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Table 8 Top ten up- and down- regulated novel isoforms expressed in rheumatoid arthritis synovial RNA

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

Gene Description Coordinates Length FPKM Wildtype FPKM RA Fold change Ensembl gene ID
FBN1 fibrillin 1 chr15:48700502-48944261 3642 0.35665 122.625 343.82 ENSG00000166147
TNXB tenascin XB chr6:31913771-32077409 10005 0.0711364 9.52612 133.91 ENSG00000168477
VCAN versican chr5:82767225-82878111 7388 0.145287 17.706 121.87 ENSG00000038427
LRP1 low density lipoprotein receptor-related protein 1 chr12:57522228-57607140 6609 0.223758 19.9154 89.00 ENSG00000123384
DPYSL2 dihydropyrimidinase-like 2 chr8:26435420-26515693 3416 0.287829 23.9348 83.16 ENSG00000092964
- Genes nearby:FAM198B: family with sequence similarity 198, member B chr4:159045731-159093718 1964 0.064901 5.20752 80.24 ENSG00000164125
- Genes nearby:TGFBR3: transforming growth factor, beta receptor III chr1:92145899-92351836 1323 0.137404 11.0015 80.07 ENSG00000069702
ALDH1L2 aldehyde dehydrogenase 1 family, member L2 chr12:105413561-105478341 4568 0.0522639 3.45172 66.04 ENSG00000136010
- NA chr14:74964883-75079368 2880 0.114262 6.82866 59.76 NA
  Genes nearby: ISCA2: iron-sulfur cluster assembly 2 homolog       ENSG00000165898
SNED1 LTBP2: latent transforming growth factor beta binding protein 2 chr2:241936998-242041710 8107 0.15755 9.34599 59.32 ENSG00000119681
TINAGL1 tubulointerstitial nephritis antigen-like 1 chr1:32041807-32053290 995 129.883 0.462813 −280.64 ENSG00000142910
TPM2 tropomyosin 2 (beta) chr9:35681989-35690053 1083 78.6638 0.329924 −238.43 ENSG00000198467
MT2A metallothionein 2A chr16:56642376-56692994 248 701.232 5.35657 −130.91 ENSG00000125148
FSTL1 follistatin-like 1 chr3:120113060-120169918 1640 10.7318 0.0822263 −130.52 ENSG00000163430
ITPRIP inositol 1,4,5-trisphosphate receptor interacting protein chr10:106069730-106098576 6523 18.5495 0.146115 −126.95 ENSG00000148841
- NA chr13:41958154-41958844 690 51.6499 0.522452 −98.86 NA
SPTBN1 spectrin, beta, non-erythrocytic 1 chr2:54683453-54898583 7086 12.396 0.126624 −97.90 ENSG00000115306
HLA-DRB1 major histocompatibility complex, class II, DR beta 5 chr6:32441211-32557589 513 12.6351 0.129095 −97.87 ENSG00000198502
SEMA3F sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F chr3:50192454-50226507 3394 6.92733 0.0764133 −90.66 ENSG00000001617
CNN1 calponin 1, basic, smooth muscle chr19:11649578-11661139 659 67.4653 0.799449 −84.39 ENSG00000130176
  1. Novel isoforms which were differentially expressed as determined by CuffDiff after Benjamini-Hochberg correction. The fold change is the ratio of RASF FPKM to control FPKM. Novel isoforms with a fold change of 1.2-fold or greater were defined as significant. The isoforms were ranked on their fold change and the 10 with the highest or lowest fold changes are listed here.