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Table 1 ChIPtig statistics and results of motif finding in the mouse ESC dataset using Velvet

From: De novo ChIP-seq analysis

TF

No. ChIPtigs

Mapped ChIPtigs (%)

Motif rank with peak-calling

Motif rank with de novo pipeline

Motif rank with random ChIPtigs

c-MYC

5,159

92.9

1

1

4

CTCF

2,152

92.9

1

2

1

ESRRB

30,278

95.9

1

1

1

KLF4

1,660

90.4

1

1

1

NANOG

5,163

94.3

1

N

N

n-MYC

3,610

86.8

1

1

1

POU5F1

2,528

92.9

1

1

N

SMAD1

596

96.1

7

N

N

SOX2

2,511

92.5

1

1

N

STAT3

4,329

94.8

1

1

N

TCFCP2I1

20,566

95.7

N

N

N

ZFX

3,348

93.5

1

1

1

  1. Three settings were evaluated for motif finding performance: peak-calling using reference genome (MACS), top 1,000 ChIPtigs from the de novo pipeline, and 1,000 random ChIPtigs from the same experiment assembled by Velvet. The rank of the known motif (from JASPAR) in the DREME results is shown for each TF. ‘N’ in a row means that either DREME did not find any motif, or none of the motifs found by DREME matches the known motif for the TF in that row
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Genome Biology

ISSN: 1474-760X

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