An object of class "Anno" that contains information about domain repertoires (a complete set of domains: domain-ome) in Eukaryotes (including extant and ancestral genomes). This data is prepared based on 1) SUPERFAMILY database which provides domain and architecture assignments to all completely sequenced genomes including eukaryotic genomes; 2) ancestral domain architecture repertoires inferred by applying Dollo parsimony to eukaryotic part of species tree of life (sTOL), from which ancestral superfamily domain and architecture repertoires at all branching points in eukaryotic evolution are inferred. This allows us to list ancestral domain and architecture repertoires that were present at these points. Based on the observed/inferred domain and architecture repertoires, we also define genome-specific plasticity potential for an individual domain as how many different architectures (or architecture diversity) it can be formed in an extant/ancestral genome. As a result, for each genome, domain repertoires (domainome) are represented as a profile of states on domains, where non-zero entry indicates a domain for which how many different architectures have occurred in the genome.
data(Ancestral_domainome)
an object of class Anno. It has slots for "annoData",
"termData" and "domainData":
annoData: a sparse matrix of 2019 domains X 875
terms/genomes (including 438 extant genomes and 437 ancestral genomes),
with each entry telling how many different architectures a domain has
in a genome. Note: zero entry also means that this domain is absent in
the genome
termData: variables describing terms/genomes (i.e. columns
in annoData), including extant/ancestral genome information: "left_id"
(unique and used as internal id), "right_id" (used in combination with
"left_id" to define the post-ordered binary tree structure), "taxon_id"
(NCBI taxonomy id, if matched), "genome" (2-letter genome identifiers
used in SUPERFAMILY, if being extant), "name" (NCBI taxonomy name, if
matched), "rank" (NCBI taxonomy rank, if matched), "branchlength"
(branch length in relevance to the parent), and "common_name" (NCBI
taxonomy common name, if matched and existed)
domainData: variables describing domains (i.e. rows in
annoData), including information about domains: "sunid" for SCOP id,
"level" for SCOP level, "classification" for SCOP classification,
"description" for SCOP description
Fang et al. (2013) A daily-updated tree of (sequenced) life as a reference for genome research. Scientific reports, 3:2015.
Morais et al. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res, 39(Database issue):D427-34.
Andreeva et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res, 36(Database issue):D419-425
data(Ancestral_domainome) Ancestral_domainomeAn object of S4 class 'Anno' @annoData: 2019 domains, 875 terms @termData (InfoDataFrame) termNames: 3 4 5 ... 1743 1750 (875 total) tvarLabels: left_id right_id taxon_id ... branchlength common_name (8 total) @domainData (InfoDataFrame) domainNames: 46458 46548 46557 ... 161266 161270 (2019 total) dvarLabels: sunid level classification description# retrieve info on terms/genomes termData(Ancestral_domainome)An object of S4 class 'InfoDataFrame' rowNames: 3 4 5 ... 1743 1750 (875 total) colNames: left_id right_id taxon_id ... branchlength common_name (8 total)# retrieve info on SCOP domains domainData(Ancestral_domainome)An object of S4 class 'InfoDataFrame' rowNames: 46458 46548 46557 ... 161266 161270 (2019 total) colNames: sunid level classification description# retrieve the first 5 rows and columns of data x <- annoData(Ancestral_domainome)[1:5,1:5] x5 x 5 sparse Matrix of class "dgCMatrix" 3 4 5 6 7 46458 4 6 9 10 10 46548 13 22 24 28 29 46557 . . . . . 46561 3 4 4 4 4 46565 18 116 123 121 125# convert the above retrieval to the full matrix as.matrix(x)3 4 5 6 7 46458 4 6 9 10 10 46548 13 22 24 28 29 46557 0 0 0 0 0 46561 3 4 4 4 4 46565 18 116 123 121 125