matchedMotifs: Matched Motifs that Regulate H5-K9 Methylation

In NElnour/3dannotator: Classification of genome motifs or features to TADs

Description

The data set is obtained by scanning murine PPMs provided by Ngo et al. with FIMO against mm10 chromsome 18. The top 50 matches by q=value were selected and organized into a dataframe.

Usage

matchedMotifs

Format

A dataframe with 50 rows and 10 variables:

motif_id

chromosome 18 fragments start coordinates

motif_alt_id

chromosome 18 fragments end coordinates

sequence_name

chromsome name at which the matches were found

start

start coordinates of the matched motif on chromsome 18

stop

end coordinate of the matched motif on chromosome 18

strand

Either "+" or "-" denoting the strand orientation of the match

score

Maximum likelihood score

p.value

The probability that the motif matchs to the chromsome region bounded by start and stop coordinates.

q.value

The p-value corrected by Benjamini and Hochsberg false discvery rate for multiple testing

matched_sequence

Consensus sequence of matched motif

Source

https://www.pnas.org/content/116/9/3668

References

Ngo V, Chen Z, Zhang K, Whitaker J, Wang M, Wang W. (2019) Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse. PNAS 116(9): 3668–3677.

NElnour/3dannotator documentation built on Dec. 12, 2019, 12:55 a.m.