Table 2

Genes with reduced expression in synovial fibroblasts from DA.F344 (Cia5d) compared with highly invasive DA, including those associated with cancer-phenotypes and estrogen signaling
Gene Symbold
 Definitiona
 Accession number
 DA mean
 Cia5d mean
 Fold change
 P valueb
 Overall rankc
Cancer, Cell Cycle, DNA replication, recombination and repair
Trim16_predictede
 Tripartite motif protein 16 (predicted)
 XM_220552.3
 262.14
 82.27
 -3.2
 0.0033
 23
Cxcl10
 Chemokine (C-X-C motif) ligand 10f
 NM_139089.1
 1218.54
 434.48
 -2.8
 0.0001
 2
Dnmbp
 Similar to Dynamin binding protein (Scaffold protein Tuba)
 XM_219860.3
 739.97
 385.61
 -1.9
 0.0088
 62
Vil2
 Villin 2 (Ezrin)f
 NM_019357.1
 1642.95
 984.09
 -1.7
 0.0023
 15
Nras
 Neuroblastoma RAS viral (v-ras) oncogene homologf
 XM_579607.1
 910.25
 601.06
 -1.5
 0.0087
 60
Brms1l_predicted
 Breast cancer metastasis-suppressor 1-like (predicted)
 XM_216712.3
 187.93
 125.37
 -1.5
 0.0094
 64
Hnrpde
 Heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37 kDa)
 NM_024404.1
 2909.16
 1959.49
 -1.5
 0.0010
 8
Rpa2
 Replication protein A2
 NM_021582.1
 1583.81
 1154.73
 -1.4
 0.0074
 48
Ube2d3
 Ubiquitin-conjugating enzyme E2D 3
 NM_031237.1
 123.48
 99.45
 -1.2
 0.0017
 10
Lsm8_predictede
 LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)
 XM_216102.3
 3766.75
 3121.49
 -1.2
 0.0024
 16
Smc1l1
 Structural maintenance of chromosomes 1 like 1 (S. cerevisiae)
 NM_031683.1
 4648.45
 3923.73
 -1.2
 0.0044
 30
Rpa3_predicted
 Replication protein A3 (predicted)
 XM_216097.3
 4013.83
 3410.52
 -1.2
 0.0022
 14








Cell Signaling






Stip1
 Stress-induced phosphoprotein 1 (Stip1)
 NM_138911.2
 3478.09
 2568.75
 -1.4
 0.0028
 18








Ubiquitination






Usp24_predicted
 Ubiquitin specific protease 24 (predicted)
 XM_233260.3
 111.07
 74.14
 -1.5
 0.0037
 25
Stub1_predicted
 STIP1 homology and U-Box containing protein 1 (predicted)
 XM_213270.3
 4967.20
 4164.69
 -1.2
 0.0034
 24








Ribosomal Proteins






Rps6
 Ribosomal protein S6 (Rps6)
 NM_017160.1
 29305.46
 24538.18
 -1.2
 0.0085
 57
LOC300278
 Similar to 40S ribosomal protein S9
 XM_213106.3
 28115.69
 26209.24
 -1.1
 0.0086
 59
LOC367102
 Similar to 40S ribosomal protein S9
 XM_345948.2
 25678.47
 23353.32
 -1.1
 0.0043
 28








Others






Trpv2
 Transient receptor potential cation channel, subfamily V, member 2
 NM_017207.1
 177.90
 92.25
 -1.9
 0.0075
 49
Gins3_predictede
 GINS complex subunit 3 (Psf3 homolog)
XM_226235.2
 171.57
 89.64
 -1.9
 0.0010
 6
LOC499310
 Similar to cell division cycle associated 5
 XM_574612.1
 450.69
 270.81
 -1.7
 0.0061
 44
LOC298186
 Similar to hypothetical protein FLJ33868 (predicted)
 XM_238399.3
 271.10
 177.29
 -1.5
 0.0070
 46
Terf1_predicted
 Telomeric repeat binding factor 1 (predicted)
 XM_238387.3
 98.95
 66.02
 -1.5
 0.0048
 34
LOC308004
 Similar to hypothetical protein FLJ13188 (predicted)
 XM_217663.3
 573.01
 383.19
 -1.5
 0.0083
 56
LOC310177
 Similar to RIKEN cDNA 0610040D20
 XM_226872.2
 85.32
 58.03
 -1.5
 0.0044
 29
LOC297821
 Similar to F23N19.9 (predicted)
 XM_232684.3
 1680.52
 1185.76
 -1.4
 0.0052
 36
LOC308443
 Similar to CDNA sequence BC028440
 XM_218345.2
 426.63
 301.59
 -1.4
 0.0059
 41
Anp32b
 Acidic nuclear phosphoprotein 32 family, member B
 NM_131911.2
 454.58
 323.06
 -1.4
 0.0082
 55
Ranbp6_predicted
 RAN binding protein 6 (predicted)
 XM_219796.2
 309.74
 222.79
 -1.4
 0.0031
 22
LOC297903
 Similar to RIKEN cDNA 6720467C03 (predicted)
 XM_216357.3
 1493.92
 1088.11
 -1.4
 0.0075
 50
Qdpr
 Quinoid dihydropteridine reductase
 NM_022390.1
 983.32
 728.72
 -1.3
 0.0045
 33
Rnf134_predicted
 Ring finger protein 134 (predicted)
 XM_219963.3
 952.04
 717.85
 -1.3
 0.0059
 42
LOC316731
 Similar to hypothetical protein FLJ23017 (predicted)
 XM_237515.3
 74.86
 58.48
 -1.3
 0.0094
 65
LOC309197
 Similar to hypothetical protein
 XM_219560.3
 1413.35
 1112.64
 -1.3
 0.0050
 35
LOC316732
 Similar to RIKEN cDNA 4931400A14 (predicted)
 XM_244261.3
 251.40
 201.41
 -1.2
 0.0062
 45
Bin2_predicted
 Bridging integrator 2 (predicted)
 XM_578696.1
 57.42
 47.13
 -1.2
 0.0076
 51

aEstrogen; ER, estrogen-induced, or estrogen-receptor signaling or degradation are marked in bold. bt test. cOrder (logistic regression) in the list of 66 genes differentially expressed between DA and DA.F344(Cia5d). dCancer and invasion associated genes are in italics. eDifferentially expressed in prostate, breast, colon or pharyngeal cancers. fKnown to induce transcription or activation of gelatinases.

Laragione et al. Arthritis Research & Therapy 2008 10:R92   doi:10.1186/ar2476

Open Data