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Table 1 Genome Ontology analysis of nucleosome-unmasked regions

From: TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning

10 versus 0 min TNFα stimulation

30 versus 0 min TNFα stimulation

Annotation

GO group

log P -value

Annotation

GO group

log P -value

rRNA

Basic

−132.6

CpG island

Basic

−18,894.5

-

-

-

coding

Basic

−2,508.6

-

-

-

protein-coding

Basic

−2,202.6

-

-

-

exons

Basic

−2,175.4

-

-

-

promoters

Basic

−1,637.2

-

-

-

5′ UTR

Basic

−1,573.7

-

-

-

rRNA

Basic

−90.7

-

-

-

miscRNA

Basic

−57.6

-

-

-

TTS

Basic

−30.3

-

-

-

miRNA

Basic

−2.3

Alu

SINE

−1,010,851.5

Alu

SINE

−127,523.7

Satellite

Satellite

−138,649.4

AluY

SINE

−254,77.1

AluSx

SINE

−130,806.8

AluJb

SINE

−13,157.4

Simple

Repeat

−109,102.9

AluSx

SINE

−10,162.6

AluSz

SINE

−95,618.8

AluSx1

SINE

−9,723.1

Satellite

Satellite

−84,407.6

AluSz

SINE

−7,150.9

TGn

Repeat

−82,907.0

AluJr

SINE

−6,259.1

Can

Repeat

−82,146.3

AluJo

SINE

−5,837.8

AluSx1

SINE

−81,015.6

AluSz6

SINE

−3,989.9

CATTCn

Satellite

−77,388.9

AluSg

SINE

−3,556.9

  1. A list of the top regions unmasked at 10 and 30 min post-stimulation (looking at nucleosomes identified using findPeaks [23] that were repositioned by >10 bp at 10 or 30 compared to 0 min). Top half: regions associated with ‘basic’ genome annotation. Bottom half: repeat elements. For each entry, the annotation category, genome ontology group and identification confidence levels (log P-value) are shown; Alu repeats known to bind NF-κB [24] are in bold. GO, Gene Ontology; SINE, short interspersed nuclear elements; TNFα, tumour necrosis factor alpha.
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Genome Biology

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