Description
Filtered correlations between replicated Histone marked bins and gene promoters based on transcription.
Display Conventions and Configuration
These bigBed tracks represent correlation measures between transcription in 13 tissues and 1kb bin read counts of three separate histone marks (H3K4me3, H3K27Ac and H3K27me3).
N.B. each bin is correlated with EVERY gene within 1Mb. Currently using the TSS of the longest transcript.
For each tissue, four tracks were generated.
- Specific means correlations between bins that were replicated (see methods) in both replicates of the tissue and no other tissues.
- Selective correlations allow the bin to have been called as marked in up to half the samples.
- For both specific and selective, a subset track was also generated retaining only correlations with protein-coding genes (pcOnly).
- The pcOnly tracks are shown by default but the full tracks can be turned on.
By default only correlations greater than +/- 0.7 (bed score 700) are shown. Negative correlations are shown in red, positive correlations in blue.
Methods
This section describes the methods used to generate and analyze the data and helps users
understand how the track data was produced and sometimes has subsections if useful.
- Embryonic ChIP-seq mapped to hg38 using STAR.
- Uniquely mapped reads counted into 1kb bins using csaw
- Normalisation of read counts through downsampling using subseq with the 99th percentile as sample weight
- Table of counts binarised using a custom elbow plot threshold method arseFromElbow
- Designation of bins as tissue-specific if pass threshold in two replicated samples from same tissue and no other samples
The above steps are from the analysis set we call hg38.full.1kb.bins .
Credits
We are very grateful to all women who consented to take part in our research programme and for the assistance of research nurses and clinical colleagues at Central Manchester University Hospitals NHS Foundation Trust. We thank Ian Donaldson, Peter Briggs and Andy Hayes of the Bioinformatics and Genomic Technologies Core Facilities at the University of Manchester for assistance with RNA-sequencing. REJ is a UK Medical Research Council (MRC) clinical research training fellow. NAH is a Wellcome Trust senior fellow in clinical science (WT088566MA). This project received support from the Wellcome Trust (WT097820) with additional support from MRC project grants MR/L009986/1 to NB and NAH, the British Council (14BX15NHBG) to NAH and MR/J003352/1 to KPH.
References
This data is unpublished. Please do not share without prior permission of neil.hanley@manchester.ac.uk