CXCL8
type: EnsemblDatabaseReference

207850_at
type: EFO_0005072
part of: A-AFFY-44

225056_at
type: EFO_0005072
part of: A-AFFY-44

212977_at
type: EFO_0005072
part of: A-AFFY-44

212665_at
type: EFO_0005072
part of: A-AFFY-44

CCL2
type: EnsemblDatabaseReference

ATF3 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.432996425
p value: 9.86485090027908E-8
refers to: 202672_s_at
refers to: ATF3
t statistic: 22.7056860816495

AHRR
type: EnsemblDatabaseReference

233587_s_at
type: EFO_0005072
part of: A-AFFY-44

SOCS3
type: EnsemblDatabaseReference

DLG1
type: EnsemblDatabaseReference

CXCL3
type: EnsemblDatabaseReference

IL6
type: EnsemblDatabaseReference

202437_s_at
type: EFO_0005072
part of: A-AFFY-44

SIPA1L2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.519342725
p value: 2.87240567318213E-7
refers to: 233587_s_at
refers to: SIPA1L2
t statistic: 19.9042824968972

CYP1B1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 4.781394925
p value: 7.28211966050119E-9
refers to: 202437_s_at
refers to: CYP1B1
t statistic: 34.3953144979876

CXCL3 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.185513975
p value: 2.74309217243456E-5
refers to: 207850_at
refers to: CXCL3
t statistic: 11.1276230887109

NFATC2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.042365425
p value: 3.98817830522952E-7
refers to: NFATC2
refers to: 226991_at
t statistic: 19.0944622388484

PTGS2
type: EnsemblDatabaseReference

ROR1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.15871095
p value: 1.53612504846192E-5
refers to: ROR1
refers to: 205805_s_at
t statistic: 11.9742218964676

SLC30A1
type: EnsemblDatabaseReference

ACKR3
type: EnsemblDatabaseReference

SELE
type: EnsemblDatabaseReference

NFATC2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.424398475
p value: 1.65488811747403E-7
refers to: NFATC2
refers to: 228442_at
t statistic: 21.134750717803

PTGS2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.18716675
p value: 3.15057260385219E-7
refers to: 1554997_a_at
refers to: PTGS2
t statistic: 19.657838928605

(Sample) cell type/endothelial cell
type: CL_0000115
property type: cell type
property value: endothelial cell

DLG1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.014316875
p value: 1.36570293141879E-5
refers to: 202516_s_at
refers to: DLG1
t statistic: 12.1562332317832

SHISA2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.3193133
p value: 2.01863887070419E-5
refers to: SHISA2
refers to: 230493_at
t statistic: 11.5912569654558

NPTX1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.402958575
p value: 8.9922868405875E-6
refers to: NPTX1
refers to: 204684_at
t statistic: 12.9480410374724

CCL2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.376504625
p value: 1.35571646511153E-8
refers to: 216598_s_at
refers to: CCL2
t statistic: 30.5758782931573

SELE UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 2.08671675
p value: 5.53362324663543E-8
refers to: SELE
refers to: 206211_at
t statistic: 24.602251237321

CXCL8 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.180429
p value: 5.53362324663543E-8
refers to: 202859_x_at
refers to: CXCL8
t statistic: 24.7688883372817

HGF
type: EnsemblDatabaseReference

ATF3
type: EnsemblDatabaseReference

TNFRSF11A
type: EnsemblDatabaseReference

F3 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.43773015
p value: 3.06813148457125E-8
refers to: F3
refers to: 204363_at
t statistic: 26.6992804091668

205749_at
type: EFO_0005072
part of: A-AFFY-44

APOLD1
type: EnsemblDatabaseReference

206211_at
type: EFO_0005072
part of: A-AFFY-44

(Assay) endothelial cell_control_rep3(55)
type: Assay
identifier: endothelial cell_control_rep3(55)
has participant: A-AFFY-44

216598_s_at
type: EFO_0005072
part of: A-AFFY-44

SERPINB2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 2.114879375
p value: 5.72236487431179E-7
refers to: SERPINB2
refers to: 204614_at
t statistic: 18.3460087713068

SIPA1L2
type: EnsemblDatabaseReference

SOCS3
type: EnsemblDatabaseReference

DLG1
type: EnsemblDatabaseReference

205805_s_at
type: EFO_0005072
part of: A-AFFY-44

TIPARP UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.171369
p value: 9.86485090027908E-8
refers to: TIPARP
refers to: 212665_at
t statistic: 22.8029945568048

SECTM1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.196851075
p value: 1.29892359608224E-5
refers to: SECTM1
refers to: 213716_s_at
t statistic: 12.3156903465412

(Sample) organism part/pulmonary artery
type: UBERON_0002012
property type: organism part
property value: pulmonary artery

213716_s_at
type: EFO_0005072
part of: A-AFFY-44

(Assay) endothelial cell_control_rep1(53)
type: Assay
identifier: endothelial cell_control_rep1(53)
has participant: A-AFFY-44

ACKR3 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.066126625
p value: 9.71204394455405E-8
refers to: ACKR3
refers to: 212977_at
t statistic: 23.0338862160447

230748_at
type: EFO_0005072
part of: A-AFFY-44

CYP1A1
type: EnsemblDatabaseReference

230493_at
type: EFO_0005072
part of: A-AFFY-44

CYP1A1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.92650625
p value: 1.35571646511153E-8
refers to: CYP1A1
refers to: 205749_at
t statistic: 30.8724990039762

ACKR3
type: EnsemblDatabaseReference

SELE
type: EnsemblDatabaseReference

CCL2
type: EnsemblDatabaseReference

Analysis of 'cultured with ultrafine air pollutant particles' vs 'control'
type: MicroarrayDifferentialExpressionAnalysis

CYP1B1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 3.16982245
p value: 6.92320298215948E-10
refers to: 202436_s_at
refers to: CYP1B1
t statistic: 45.142649384304

A-AFFY-44
type: EFO_0000269

204363_at
type: EFO_0005072
part of: A-AFFY-44

CXCL3
type: EnsemblDatabaseReference

(Assay) endothelial cell_UFP treatment_rep4(60)
type: Assay
identifier: endothelial cell_UFP treatment_rep4(60)
has participant: A-AFFY-44

238846_at
type: EFO_0005072
part of: A-AFFY-44

CXCL8 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.423159625
p value: 1.65488811747403E-7
refers to: CXCL8
refers to: 211506_s_at
t statistic: 21.1088621919585

HGF
type: EnsemblDatabaseReference

(Assay) endothelial cell_control_rep4(56)
type: Assay
identifier: endothelial cell_control_rep4(56)
has participant: A-AFFY-44

CXCL2
type: EnsemblDatabaseReference

SHISA2
type: EnsemblDatabaseReference

ATF3
type: EnsemblDatabaseReference

TNFRSF11A
type: EnsemblDatabaseReference

SECTM1
type: EnsemblDatabaseReference

HMOX1
type: EnsemblDatabaseReference

PTGS2
type: EnsemblDatabaseReference

E-GEOD-4567
type: microarray 1colour mrna differential
RO_0002162: Homo sapiens
description: Epidemiology studies have linked exposure to pollutant particles to increased cardiovascular mortality and morbidity, however, the mechanism remains unknown. In this study, we hypothesized that the ultrafine fraction of ambient pollutant particles would cause endothelial cells dysfunction. We profiled gene expression of human pulmonary artery endothelial cells (HPAEC) exposed to ultrafine Chapel Hill particles (UFP) (100ÃÂÃÂ¼g/ml) or vehicle for 4h with Affymetrix HG U133 Plus 2.0 chips (N = 4 each). Using an unpaired t-test (p <0.01, 5% false discovery rate) we found 426 unique genes to be differentially expressed with 320 upregulated genes and 106 downregulated genes. Among these genes, we noted upregulation of genes related to coagulation-inflammation circuitry including tissue factor (F3), coagulation factor II receptor-like 2 (F2RL2, PAR3), interleukin (IL)-6 and IL-8. Upregulation of these genes were independently confirmed by RT-PCR and/or protein release. Genes related to the CXC chemokine family that have been implicated in the pathogenesis of vascular disease were upregulated, including MCP-1 (2.60 fold), IL-8 (2.47 fold), CXCL1 (1.41 fold), CXCL2 (1.95 fold), CXCL3 (2.28 fold) and CXCR4 (1.30 fold). In addition, genes related to clotting independent signaling of F3 were also differentially expressed, including FOS, JUN and NFKBIA. Treatment of HPAEC with UFP for 16 hours increased the release of IL6 and IL8 by 1.9-fold and 1.8-fold respectively. Pretreatment of HPAEC with a blocking antibody against F3 attenuated IL6 and IL8 release by 30% and 70% respectively. Thus using gene profiling, we uncovered that UFP may induce vascular endothelial cells to express genes related to clotting and angiogenesis. These results provide a novel hypothesis that PM may cause cardiovascular adverse health effects via induction of tissue factor in vascular endothelial cells which then triggers clotting dependent and independent downstream signaling. Experiment Overall Desig…
uses data from: http://identifiers.org/pubmed/17450221

228181_at
type: EFO_0005072
part of: A-AFFY-44

209774_x_at
type: EFO_0005072
part of: A-AFFY-44

(Assay) endothelial cell_UFP treatment_rep1(57)
type: Assay
identifier: endothelial cell_UFP treatment_rep1(57)
has participant: A-AFFY-44

(Assay) endothelial cell_UFP treatment_rep3(59)
type: Assay
identifier: endothelial cell_UFP treatment_rep3(59)
has participant: A-AFFY-44

ROR1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.603281075
p value: 7.24961063448102E-8
refers to: ROR1
refers to: 232060_at
t statistic: 23.8221182245032

CYP1B1
type: EnsemblDatabaseReference

SIPA1L2
type: EnsemblDatabaseReference

Homo sapiens
type: OBI_0100026

203665_at
type: EFO_0005072
part of: A-AFFY-44

SLC30A1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.0852441
p value: 7.6991607450867E-6
refers to: 228181_at
refers to: SLC30A1
t statistic: 13.1724049686489

CYP1A1
type: EnsemblDatabaseReference

GCLM UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.09435025
p value: 8.4386629212872E-7
refers to: 236140_at
refers to: GCLM
t statistic: 17.3827520886337

202435_s_at
type: EFO_0005072
part of: A-AFFY-44

TIPARP
type: EnsemblDatabaseReference

202859_x_at
type: EFO_0005072
part of: A-AFFY-44

NFATC2
type: EnsemblDatabaseReference

GCLM UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.02732315
p value: 1.14071370730852E-6
refers to: 234986_at
refers to: GCLM
t statistic: 16.7315109759902

APOLD1
type: EnsemblDatabaseReference

202672_s_at
type: EFO_0005072
part of: A-AFFY-44

ROR1
type: EnsemblDatabaseReference

202436_s_at
type: EFO_0005072
part of: A-AFFY-44

234986_at
type: EFO_0005072
part of: A-AFFY-44

SLC16A6
type: EnsemblDatabaseReference

CXCL2
type: EnsemblDatabaseReference

SECTM1
type: EnsemblDatabaseReference

HMOX1
type: EnsemblDatabaseReference

229354_at
type: EFO_0005072
part of: A-AFFY-44

211506_s_at
type: EFO_0005072
part of: A-AFFY-44

SERPINB2
type: EnsemblDatabaseReference

TNFRSF11A UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.0114153
p value: 2.6776017928964E-6
refers to: TNFRSF11A
refers to: 238846_at
t statistic: 15.0970496759963

209960_at
type: EFO_0005072
part of: A-AFFY-44

221031_s_at
type: EFO_0005072
part of: A-AFFY-44

SOCS3 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.5939912
p value: 1.56268053804475E-7
refers to: SOCS3
refers to: 227697_at
t statistic: 21.533946005924

NPTX1
type: EnsemblDatabaseReference

F3
type: EnsemblDatabaseReference

(Sample) organism/Homo sapiens
type: Homo sapiens
property type: organism
property value: Homo sapiens

226991_at
type: EFO_0005072
part of: A-AFFY-44

(Assay) endothelial cell_control_rep2(54)
type: Assay
identifier: endothelial cell_control_rep2(54)
has participant: A-AFFY-44

SIPA1L2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.5446965
p value: 1.82161246912612E-8
refers to: 225056_at
refers to: SIPA1L2
t statistic: 28.5951027613683

IL6
type: EnsemblDatabaseReference

205207_at
type: EFO_0005072
part of: A-AFFY-44

GCLM
type: EnsemblDatabaseReference

SHISA2
type: EnsemblDatabaseReference

1554997_a_at
type: EFO_0005072
part of: A-AFFY-44

CEBPD UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.1817085
p value: 5.63255441697111E-7
refers to: 203973_s_at
refers to: CEBPD
t statistic: 18.4360233362815

204614_at
type: EFO_0005072
part of: A-AFFY-44

APOLD1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.105973925
p value: 1.61511484873242E-7
refers to: 221031_s_at
refers to: APOLD1
t statistic: 21.3586363823978

AHRR UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.404470625
p value: 1.82161246912612E-8
refers to: AHRR
refers to: 229354_at
t statistic: 28.317962432718

CEBPD
type: EnsemblDatabaseReference

NFATC2
type: EnsemblDatabaseReference

SLC16A6 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.28984015
p value: 1.72086412473337E-5
refers to: SLC16A6
refers to: 230748_at
t statistic: 11.8230015870475

CXCL8
type: EnsemblDatabaseReference

ROR1
type: EnsemblDatabaseReference

CYP1B1
type: EnsemblDatabaseReference

(Assay) endothelial cell_UFP treatment_rep2(58)
type: Assay
identifier: endothelial cell_UFP treatment_rep2(58)
has participant: A-AFFY-44

AHRR
type: EnsemblDatabaseReference

227697_at
type: EFO_0005072
part of: A-AFFY-44

CXCL2 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.235863125
p value: 5.87455311538894E-6
refers to: 209774_x_at
refers to: CXCL2
t statistic: 13.6809929663921

232060_at
type: EFO_0005072
part of: A-AFFY-44

(Factor value) GROWTH_CONDITION/cultured with ultrafine air pollutant particles
type: EFO_0000001
property type: GROWTH_CONDITION
property value: cultured with ultrafine air pollutant particles

SERPINB2
type: EnsemblDatabaseReference

204684_at
type: EFO_0005072
part of: A-AFFY-44

TIPARP
type: EnsemblDatabaseReference

203973_s_at
type: EFO_0005072
part of: A-AFFY-44

IL6 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.194063375
p value: 3.5993163118065E-8
refers to: 205207_at
refers to: IL6
t statistic: 26.0409297809273

SLC30A1
type: EnsemblDatabaseReference

NPTX1
type: EnsemblDatabaseReference

202516_s_at
type: EFO_0005072
part of: A-AFFY-44

F3
type: EnsemblDatabaseReference

HGF UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.12893775
p value: 9.47810432103219E-5
refers to: 209960_at
refers to: HGF
t statistic: 9.44474371504383

CYP1B1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 2.5267923
p value: 7.88105734392846E-7
refers to: CYP1B1
refers to: 202435_s_at
t statistic: 17.592572732306

(Factor value) GROWTH_CONDITION/control
type: EFO_0001461
property type: GROWTH_CONDITION
property value: control

228442_at
type: EFO_0005072
part of: A-AFFY-44

SLC16A6
type: EnsemblDatabaseReference

GCLM
type: EnsemblDatabaseReference

HMOX1 UP in 'cultured with ultrafine air pollutant particles' vs 'control'
type: IncreasedDifferentialExpressionRatio
fold change: 1.34664175
p value: 1.82161246912612E-8
refers to: HMOX1
refers to: 203665_at
t statistic: 28.8846124080669

236140_at
type: EFO_0005072
part of: A-AFFY-44

CEBPD
type: EnsemblDatabaseReference