example_chip_summits {memes} | R Documentation

## Annotated Transcription Factor ChIP-seq summits

### Description

ChIP-seq summit positions on Drosophila melanogaster chromosome 3 for the transcription factor E93 using a union set of peaks from third-instar larval wings ("Early") and 24 hour Pupal ("Late") wings.

### Usage

    example_chip_summits

### Format

A GRanges object of ChIP summit position with 2 metadata columns

peak_binding_description

  Binding profiles between Early and Late E93 were compared. Peaks are annotated as whether they are bound in Early wings only ("ectopic"), both Early and Late wings ("entopic"), or only bound in Late wings ("orphan").

e93_sensitive_behavior

  change in chromatin accessibility in response to E93 binding: Increasing, Decreasing, or Static

### Details

E93 is a transcription factor normally present only in Late wings. An experimental perturbation precociously expressed E93 during Early stages. Binding profiles between Early and Late E93 were compared. Peaks are annotated as whether they are bound in Early wings only ("ectopic"), both Early and Late wings ("entopic"), or only bound in Late wings ("orphan").

DNA elements can be made "open" or "closed" in response to binding of transcription factors like E93. Accessibility of E93 binding sites before and after E93 expression was measured using FAIRE-seq. ChIP peaks are annotated by how their accessibility changes in response to E93 binding . Peaks can become more open ("Increasing"), more closed ("Decreasing"), or unchanged in accessibility ("Static"). These experiments demonstrate a causal relationship between E93 binding and both opening and closing of DNA elements.

### Source

https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE141738&format=file&file=GSE141738

[Package memes version 1.0.4 Index]