Today we will focus on the exploration of hg38 assembly, HepG2 cell line (see https://depmap.org/portal/cell_line/HEPG2_LIVER?tab=mutation if you want to deepen) and MYC regulation.

  1. Load TxDb.Hsapiens.UCSC.hg38.knownGene. Plot the density of transcripts. Use plot.type=1.
  1. Read file CCLE_RRBS_TSS1kb_20181022_HepG2.rds in Datasets/karyoploteR/. This file contains DNA methylation values in proximity of transcription start sites (TSS) for HepG2 cell line. It has been retrieved from depmap @ https://depmap.org/portal/download/all/ and slighly modified. Make a lollipop plot representing DNA methylation values across chromosomes chr1, chr2 and chr3. Scale colors according to values. Use plot.type=1.
  1. Read file HEPG2_mutations.csv in Datasets/karyoploteR/. This file contains mutations that characterize HepG2 cell line. It has been retrieved from depmap @ https://depmap.org/portal/download/all/ and slightly modified. Use plot.type=6 and plot points at mutation location. Assign a different color to each Variant.Info and a shape to each Variant.Type.
  1. Read file Hepg2_copy_number_segments.csv in Datasets/karyoploteR/. This file contains copy numbers of HepG2 cell line and has been retrieved from depmap @ https://depmap.org/portal/download/all/ and slighly modified. Plot segments. Use plot.type=4 and color segments according to values (black if ==2, red if >2 and blue if <2).

  1. Read file ENCSR000DLR.MYC.Hep-G2.bed in Datasets/karyoploteR/. This file contains ChIP-seq significant peaks of the transcription factor MYC in HepG2 cell line. It has been retrieved from Remap @ https://remap2022.univ-amu.fr/biotype_page/Hep-G2:9606 and slightly modified. Plot density of regions and insert a marker, indicating were MYC gene is located.

  2. Read file chr1_hg38_geneHancer.csv in Datasets/karyoploteR/. This file contains Enhancer positions together with putative regulated genes for chr1. It has been retrieved from UCSC geneHancer @ https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1563652731_GeAnj3cf9S70pGQWKAUtajUAdUTn&clade=mammal&org=Human&db=hg38&hgta_group=regulation&hgta_track=geneHancer&hgta_table=geneHancerInteractionsDoubleElite&hgta_regionType=range&position=chr1%3A1-248%2C956%2C422&hgta_outputType=primaryTable&hgta_outFileName= and slighly modified. Randomly choose 50 links and plot them.

  3. Extract promoters from TxDb.Hsapiens.UCSC.hg38.knownGene by extending TSS of 500 bps upstream and 500 bps downstream.

  1. Find overlaps between MYC ChIP-seq peaks and enhancers. Extract unique peaks that overlap and unique enhancers that overlap.
  1. Find overlaps between MYC ChIP-seq peaks and promoters. Extract unique peaks that overlap and unique promoters that overlap.
  1. Concatenate peaks that overlapped with promoters and enhancer and merge regions that overlap.
  1. Plot density of chip regions that overlap with promoters and enhancers.