Transcriptome-wide analysis of blood vessels laser captured from human skin and chronic wound-edge tissue
Roy et al. 10.1073/pnas.0706793104.
Supporting Information
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SI Table 1SI Table 2
SI Figure 7
SI Table 3
SI Figure 8
Fig. 7. Protocol for tissue sectioning, staining, and LMPC. Outline of protocols and procedures used for sectioning, staining, and LMPC capture of blood vessels from human wound tissue.
Fig. 8. GeneChip data analysis scheme used to identify differentially expressed genes in wound blood vessels vs. skin blood vessels. Image acquisition and processing was performed by using GCOS (GeneChip operating software; Affymetrix). GC-RMA was applied for data normalization and background correction. ArrayAssist software, Version 5.1 was used to identify significant (P < 0.05; FDR corrected) differentially expressed genes in wound vessels compared to skin vessels captured using LMPC. Details of software and other resources for data analysis have been provided in Materials and Methods in the main text. , increase; ¯, decrease in wound vessels vs. skin vessels
Table 1. Genes upregulated in wound vessels compared to skin vessels
|
Probe ID |
Abbreviation |
Description |
Mean |
SD |
P |
|
210809_s_at |
POSTN |
Periostin |
96.3 |
27.8 |
0.04 |
|
212354_at |
SULF1 |
Sulfatase 1 |
42.3 |
17.8 |
0.05 |
|
204368_at |
SULF1 |
Solute carrier organic anion transporter family, member 2A1 |
38.9 |
18.8 |
0.05 |
|
211980_at |
COL4A1 |
Collagen, type IV, alpha 1 |
37.5 |
4.2 |
0.05 |
|
209728_at |
HLA-DRB4 |
Major histocompatibility complex, class II |
31.4 |
3.3 |
0.00 |
|
205303_at |
KCNJ8 |
Potassium inwardly-rectifying channel |
26.7 |
7.3 |
0.05 |
|
208850_s_at |
THY1 |
Thy-1 cell surface antigen |
23.8 |
6.3 |
0.05 |
|
212624_s_at |
CHN1 |
Chimerin 1 |
23.6 |
7.2 |
0.05 |
|
214081_at |
PLXDC1 |
Plexin domain containing 1 |
23.4 |
7.7 |
0.05 |
|
219700_at |
PLXDC1 |
Plexin domain containing 1 |
19.6 |
1.3 |
0.00 |
|
220122_at |
MCTP1 |
Multiple C2 domains, transmembrane 1 |
19.0 |
1.9 |
0.05 |
|
221730_at |
COL5A2 |
Collagen, type V, alpha 2 |
18.3 |
2.6 |
0.05 |
|
211161_s_at |
COL3A1 |
Collagen, type III, alpha 1 |
17.7 |
2.2 |
0.05 |
|
201666_at |
TIMP1 |
TIMP metallopeptidase inhibitor 1 |
16.9 |
4.0 |
0.05 |
|
201289_at |
CYR61 |
Cysteine-rich, angiogenic inducer, 61 |
15.2 |
4.4 |
0.05 |
|
217762_s_at |
RAB31 |
RAB31, member RAS oncogene family |
13.7 |
1.1 |
0.05 |
|
205656_at |
PCDH17 |
Protocadherin 17 |
13.1 |
3.2 |
0.05 |
|
221729_at |
COL5A2 |
Collagen, type V, alpha 2 |
13.1 |
2.4 |
0.03 |
|
203186_s_at |
S100A4 |
S100 calcium binding protein A4 |
12.3 |
2.6 |
0.05 |
|
205120_s_at |
SGCB |
Sarcoglycan, beta |
11.4 |
0.9 |
0.00 |
|
215785_s_at |
CYFIP2 |
Cytoplasmic FMR1 interacting protein 2 |
11.1 |
0.2 |
0.00 |
|
211981_at |
COL4A1 |
Collagen, type IV, alpha 1 |
11.0 |
2.0 |
0.04 |
|
213001_at |
ANGPTL2 |
Angiopoietin-like 2 |
10.8 |
3.3 |
0.05 |
|
212314_at |
KIAA0746 |
KIAA0746 protein |
10.7 |
1.4 |
0.04 |
|
204475_at |
MMP1 |
Matrix metallopeptidase 1 (interstitial collagenase) |
10.2 |
2.2 |
0.05 |
|
201744_s_at |
LUM |
Lumican |
9.1 |
2.6 |
0.05 |
|
212822_at |
HEG1 |
HEG homolog 1 (zebrafish) |
8.5 |
1.3 |
0.04 |
|
201060_x_at |
STOM |
Stomatin |
8.4 |
1.4 |
0.04 |
|
204620_s_at |
CSPG2 |
Chondroitin sulfate proteoglycan 2 (versican) |
8.2 |
1.4 |
0.05 |
|
206700_s_at |
SMCY |
Smcy homolog, Y-linked (mouse) |
6.5 |
1.1 |
0.05 |
|
202701_at |
BMP1 |
Bone morphogenetic protein 1 |
5.9 |
1.2 |
0.05 |
|
205932_s_at |
MSX1 |
msh homeobox homolog 1 (Drosophila) |
5.1 |
0.8 |
0.04 |
|
200982_s_at |
ANXA6 |
annexin A6 |
4.5 |
0.6 |
0.04 |
|
206133_at |
BIRC4BP |
XIAP associated factor-1 |
4.4 |
0.7 |
0.05 |
|
205572_at |
ANGPT2 |
Angiopoietin 2 |
4.3 |
0.2 |
0.05 |
|
204677_at |
CDH5 |
Cadherin 5, type 2, VE-cadherin (vascular epithelium) |
4.3 |
0.2 |
0.04 |
|
204595_s_at |
STC1 |
Stanniocalcin 1 |
4.2 |
0.4 |
0.05 |
|
52255_s_at |
COL5A3 |
Collagen, type V, alpha 3 |
3.8 |
0.4 |
0.04 |
|
202269_x_at |
GBP1 |
Guanylate binding protein 1, interferon-inducible |
3.8 |
0.5 |
0.05 |
|
204026_s_at |
ZWINT |
ZW10 interactor |
3.7 |
0.4 |
0.05 |
|
206857_s_at |
FKBP1B |
FK506 binding protein 1B |
3.6 |
0.3 |
0.04 |
|
204114_at |
NID2 |
Nidogen 2 (osteonidogen) |
3.5 |
0.6 |
0.05 |
|
210510_s_at |
NRP1 |
Neuropilin 1 |
3.5 |
0.3 |
0.05 |
|
205479_s_at |
PLAU |
Plasminogen activator, urokinase |
3.4 |
0.4 |
0.04 |
|
221737_at |
GNA12 |
Guanine nucleotide binding protein (G protein) alpha 12 |
3.3 |
0.4 |
0.05 |
|
213249_at |
FBXL7 |
F-box and leucine-rich repeat protein 7 |
3.1 |
0.2 |
0.05 |
|
200788_s_at |
PEA15 |
Phosphoprotein enriched in astrocytes 15 |
2.7 |
0.3 |
0.05 |
|
202860_at |
DENND4B |
DENN/MADD domain containing 4B |
2.6 |
0.3 |
0.05 |
|
213115_at |
ATG4A |
ATG4 autophagy related 4 homolog A (S. cerevisiae) |
2.6 |
0.3 |
0.05 |
|
202719_s_at |
TES |
Testis derived transcript (3 LIM domains) |
2.6 |
0.1 |
0.03 |
|
210619_s_at |
HYAL1 |
Hyaluronoglucosaminidase 1 |
2.2 |
0.2 |
0.05 |
|
200686_s_at |
SFRS11 |
Splicing factor, arginine/serine-rich 11 |
2.0 |
0.1 |
0.05 |
|
217788_s_at |
GALNT2 |
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2) |
1.8 |
0.0 |
0.04 |
Data presented indicate fold-change (mean ± SD) in gene expression. Probe ID, Affymetrix probe identifications.
Table 2. Genes downregulated in wound vessels compared to skin vessels
|
Probe ID |
Abbreviation |
Description |
Mean |
SD |
P |
|
209351_at |
KRT14 |
Keratin 14 |
1149.5 |
356.1 |
0.05 |
|
206378_at |
SCGB2A2 |
Secretoglobin, family 2A, member 2 |
944.3 |
2.4 |
0.05 |
|
202037_s_at |
SFRP1 |
Secreted frizzled-related protein 1 |
273.9 |
26.5 |
0.04 |
|
202935_s_at |
SOX9 |
SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) |
148.3 |
96.9 |
0.05 |
|
204734_at |
KRT15 |
Keratin 15 |
130.8 |
11.6 |
0.04 |
|
219476_at |
C1orf116 |
Chromosome 1 open reading frame 116 |
110.7 |
26.0 |
0.03 |
|
LOC653098 |
similar to chromosome 1 open reading frame 116 |
||||
|
200606_at |
DSP |
Desmoplakin |
93.0 |
15.2 |
0.05 |
|
216379_x_at |
CD24 |
CD24 molecule |
88.3 |
4.0 |
0.05 |
|
201243_s_at |
ATP1B1 |
ATPase, Na+/K+ transporting, beta 1 polypeptide |
87.4 |
7.0 |
0.04 |
|
203074_at |
ANXA8 |
Annexin A8 |
87.1 |
0.9 |
0.05 |
|
LOC653107 |
annexin A8-like |
||||
|
ANXA8L1 |
annexin A8-like 1 |
||||
|
205044_at |
GABRP |
Gamma-aminobutyric acid (GABA) A receptor, pi |
76.9 |
27.0 |
0.04 |
|
204351_at |
S100P |
S100 calcium binding protein P |
76.7 |
14.6 |
0.05 |
|
202036_s_at |
SFRP1 |
Secreted frizzled-related protein 1 |
60.7 |
8.6 |
0.05 |
|
211657_at |
CEACAM6 |
Carcinoembryonic antigen-related cell adhesion molecule 6 |
39.3 |
1.8 |
0.04 |
|
220161_s_at |
EPB41L4B |
Erythrocyte membrane protein band 4.1 like 4B |
33.3 |
1.0 |
0.04 |
|
209212_s_at |
KLF5 |
Kruppel-like factor 5 (intestinal) |
17.7 |
1.7 |
0.04 |
|
219795_at |
SLC6A14 |
Solute carrier family 6 (amino acid transporter), member 14 |
11.6 |
2.7 |
0.05 |
|
202454_s_at |
ERBB3 |
v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) |
7.7 |
0.2 |
0.03 |
|
212991_at |
FBXO9 |
F-box protein 9 |
5.5 |
0.9 |
0.05 |
|
204304_s_at |
PROM1 |
Prominin 1 |
4.2 |
0.3 |
0.05 |
|
204713_s_at |
F5 |
Coagulation factor V |
3.7 |
0.5 |
0.05 |
|
218704_at |
RNF43 |
Ring finger protein 43 |
3.4 |
0.6 |
0.05 |
|
221582_at |
HIST3H2A |
Histone 3, H2a |
3.1 |
0.0 |
0.05 |
|
214594_x_at |
ATP8B1 |
ATPase, Class I, type 8B, member 1 |
2.1 |
0.2 |
0.05 |
Data presented indicate fold-change (mean ± SD) in gene expression. Probe ID, Affymetrix probe identifications.
This Article
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PNAS September 4, 2007 vol. 104 no. 36 14472-14477