Exercises

  1. Check what kind of annotation data can be extracted using org.Hs.eg.db package

  2. Print few gene names from org.Hs.eg.db

  3. Retrieve gene name, chromosome and Ensembl gene identifiers for “HEBP2” and “PRND” from org.Hs.eg.db

  4. How many annotation datasets available in Ensembl Biomart?

  5. Retrieve genomic coordinates for human genes from Ensembl biomart and build a GRanges object.

    • Subset the above GRanges object to include only protein coding genes
    • Subset the GRanges object again with genes in main chromsomes (1-22,X,Y)
    • Create another GRanges object with genes in chr1:1544000-2371000

  6. Retrieve 200 bp upstream promoter sequences for the given gene symbols AQP1, ASNSP2, KPNA2, FRMD4A, NSUN5, VAC14 from Ensembl human biomart.

    • Tips:
    • Read documentation for getSequence
    • Use type="hgnc_symbol" and seqType="coding_gene_flank"

  7. Retrieve the transcript coordinates for genes as GRangesList from TxDb.Hsapiens.UCSC.hg19.knownGene (install it from Bioconductor if required)

  8. Retrieve exon coordiantes for genes from TxDb.Hsapiens.UCSC.hg19.knownGene