Systems Biology (Methods in Molecular Biology)

(Tina Sui) #1
management system based on the Comprehensive R Archive
Network (CRAN) [17]. The R installation should have the
following software packages installed (including all of their
dependencies): reshape2 [18], GSEABase {GSEABaseGen-
esete:tz}, GSVA [13], ggplot2 [19], and DESeq2 [20], using
the built-in "install.packages" function in R.


  1. A data set of ortholog-based mappings of Ensembl gene iden-
    tifiers for the non-human species (in the example vignette
    shown here, dog) to Human Gene Nomenclature Committee
    (HGNC) Gene Symbols. Such a mapping can be obtained
    using the BioMart tool [21] through the Ensembl genome
    portal [22]. This information should be contained in a single-
    column data frame "dog_ensgene_to_symbol" in which the
    Ensembl gene identifiers are the row names, as shown here
    (in this chapter, blue text indicates screen output from an R
    session):


>head(dog_ensgene_to_symbol)
Associated.Gene.Name
ENSCAFG00000022708
ENSCAFG00000022709
ENSCAFG00000022710
ENSCAFG00000022711
ENSCAFG00000022712
ENSCAFG00000022713 ND1
(seeNote 1). In the above, the R function "head" is used; this
function prints out the firstnlines (the default isn¼6 lines) of
whatever object is the function argument.


  1. A data set of human gene annotations mapping Ensembl gene
    identifiers to HGNC gene symbols. Such a mapping can be
    obtained using Ensembl BioMart. This information should be
    contained in a single-column data frame "human_ensgen-
    e_to_symbol" in which the Ensembl gene identifiers are the
    row names:


>head(human_ensgene_to_symbol)
Associated.Gene.Name
ENSG00000210049 MT-TF
ENSG00000211459 MT-RNR1
ENSG00000210077 MT-TV
ENSG00000210082 MT-RNR2
ENSG00000209082 MT-TL1
ENSG00000198888 MT-ND1


  1. A file containing mappings of HGNC gene symbols to gene
    functional annotation categories, in Gene Matrix Transposed
    (GMT) format {GSEATeam:wt}. A comprehensive file of
    human gene annotations (for the Gene Ontology functional
    annotation categories [23]) can be obtained from the Molecu-
    lar Signatures Database (MSigDB [24, 25]) web site [26] via a
    downloadable file "c5.all.v5.2.symbols.gmt."


Cross-Species RNA-Seq Analysis 293
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