Table 2 Enrichment of PD risk variants within motif-containing open chromatin region sets identified with HOMER.

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

Olig2*

0.025 (1.10 × 10–03)

1.39 × 10–03 (6.05 × 10–05)

21924

POL010.1_DCE

0.064 (2.80 × 10–03)

7.18 × 10–05 (3.12 × 10–06)

37574

NRF1

0.407 (0.018)

6.26 × 10–03 (2.72 × 10–04)

7729

NFIA

0.580 (0.025)

0.022 (9.51 × 10–04)

37903

Sp2

1 (0.052)

0.147 (6.39 × 10–03)

7566

Egr2

1 (0.073)

0.103 (4.46 × 10–03)

25202

NFY

1 (0.078)

0.152 (6.63 × 10–03)

5806

PB0080.1_Tbp_1

1 (0.087)

0.774 (0.034)

5118

ETV2

1 (0.171)

0.113 (4.91 × 10–03)

10961

CTCF

1 (0.189)

1 (0.091)

6257

Mef2c

1 (0.205)

1 (0.050)

17566

PB0013.1_Eomes_1

1 (0.221)

1 (0.053)

29438

Atf1

1 (0.297)

0.331 (0.014)

5809

BORIS

1 (0.333)

1 (0.138)

6018

POL002.1_INR

1 (0.336)

1 (0.136)

34917

SPDEF

1 (0.390)

0.172 (0.007)

18884

MafF

1 (0.523)

1 (0.219)

34091

GFY

1 (0.683)

1 (0.543)

1196

Rfx5

1 (0.759)

1 (0.382)

7410

Fra1

1 (0.851)

1 (0.601)

9557

NFIL3

1 (0.901)

1 (0.723)

4431

Rfx1

1 (1)

1 (1)

3337

noMotif

1 (1)

0.542 (0.024)

1196

  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 23 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 OCR 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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