This project aims to identify potential transcription factors (TFs) involved in PXDN regulation using publicly available ChIP-Seq data. PXDN is a gene that encodes the peroxidasin protein, which has been linked to several prominent diseases worldwide. These include breast and prostate cancers, as well as kidney fibrosis and cardiovascular disease. Thus, these four tissue types - breast, prostate, kidney and cardiovascular - are used in this analysis to better understand the regulation of PXDN in each.
The raw data for this project was sourced from the ChIP-Atlas database, with the help of Prof. Shinya Oki - the co-author of these tools @inutano/chip-atlas. The ChIP-Seq reads were collected from major projects (such as ENCODE) as well as from smaller projects stored in the SRA. The reads were aligned to the human reference genome with Bowtie2 and MACS2 was used for peak calling of the significantly enriched aligned reads (link to ChIP-Atlas publication: https://www.embopress.org/doi/full/10.15252/embr.201846255).
These results were downloaded in BED file format for the region of PXDN (hg19::chr2:1,577,805-1,806,141) for each tissue at a q-value greater than 1x10-5. Each of these files are available in the the TF folder.
This script includes the steps of the downstream analysis of this data using a number of R packages from Bioconductor (ChIPseeker in particular). This includes the functional annotation, further filtering and visualisation of the data. The results generated here were used to find the known and de novo binding sites for the final TFs using the MEME Suite command line tool (not included in this script).
This is my first time conducting bioinformatic analysis in R so all comments and suggestions are most welcome.