --2.0.E-05 Fc receptor-like 5
6.9.E-05
HS6ST2
chrXq26.2
sulfotransferase activity
--FCRL5
chr22q11.1-q11.
2
--chr1q21
4.8.E-05 --Ras association
1.2.E-04 (RalGDS/AF-6) domain
family member 6
immunoglobulin lambda
2.2.E-05
locus
Immunoglobulin heavy
---
---
---
RASSF6
chr4q13.3
protein binding
IGL@
chr22q11.1-q11.
2
---
2.1.E-04 constant gamma 1 (G1m
marker)
immunoglobulin heavy
1.7.E-04
locus
immunoglobulin heavy
4.5.E-04
constant alpha 1
Immunoglobulin lambda
2.1.E-05
variable 1-44
immunoglobulin heavy
2.9.E-04
constant alpha 1
IGHG1
chr14q32.33
antigen binding
IGH@
chr14q32.33
antigen binding
IGHA1
chr14q32.33
antigen binding
IGLV1-44
chr22q11.2
---
IGHA1
chr14q32.33
antigen binding
IGL@
----receptor activity
234884_x_at
1.9
235075_at
3.6
242680_at
1552797_s_at
1.8
2.2
1556183_at
1557383_a_at
1.7
1.6
1558290_a_at
1.2
1561937_x_at
1.4
1568868_at
1.8
1569040_s_at
2.0
Immunoglobulin lambda
locus
desmoglein 3 (pemphigus
2.9.E-05
vulgaris antigen)
2.9.E-04 --3.3.E-05 prominin 2
--PROM2
chr22q11.1-q11.
2
chr18q12.1-q12.
2
--chr2q11.1
8.0.E-05 hypothetical LOC645784
4.0.E-05 --Pvt1 oncogene (non-protein
2.1.E-04
coding)
immunoglobulin heavy
3.1.E-05
constant alpha 1
cytochrome P450, family
FLJ40330
---
chr2p11.2
---
-----
PVT1
chr8q24
---
IGHA1
chr14q32.33
antigen binding
9.9.E-04 27, subfamily C,
polypeptide 1
2.0.E-05 hypothetical LOC645784
CYP27C1
chr2q14.3
monooxygenase activity
FLJ40330
chr2p11.2
---
1.4.E-03
IGL@
DSG3
--calcium ion binding
-----
*
Probe name in Affymetrix.
†
SLR = signal log ratio. The SLR algorithm measures the magnitude and direction of the change between signal levels of the fibrotic
lesions versus emphysematous lesions.
‡
The significance of the signal changes between the fibrotic lesions versus emphysematous lesions. For example, P=2.0.E-05 indicates
P= 2.0 x 10-5.
--- Unknown or undetected.