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Table 5 Top ten up- and down- regulated isoforms 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 Locus Length RA1FPKM RA2FPKM WT1FPKM WT2FPKM Avg. RA Avg. WT Ensembl gene ID
SCARA5 Scavenger receptor class A, member 5 chr8 4151 11.36 353.51 -- -- 182.43 -- ENSG00000168079
PLA2G2A Phopholipase A2, group IIA chr1 969 3.81 264.84 -- -- 134.33 -- ENSG00000188257
SPCS1 Signal peptidase complex subunit 1 homolog chr3 1084 81.32 112.54 -- -- 96.93 -- ENSG00000114902
CITED2 Cbp/p300-interacting transactivator, 2 chr6 1929 69.03 119.73 -- -- 94.38 -- ENSG00000164442
IL13RA2 Interleukin 13 receptor, alpha 2 chrX 1373 9.94 90.27 -- -- 50.10 -- ENSG00000123496
SLPI Secretory leukocyte peptidase inhibitor chr20 598 1.36 98.75 -- -- 50.06 -- ENSG00000124107
KYNU Kynureninase chr2 1672 16.46 79.31 -- -- 47.88 -- ENSG00000115919
FAM20A Family with sequence similarity 20, member A chr17 4275 28.98 60.54 -- -- 44.76 -- ENSG00000108950
NUMA1 Nuclear mitotic apparatus protein 1 chr11 7182 40.51 45.42 -- -- 42.96 -- ENSG00000137497
PRG4 Proteoglycan 4 chr1 4765 1.27 81.59 -- -- 41.43 -- ENSG00000116690
ACTG2 Actin, gamma 2, smooth muscle, enteric chr2 1331 -- -- 1046.45 2.16 -- 524.30 ENSG00000163017
PSAP Prosaposin chr10 2822 -- -- 234.56 510.86 -- 372.71 ENSG00000197746
RPS24 Ribosomal Protein S24 chr10 655 -- -- 149.70 298.29 -- 224.00 ENSG00000138326
LRRC59 Leucine rich repeat containing 59 chr17 2915 -- -- 116.95 88.57 -- 102.76 ENSG00000108829
HMGA1 High mobility group box 1 chr6 1846 -- -- 44.78 99.59 -- 72.19 ENSG00000189403
CD59 CD59 molecule, complement regulatory protein chr11 7619 -- -- 68.61 75.31 -- 71.96 ENSG00000085063
PPP1R14A Protein phosphatase 1, regulatory (inhibitor) subunit 14A chr19 718 -- -- 142.49 1.10 -- 71.79 ENSG00000167641
HMGA1 High mobility group box 1 chr6 1993 -- -- 43.81 93.26 -- 68.54 ENSG00000189403
RPS24 Ribosomal Protein S24 chr10 633 -- -- 80.53 47.31 -- 63.92 ENSG00000138326
SNHG6 Small nucleolar RNA host gene 6 chr8 472 -- -- 46.68 65.62 -- 56.15 ENSG00000245910
  1. Isoforms which were differentially expressed as determined by Cufflinks, after normalization to a panel of housekeeping genes.
  2. The isoforms were ranked by FPKM and the 10 with the highest or lowest values are listed here.