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Table 3 Top ten up- and down- regulated genes expressed only in normal synovial RNA or only in rheumatoid arthritis synovial RNA

From: RNA-seq analysis of synovial fibroblasts brings new insights into rheumatoid arthritis

Gene Description Chr RA FPKM RA2 FPKM WT1 FPKM WT2 FPKM Avg.RA Avg.WT Ensembl gene ID
HLA-B Major histocompatibility complex, class 1, B chr6 704.3 728.3 -- -- 716.3 -- ENSG00000228964
HLA-A Major histocompatibility complex, class 1, A chr6 778.2 585.6 -- -- 681.9 -- ENSG00000223980
HLA-C Major histocompatibility complex, class 1, C chr6 534.8 452.1 -- -- 493.5 -- ENSG00000206435
TUBB Tubulin, beta class I chr6 405.3 416.7 -- -- 411 -- ENSG00000232421
CLIC1 Chloride intracellular channel 1 chr6 350.5 369.6 -- -- 360 -- ENSG00000223639
RPS18 Ribosomal Protein S18 chr6 260.4 269.1 -- -- 264.8 -- ENSG00000227794
HLA-E Major histocompatibility complex, class 1, E chr6 243.5 260.2 -- -- 251.9 -- ENSG00000230254
C6orf48 Chromosome 6 open reading frame 48 chr6 119.5 225.8 -- -- 172.6 -- ENSG00000206380
SCARA5 Scavenger receptor class A, member 5 chr8 11.36 316 -- -- 163.7 -- ENSG00000168079
CUTA CutA divalent cation tolerance homolog chr6 168.7 133.7 -- -- 151.2 -- ENSG00000226492
ACTG2 Actin, gamma 2, smooth muscle, enteric chr2 -- -- 1087.76 2.58 -- 545.17 ENSG00000163017
RPS24 Ribosomal Protein S24 chr10 -- -- 407.72 429.08 -- 418.40 ENSG00000138326
PSAP Prosaposin chr10 -- -- 236.86 519.83 -- 378.35 ENSG00000197746
HMGA1 High mobility group box 1 chr6: -- -- 139.35 265.81 -- 202.58 ENSG00000189403
CD59 CD59 molecule, complement regulatory protein chr11 -- -- 111.47 149.28 -- 130.38 ENSG00000085063
LRRC59 Leucine rich repeat containing 59 chr17 -- -- 116.95 88.57 -- 102.76 ENSG00000108829
PPP1R14A Protein phosphatase 1, regulatory (inhibitor) subunit 14A chr19 -- -- 142.49 1.10 -- 71.79 ENSG00000167641
LTBP1 Latent transforming growth factor beta binding protein 1 chr2 -- -- 54.38 66.08 -- 60.23 ENSG00000049323
SNHG6 Small nucleolar RNA host gene 6 chr8 -- -- 46.68 65.62 -- 56.15 ENSG00000245910
HNRNPC Heterogeneous nuclear ribonucleoprotein C (C1/C2) chr14 -- -- 52.08 58.46 -- 55.27 ENSG00000092199
  1. Genes which were differentially expressed as determined by Cufflinks, after normalization to a panel of housekeeping genes.
  2. The genes were ranked by FPKM and the 10 with the highest or lowest values are listed here.