Table 1 Gene ontology analysis based on the microarray data analysis from LCLs, ATR-X cases vs unaffected donors showing the top enriched pathways based on the count with a p-value < 0.05 (p-values based on EASE Score DAVID 6.8)60.

From: The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin

Gene list

Term

Count

p-value

Genes

DEGs p < 0.05

Transcription, DNA-templated

32

0.042

ZNF555, ZNF57, ZNF347, CNOT6, ZNF32, ZBTB38, ZNF30, HOXA1, LPXN, STAT4, LBH, TEAD4, VPS36, ZNF595, TXNIP, MBD3L3, L3MBTL4, TRNP1, ZNF506, ARID5A, ZNF649, MAPK11, MBD2, ZNF626, MXD1, ATF7IP2, PURA, MSL3, ZNF718, ADNP2, MAFIP, ZNF418

 

Regulation of transcription, DNA-templated

27

0.025

ZNF555, ZNF57, ZNF347, CNOT6, ZNF32, ZNF30, HOXA1, LPXN, STAT4, MEIS2, LBH, MYB, VPS36, ZNF595, L3MBTL4, TRNP1, ZNF506, ZNF649, ZNF626, ATF7IP2, MSL3, RPS6KA5, ZNF718, ADNP2, TCFL5, MAFIP, ZNF418

 

Angiogenesis

7

0.045

KLF5, FMNL3, NUS1, LEPR, SOX18, ENPEP, PNPLA6

 

T cell costimulation

6

0.002

BTLA, TRAC, CD80, KLRK1, KLRC4-KLRK1, CD28

 

Peptidyl-tyrosine dephosphorylation

6

0.006

PTPRC, PTPRG, DNAJC6, PTPDC1, PTPRO, RNGTT

 

Negative regulation of gene expression

6

0.021

SLC35C2, BAK1, AIF1, TRIM6, CCR1, CD28

DEGs p < 0.05 Intragenic ATRX binding site

Transcription, DNA-templated

20

3.62E−04

ZNF595, ZBTB38, MBD2, CTR9, ATF7IP2, ARID5A, ZNF32, ZNF57, CNOT6, LBH, ZNF718, ZNF649, ZNF418, ZNF506, ZNF626, ZNF30, ADNP2, ZNF347, ZNF555, L3MBTL4

 

Regulation of transcription, DNA-templated

19

3.86E−05

ZNF595, CTR9, ATF7IP2, ZNF32, ZNF57, MEIS2, CNOT6, LBH, ZNF718, ZNF649, ZNF418, ZNF506, ZNF626, ZNF30, MYB, ADNP2, ZNF347, ZNF555, L3MBTL4

DEGs p < 0.05 ATRX binding site within 10 kb

Transcription, DNA-templated

22

4.98E−04

ZNF595, ZBTB38, MBD2, CTR9, ATF7IP2, ARID5A, ZNF32, ZNF57, CNOT6, LBH, ZNF718, ZNF649, ZNF418, ZNF506, ZNF626, ZNF30, STAT4, ADNP2, LPXN, ZNF347, ZNF555, L3MBTL4

 

Regulation of transcription, DNA-templated

21

3.91E−05

ZNF595, CTR9, ATF7IP2, ZNF32, ZNF57, MEIS2, CNOT6, LBH, ZNF718, ZNF649, ZNF418, ZNF506, ZNF626, ZNF30, MYB, STAT4, ADNP2, LPXN, ZNF347, ZNF555, L3MBTL4

DEGs p < 0.05 ATRX binding site within 50 kb

Transcription, DNA-templated

26

6.26E−4

ZNF595, CTR9, ATF7IP2, MBD3L4, MBD3L3, LBH, ZNF506, ZNF649, ZNF626, STAT4, ADNP2, LPXN, ZNF347, ZBTB38, MBD2, ARID5A, ZNF32, MSL3, ZNF57, CNOT6, ZNF718, ZNF418, ZNF30, TXNIP, ZNF555, L3MBTL4

 

Regulation of transcription, DNA-templated

23

2.28E−04

ZNF595, CTR9, ATF7IP2, ZNF32, MSL3, ZNF57, MEIS2, CNOT6, LBH, ZNF718, ZNF649, ZNF418, ZNF506, ZNF626, ZNF30, MYB, STAT4, ADNP2, LPXN, ZNF347, ZNF555, L3MBTL4, TCFL5

 

Negative regulation of transcription from RNA polymerase II promoter

10

0.044

ZNF649, MBD2, MYB, CTR9, TXNIP, MBD3L4, MBD3L5, MBD3L2, MBD3L3, MEIS2

DEGs p < 0.05 ATRX binding site within 100 kb

Transcription, DNA-templated

27

0.0049

ZNF595, CTR9, ATF7IP2, MBD3L4, MBD3L3, LBH, ZNF506, ZNF649, ZNF626, STAT4, ADNP2, LPXN, ZNF347, ZBTB38, MBD2, ARID5A, ZNF32, MSL3, ZNF57, MAPK11, CNOT6, ZNF718, ZNF418, ZNF30, TXNIP, ZNF555, L3MBTL4

 

Regulation of transcription, DNA-templated

23

0.0032

ZNF595, CTR9, ATF7IP2, ZNF32, MSL3, ZNF57, MEIS2, CNOT6, LBH, ZNF718, ZNF649, ZNF418, ZNF506, ZNF626, ZNF30, MYB, STAT4, ADNP2, LPXN, ZNF347, ZNF555, L3MBTL4, TCFL5

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