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Table 5 Alterations in TAD structure after TNF stimulation and genes in stimulation-specific TADs

From: Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability

Locus

Chr

TAD_diff

Type of difference

Enriched_in

Expressed in FLS

Differential expressed in FLS (p adj < 0.05)

9

chr1

Differential

Strength Change

Basal

RC3H1; RABGAP1L; PRDX6; KLHL20; GAS5-AS1; GAS5; ZBTB37

GAS5; PRDX6; ZBTB37; RABGAP1L; RC3H1

10

chr2

Differential

Complex

Basal

LBH; LCLAT1; YPEL5

LBH; LCLAT1

13

chr2

Differential

Merge

Stim

NPAS2

NPAS2

19

chr3

Differential

Strength Change

Basal

CMC1; SLC4A7; AZI2

CMC1

20

chr3

Differential

Split

Basal

SLMAP; FLNB; FLNB-AS1; PXK; PDHB

PXK; FLNB

21

chr3

Differential

Strength Change

Basal

PCCB; PPP2R3A; MSL2; STAG1

PCCB

22

chr4

Differential

Strength Change

Basal

WDR1; ZNF518B

 

27

chr6

Differential

Strength Change

Basal

SRPK1; MAPK14; PI16; LHFPL5; BRPF3; KCTD20; STK38; SRSF3; PANDAR; CDKN1A; C6orf89; MTCH1

SRPK1; C6orf89; STK38; MTCH1; KCTD20; BRPF3; CDKN1A; SRSF3

28

chr6

Differential

Strength Change

Stim

RSPH9; VEGFA; CDC5L; TMEM63B; HSP90AB1; SLC35B2

TMEM63B; CDC5L

29

chr6

Differential

Strength Change

Stim

IFNGR1; WAKMAR2; TNFAIP3

TNFAIP3; IFNGR1

30

chr6

Differential

Strength Change

Stim

IFNGR1; WAKMAR2; TNFAIP3

TNFAIP3; IFNGR1

32

chr6

Differential

Strength Change

Basal

RPS6KA2; AFDN

 

33

chr7

Differential

Strength Change

Stim

CREB5; TAX1BP1; JAZF1

JAZF1; TAX1BP1

47

chr11

Differential

Strength Change

Basal

TRIM44; FJX1; COMMD9

COMMD9

48

chr11

Differential

Strength Change

Basal

FADS2; SLC15A3; TKFC; INCENP; AHNAK; INTS5; CCDC86; PRPF19; TMEM109; TMEM132A; VPS37C; DDB1; CYB561A3; TMEM138; CPSF7; MYRF; FEN1; FADS1; FADS3; RAB3IL1; BEST1; FTH1; EEF1G; TUT1; MTA2; EML3; ROM1; GANAB; LBHD1; CSKMT; UQCC3; UBXN1; LRRN4CL; HNRNPUL2-BSCL2; HNRNPUL2; TMEM179B; TMEM223; NXF1; STX5; RNU2-2P; SLC3A2

TMEM132A; FTH1; SLC15A3; FADS1; AHNAK; VPS37C; INCENP; RAB3IL1; LRRN4CL; EEF1G; TMEM138; ROM1; TUT1; DDB1; FADS2; CCDC86; MTA2; TMEM109

49

chr11

Differential

Strength Change

Basal

ACAT1; ATM; CUL5; NPAT; POGLUT3

ATM; ACAT1; NPAT; CUL5

57

chr14

Differential

Strength Change

Basal

ZFYVE26; ZFP36L1

 

65

chr18

Differential

Split

Basal

SPIRE1; SEH1L; CEP192; AFG3L2; CEP76

CEP76; CEP192; SPIRE1; SEH1L

72

chr22

Differential

Strength Change

Basal

MAPK1; UBE2L3; PPIL2; YPEL1; PPM1F

MAPK1; UBE2L3

73

chr22

Differential

Strength Change

Basal

JOSD1; GTPBP1; SUN2; CBX6; APOBEC3C; CBX7; RPL3; MIEF1; ATF4; RPS19BP1

GTPBP1; RPL3; SUN2; ATF4; CBX6