BioMed Research International / 2015 / Article / Tab 1

Research Article

Cross-Omics Comparison of Stress Responses in Mesothelial Cells Exposed to Heat- versus Filter-Sterilized Peritoneal Dialysis Fluids

Table 1

Proteins and transcripts analyzed by 2D-DIGE and mRNA expression microarrays.

Gene nameGene IDProtein nameTranscriptomics dataProteomics data
RefSeqHeat/filter SwissProt
entry name
HeatFilterHeat/filter
Mean ratioSDCVChip CVMean spot volumeSDMean spot volumeSDRatio value

Increased protein abundance (proteomics ratio > 1)

Increased gene expression (transcriptomics ratio > 1)
HSPA83312Heat shock cognate 71 kDa proteinNM_006597 NM_1532011.600.023%4%HSP7C_HUMAN132.8939.736112.89911.8381.1770.203
HSPB13315Heat shock protein beta-1NM_0015401.320.1317%4%HSPB1_HUMAN207.83035.16271.97517.3352.8880.061
GSTP12950Glutathione S-transferase PNM_0008521.160.045%4%GSTP1_HUMAN88.02966.62561.65410.3431.4280.562
GSR2936Glutathione reductase, mitochondrialNM_0006371.190.079%0%GSHR_HUMAN140.74312.299129.5124.9311.0870.438
PDIA32923Protein disulfide-isomerase A3NM_0053131.070.1414%14%PDIA3_HUMAN185.9973.950125.44420.0511.4830.031
PDIA32923Protein disulfide-isomerase A3NM_0053131.070.1414%14%PDIA3_HUMAN147.4174.727115.85216.5241.2720.094

Decreased gene expression (transcriptomics ratio < 1)
CCT522948T-complex protein 1 subunit epsilonNM_0120730.820.097%9%TCPE_HUMAN177.98810.033122.6978.4151.4510.019
PSMB25690Proteasome subunit beta type-2NM_0027940.870.097%18%PSB2_HUMAN100.1677.49283.67013.5591.1970.161
HSPA5330978 kDa glucose-regulated proteinNM_0053470.810.1411%4%GRP78_HUMAN254.1215.404106.67615.4502.3820.001
P4HB5034Protein disulfide-isomeraseNM_0009180.560.3520%7%PDIA1_HUMAN192.7106.746112.93826.3341.7060.025
PDIA610130Protein disulfide-isomerase A6NM_0057420.650.042%4%PDIA6_HUMAN125.9402.434106.14811.4781.1860.090
COPS451138COP9 signalosome complex subunit 4NM_0161290.770.118%7%CSN4_HUMAN151.48417.903108.44017.3681.3970.139
HSPD1332960 kDa heat shock protein, mitochondrialNM_002156 NM_1994400.820.065%3%CH60_HUMAN275.6621.224155.2338.9621.7760.001
RPSA392140S ribosomal protein SANM_0022950.750.2418%0.05RSSA_HUMAN111.01923.693110.8459.4741.0020.993

Decreased protein abundance (proteomics ratio < 1)

Increased gene expression (transcriptomics ratio > 1)
HSPA93313Stress-70 protein, mitochondrialNM_0041341.320.079%4%GRP75_HUMAN108.0499.256123.2535.8430.8770.156
HSPA1A3303Heat shock 70 kDa protein 1NM_005345 NM_0053462.590.0717%6%HSP71_HUMAN108.0499.256123.2535.8430.8770.156
HSPA83312Heat shock cognate 71 kDa proteinNM_006597 NM_1532011.600.023%4%HSP7C_HUMAN108.0499.256123.2535.8430.8770.156
HSPA1A3303Heat shock 70 kDa protein 1NM_005345 NM_0053462.590.0717%6%HSP71_HUMAN104.25414.587130.0414.8120.8020.091
HSPA83312Heat shock cognate 71 kDa proteinNM_006597 NM_1532011.600.023%4%HSP7C_HUMAN106.85310.219123.1206.4120.8680.163
HSPA1A3303Heat shock 70 kDa protein 1NM_005345 NM_0053462.590.0717%6%HSP71_HUMAN87.59112.214113.8585.9480.7690.043
G6PD2539Glucose-6-phosphate 1-dehydrogenaseNM_0004021.020.088%6%G6PD_HUMAN80.83616.641121.33010.2290.6660.035
GSTP12950Glutathione S-transferase PNM_0008521.160.045%4%GSTP1_HUMAN65.2687.17485.96420.8850.7590.190
CCT210576T-complex protein 1 subunit betaNM_0064311.190.033%2%TCPB_HUMAN104.7146.378119.18712.0880.8790.267
TXNRD17296Thioredoxin reductase 1, cytoplasmicNM_001093771 NM_003330 NM_182729 NM_182742 NM_1827431.470.1217%6%TRXR1_HUMAN104.7146.378119.18712.0880.8790.267
G6PD2539Glucose-6-phosphate 1-dehydrogenaseNM_0004021.020.088%6%G6PD_HUMAN85.8488.356124.1405.5060.6920.005
HSPB13315Heat shock protein beta-1NM_0015401.320.1317%4%HSPB1_HUMAN69.93023.92186.8138.0600.8060.258
NME14830Nucleoside diphosphate kinase ANM_000269 NM_1981751.140.089%8%NDKA_HUMAN59.78920.657144.62766.4110.4130.283

Decreased gene expression (transcriptomics ratio < 1)
CCT710574T-complex protein 1 subunit etaNM_0064290.810.043%2%TCPH_HUMAN95.3817.45995.73110.2800.9960.969
PSMA25683Proteasome subunit alpha type-2NM_0027870.690.1510%4%PSA2_HUMAN116.47711.780148.56914.4660.7840.150
FKBP1A2280Peptidyl-prolyl cis-trans-isomerase FKBP1ANM_0540140.650.2617%15%FKB1A_HUMAN473.565141.421 65245.93699.9460.0070.275
PPIA5478Peptidyl-prolyl cis-trans-isomerase ANM_0211300.860.044%6%PPIA_HUMAN60.34016.561121.6039.7850.4960.005
PCNA5111Proliferating cell nuclear antigenNM_002592 NM_1826490.460.2612%7%PCNA_HUMAN87.2968.040123.9096.4260.7050.008
HADHA3030Trifunctional enzyme subunit alpha, mitochondrialNM_0001820.850.054%5%ECHA_HUMAN85.56423.72390.07312.5980.9500.798
PPIA5478Peptidyl-prolyl cis-trans-isomerase ANM_0211300.860.044%6%PPIA_HUMAN62.91911.686115.73810.4980.5440.006
PSMD4571026S proteasome non-ATPase regulatory subunit 4NM_002810 NR_0023190.740.097%8%PSMD4_HUMAN85.45514.214148.81210.0630.5740.010
HSPD1332960 kDa heat shock protein, mitochondrialNM_002156 NM_1994400.820.065%3%CH60_HUMAN101.42311.218170.5527.4720.5950.005
HSP90B17184EndoplasminNM_0032990.590.1911%5%ENPL_HUMAN92.81833.37693.65122.9140.9910.977
HSPA43308Heat shock 70 kDa protein 4NM_0021540.684%HSP74_HUMAN123.82930.682141.98616.3240.8720.595

Proteins and transcripts, which could be mapped and analyzed by both proteomics by 2D-DIGE combined with MS protein identification and topic defined mRNA expression microarray analysis (Miltenyi PIQOR toxicology array). Ratio: fold-change of mRNA expression of cells treated with H-PDF versus cells treated with F-PDF as obtained from the PIQOR microarray service. Standard deviation of mRNA expression ratios of cells treated with H-PDF versus cells treated with F-PDF. Coefficient variation: relative standard deviation in percent of mRNA expression ratios of cells treated with H-PDF versus cells treated with F-PDF. Chip CV: the column contains the relative standard deviation in percent for the respective rRNA by the number of multiple features on the microarray () as obtained from the PIQOR microarray service. Mean spot volume: mean of the spot quantification data over the biological replicates within the given groups.   Standard deviation of the spot quantification data within the given groups. Ratio: fold-change of protein spot abundance in cells treated with H-PDF versus cells treated with F-PDF as obtained from 2D-DIGE analysis. The column contains the value of the -test comparing relative spot abundance of cells treated with H-PDF versus cells treated with F-PDF. Protein quantifications, reaching the according levels of statistical significance, are marked with asterisks (, , and ) after the protein name.