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Table 3 Chemokine and chemokine receptor expression data analysis

From: Chemokine receptors in the rheumatoid synovium: upregulation of CXCR5

Gene RA Non-RA Regulation (ratio RA/non-RA)
Receptors
Array column 3 (Fig. 1, C3)
   CCR1 0.050 0.023 Up (2.2 ± 0.2)
   CCR2a 0.031 0.012 Up (2.7 ± 0.2)
   CCR2b 0.000 0.000 Not visible (NA)
   CCR3 0.000 0.000 Not visible (NA)
   CCR4 0.003 0.000 Not visible (NA)
   CCR5 0.042 0.000 Up (NA)
   CCR6 0.001 0.000 Not visible (NA)
   CCR7 0.022 0.011 Not visible (2.5 ± 0.9)
   CCR9 0.001 0.000 Not visible (NA)
   CX3CR1 0.028 0.019 Not visible (1.5 ± 0.1)
   CXCR1 0.036 0.008 Not visible (9.6 ± 5.6)
   CXCR2 0.651 0.000 Up (NA)
   CXCR4 0.190 0.055 Up (3.5 ± 0.1)
   CXCR5 1.328 0.059 Up (22.6 ± 0.7)
   CXCR6 (STRL33) 0.016 0.025 Not visible (0.7 ± 0.0)
   Bob 0.034 0.000 Up (NA)
Chemokines
Array column 1 (Fig. 1, C1)
   CCL21 (6Ckine) 0.030 0.019 Up (1.6 ± 0.1)
   CXCL13 (BLC/BCA-1) 0.052 0.020 Up (2.8 ± 0.4)
   CXCL10 (IP-10) 0.031 0.019 Up (1.6 ± 0.1)
   CXCL5 (ENA-78) 0.050 0.015 Up (3.5 ± 0.3)
   CCL11 (eotaxin) 0.050 0.052 Not visible (1.0 ± 0.0)
   CCL24 (eotaxin-2) 0.032 0.013 Up (2.5 ± 0.3)
   CX3CL1 (fractalkine) 0.030 0.012 Not visible (2.5 ± 0.2)
   CXCL1 (GRO-α) 0.090 0.057 Up (1.6 ± 0.0)
   CXCL2 (GRO-β) 0.151 0.101 Up (1.5 ± 0.0)
   CXCL3 (GRO-γ) 0.101 0.055 Up (1.8 ± 0.0)
   CCL14 (HCC-1) 0.202 0.296 Down (0.7 ± 0.0)
   CCL16 (HCC-4) 0.006 0.000 Not visible (NA)
   CCL1 (I-309) 0.007 0.000 Not visible (NA)
   CXCL8 (IL-8) 0.086 0.026 Up (3.3 ± 0.2)
   CXCL7 (LDGF) 0.005 0.000 Not visible (NA)
   CCL15 (MIP-1δ) 0.009 0.008 Not visible (11 ± 13)
   XCL1 (lymphotactin) 0.048 0.031 Up (1.6 ± 0.0)
   CCL2 (MCP-1) 0.482 0.545 Not visible (0.9 ± 0.0)
   CCL8 (MCP-2) 0.053 0.062 Not visible(0.9 ± 0.0)
   CCL7 (MCP-3) 0.066 0.047 Up (1.4 ± 0.1)
   CCL13 (MCP-4) 0.000 0.002 Not visible (0.0)
   CCL22 (MDC) 0.000 0.008 Not visible (0.0)
Array column 2 (Fig. 1, C2)
   Midkine 0.299 0.155 Up (1.9 ± 0.0)
   CXCL9 (MIG) 0.166 0.047 Up (3.6 ± 0.1)
   CCL3 (MIP-1α) 0.040 0.042 Not visible (1.0 ± 0.0)
   CCL4 (MIP-1β) 0.023 0.018 Up (1.3 ± 0.2)
   CCL20 (MIP-3α) 0.000 0.013 Not visible(0.0)
   CCL19 (MIP-3β) 0.023 0.042 Not visible (0.6 ± 0.0)
   CCL23 (MPIF-1) 0.039 0.042 Up (0.9 ± 0.0)
   CCL18 (PARC) 0.146 0.033 Up (4.5 ± 0.4)
   CCL5 (RANTES) 0.037 0.031 Up (1.2 ± 0.1)
   CXCL12 (SDF-1) 0.409 0.573 Down (0.7 ± 0.0)
   CCL17 (TARC) 0.000 0.000 Not visible (NA)
   CCL25 (TECK) 0.000 0.000 Not visible (NA)
  1. Following hybridization to labelled mRNA extracted from rheumatoid arthritis (RA) and non-RA synovia, a pair of array membranes was autoradiographed for varying lengths of time. The autoradiograms were scanned and analysed with the ArrayVision software (version 6.0; Imaging Research Inc., Haverhill, UK). For each RA/non-RA pair the housekeeping genes on the membranes showed very similar intensities, were not saturated and were used to normalize the data. The analysis measured the 'volume' of each spot (i.e. the density value of each spot multiplied by its area). The background was measured using the 'corners between spots' protocol of the software and was deducted from the 'volumes'. The ratio of RA synovia versus non-RA synovia was also calculated for each spot. The analysis was repeated eight times for each pair of autoradiograms, providing 16 values for each gene (each gene is spotted in duplicate) on each pair. Figures in the columns RA, non-RA and ratio RA/non-RA represent the average of 16 values. For each average ratio the 95% confidence level was calculated, and the results presented are those from the autoradiogram pair giving the smallest variation. , spot was not visible by eye on the corresponding autoradiogram; , spot was visible after prolonged exposure. The mRNA regulation of RA versus non-RA as observed by eye at the time point used for quantification is indicated by not visible, up or down. NA, ratio could not be calculated due to the presence of zero values. The recent systematic nomenclature of chemokines is used, with the former names in parentheses. The order of the genes presented is the same as that appearing on the microarray in Fig. 1.