Table 3 Enrichment of PD risk variants within open chromatin region sets containing known motifs identified with MEME-ChIP.

From: Integrative analysis identifies bHLH transcription factors as contributors to Parkinson’s disease risk mechanisms

Motif-containing OCR sets

GoShifter Adj. p-val (p-val)

GREGOR Adj. p-val (p-val)

No. ATAC-seq peaks

NEUROD1*

7.20 × 10–03 (4.00 × 10–04)

7.63 × 10–04 (4.24 × 10–05)

12197

SP1

0.058 (3.20 × 10–03)

5.79 × 10–06 (3.21 × 10–07)

19373

ZNF263

0.472 (0.026)

2.85 × 10–03 (1.59 × 10–04)

27496

NHLH1

0.770 (0.043)

0.552 (0.031)

8288

TEAD2

1 (0.133)

0.097 (5.41 × 10–03)

7000

RBPJ

1 (0.137)

0.790 (0.044)

11637

KLF9

1 (0.206)

0.188 (0.010)

12364

NRF1

1 (0.254)

0.071 (3.92 × 10–03)

7740

SPIC

1 (0.261)

1 (0.075)

8737

SPIB

1 (0.291)

0.422 (0.023)

9300

ZIC1

1 (0.335)

0.221 (0.012)

6952

Stat5a::Stat5b

1 (0.457)

1 (0.140)

9783

ZNF384

1 (0.510)

1 (0.644)

14373

MEF2C

1 (0.557)

1 (0.279)

16923

FOSL2

1 (0.854)

1 (0.519)

9141

FOXP1

1 (0.888)

1 (0.919)

6847

TBP

1 (0.911)

1 (0.816)

5011

CREB1

1 (0.911)

1 (0.363)

2994

  1. The motif-containing OCR set passing the significance threshold with both GoShifter and GREGOR is marked with a star and is reported in the text as significantly enriched with PD risk variants. We adjusted for multiple testing by Bonferroni correction, adjusting for 18 tests. Unadjusted p-values are provided in parenthesis. Adjusted p-val < 0.05 are written in bold. No. ATAC-seq peaks refers to the total number of peaks, representing OCRs, in the analysed motif-containing open chromatin sets. The total number of ATAC-seq peaks in superior temporal cortex neurons is 76145.
  2. PD, Parkinson’s disease; OCR, Open chromatin region.
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