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_predicted e | 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.