biomartrEvolutionary Transcriptomics defines the concept of combining genetic sequence conservation information with gene expression levels to quantify transcriptome conservation throughout biological processes (Domazet-Loso and Tautz, 2010 Nature ; Quint, Drost et al., 2012 Nature ; Drost et al., 2015 Mol. Biol. Evol. ; Drost et al., 2016 Mol. Biol. Evol.).
The Introduction to Evolutionary Transcriptomics vignette provided by the myTAI package will give users a broad overwiew of phylotranscriptomics as scientific discipline.
The biomartr package aims to provide an interface for functional annotation queries. Hence, combining functional annotation with the detection of evolutionary signals in biological processes with orthologr and myTAI allows users to correlate biological functions and constraints with their evolutionary origin.
This vignette aims to provide use cases for combining functional annotation of genes (biomartr) with their role in development (myTAI) in an evolutionary context (orthologr).
Evolutionary Transcriptomics aims to predict stages or periods of evolutionary conservation in biological processes on the transcriptome level. However, finding genes sharing a common evolutionary history could reveal how the the biological process might have evolved in the first place.
In this Use Case we will combine functional and biological annotation obtained with biomartr with enriched genes obtained with PlotEnrichment().
For the following example we will use the dataset an enrichment analyses found in PlotEnrichment().
Install and load the myTAI package:
# install myTAI
install.packages("myTAI")
# load myTAI
library(myTAI)Download the Phylostratigraphic Map of D. rerio:
# download the Phylostratigraphic Map of Danio rerio
# from Sestak and Domazet-Loso, 2015
download.file( url = "http://mbe.oxfordjournals.org/content/suppl/2014/11/17/msu319.DC1/TableS3-2.xlsx",
destfile = "MBE_2015a_Drerio_PhyloMap.xlsx" )Read the *.xlsx file storing the Phylostratigraphic Map of D. rerio and format it for the use with myTAI:
# install the readxl package
install.packages("readxl")
# load package readxl
library(readxl)
# read the excel file
DrerioPhyloMap.MBEa <- read_excel("MBE_2015a_Drerio_PhyloMap.xlsx", sheet = 1, skip = 4)
# format Phylostratigraphic Map for use with myTAI
Drerio.PhyloMap <- DrerioPhyloMap.MBEa[ , 1:2]
# have a look at the final format
head(Drerio.PhyloMap) Phylostrata ZFIN_ID
1 1 ZDB-GENE-000208-13
2 1 ZDB-GENE-000208-17
3 1 ZDB-GENE-000208-18
4 1 ZDB-GENE-000208-23
5 1 ZDB-GENE-000209-3
6 1 ZDB-GENE-000209-4Now, Drerio.PhyloMap stores the Phylostratigraphic Map of D. rerio which is used as background set to perform enrichment analyses with PlotEnrichment() from myTAI.
Now, the PlotEnrichment() function visualizes the over- and underrepresented Phylostrata of brain specific genes when compared with the total number of genes stored in the Phylostratigraphic Map of D. rerio.
library(readxl)
# read expression data (organ specific genes) from Sestak and Domazet-Loso, 2015
Drerio.OrganSpecificExpression <- read_excel("MBE_2015a_Drerio_PhyloMap.xlsx", sheet = 2, skip = 3)
# select only brain specific genes
Drerio.Brain.Genes <- unlist(unique(na.omit(Drerio.OrganSpecificExpression[ , "brain"])))
# visualize enriched Phylostrata of genes annotated as brain specific
PlotEnrichment(Drerio.PhyloMap,
test.set = Drerio.Brain.Genes,
measure = "foldchange",
use.only.map = TRUE,
legendName = "PS")Users will observe that for example brain genes deriving from PS5 are significantly enriched.
Now we can select all brain genes originating in PS5 using the SelectGeneSet() function from myTAI. Please notice that SelectGeneSet() can only be used with phylostratigraphic maps only (use.map.only = TRUE argument) since myTAI version > 0.3.0.
BrainGenes <- SelectGeneSet(ExpressionSet = Drerio.PhyloMap,
gene.set = Drerio.Brain.Genes,
use.only.map = TRUE)
# select only brain genes originating in PS5
BrainGenes.PS5 <- BrainGenes[which(BrainGenes[ , "Phylostrata"] == 5), ]
# look at the results
head(BrainGenes.PS5) Phylostrata ZFIN_ID
14851 5 ZDB-GENE-000210-6
14852 5 ZDB-GENE-000210-7
14853 5 ZDB-GENE-000328-4
14856 5 ZDB-GENE-000411-1
14857 5 ZDB-GENE-000427-4
14860 5 ZDB-GENE-000526-1Now users can perform the biomart() function to obtain the functional annotation of brain genes originating in PS5.
For this purpose, first we need to find the filter name of the corresponding gene ids such as ZDB-GENE-000210-6.
# find filter for zfin.org ids
organismFilters("Danio rerio", topic = "zfin_id") name description dataset
52 with_zfin_id with ZFIN ID(s) drerio_gene_ensembl
53 with_zfin_id_transcript_name with ZFIN transcript name(s) drerio_gene_ensembl
103 zfin_id ZFIN ID(s) [e.g. ZDB-GENE-060825-136] drerio_gene_ensembl
274 with_zfin_id with ZFIN ID(s) drerio_gene_vega
286 zfin_id ZFIN ID(s) [e.g. ZDB-GENE-121214-212] drerio_gene_vega
366 with_zfin_id with ZFIN ID(s) drerio_gene_ensembl
367 with_zfin_id_transcript_name with ZFIN transcript name(s) drerio_gene_ensembl
417 zfin_id ZFIN ID(s) [e.g. ZDB-GENE-060825-136] drerio_gene_ensembl
588 with_zfin_id with ZFIN ID(s) drerio_gene_vega
600 zfin_id ZFIN ID(s) [e.g. ZDB-GENE-121214-212] drerio_gene_vega
680 with_zfin_id with ZFIN ID(s) drerio_gene_ensembl
681 with_zfin_id_transcript_name with ZFIN transcript name(s) drerio_gene_ensembl
731 zfin_id ZFIN ID(s) [e.g. ZDB-GENE-060825-136] drerio_gene_ensembl
902 with_zfin_id with ZFIN ID(s) drerio_gene_vega
914 zfin_id ZFIN ID(s) [e.g. ZDB-GENE-121214-212] drerio_gene_vega
mart
52 ENSEMBL_MART_ENSEMBL
53 ENSEMBL_MART_ENSEMBL
103 ENSEMBL_MART_ENSEMBL
274 ENSEMBL_MART_ENSEMBL
286 ENSEMBL_MART_ENSEMBL
366 ENSEMBL_MART_ENSEMBL
367 ENSEMBL_MART_ENSEMBL
417 ENSEMBL_MART_ENSEMBL
588 ENSEMBL_MART_ENSEMBL
600 ENSEMBL_MART_ENSEMBL
680 ENSEMBL_MART_ENSEMBL
681 ENSEMBL_MART_ENSEMBL
731 ENSEMBL_MART_ENSEMBL
902 ENSEMBL_MART_ENSEMBL
914 ENSEMBL_MART_ENSEMBLNow users can retrieve the corresponding GO attribute of D. rerio with organismAttributes.
# find go attribute term for D. rerio
organismAttributes("Danio rerio", topic = "go") name description
33 go_id GO Term Accession
36 go_linkage_type GO Term Evidence Code
38 goslim_goa_accession GOSlim GOA Accession(s)
39 goslim_goa_description GOSlim GOA Description
516 ggorilla_homolog_ensembl_gene Gorilla Ensembl Gene ID
517 ggorilla_homolog_canomical_transcript_protein Canonical Protein or Transcript ID
518 ggorilla_homolog_ensembl_peptide Gorilla Ensembl Protein ID
519 ggorilla_homolog_chromosome Gorilla Chromosome Name
520 ggorilla_homolog_chrom_start Gorilla Chromosome Start (bp)
521 ggorilla_homolog_chrom_end Gorilla Chromosome End (bp)
522 ggorilla_homolog_orthology_type Homology Type
523 ggorilla_homolog_subtype Ancestor
524 ggorilla_homolog_orthology_confidence Orthology confidence [0 low, 1 high]
525 ggorilla_homolog_perc_id % Identity with respect to query gene
526 ggorilla_homolog_perc_id_r1 % Identity with respect to Gorilla gene
527 ggorilla_homolog_dn dN
528 ggorilla_homolog_ds dS
1240 go_id GO ID
1241 quick_go Quick GO ID
1370 go_id GO Term Accession
1373 go_linkage_type GO Term Evidence Code
1375 goslim_goa_accession GOSlim GOA Accession(s)
1376 goslim_goa_description GOSlim GOA Description
1853 ggorilla_homolog_ensembl_gene Gorilla Ensembl Gene ID
1854 ggorilla_homolog_canomical_transcript_protein Canonical Protein or Transcript ID
1855 ggorilla_homolog_ensembl_peptide Gorilla Ensembl Protein ID
1856 ggorilla_homolog_chromosome Gorilla Chromosome Name
1857 ggorilla_homolog_chrom_start Gorilla Chromosome Start (bp)
1858 ggorilla_homolog_chrom_end Gorilla Chromosome End (bp)
1859 ggorilla_homolog_orthology_type Homology Type
1860 ggorilla_homolog_subtype Ancestor
1861 ggorilla_homolog_orthology_confidence Orthology confidence [0 low, 1 high]
1862 ggorilla_homolog_perc_id % Identity with respect to query gene
1863 ggorilla_homolog_perc_id_r1 % Identity with respect to Gorilla gene
1864 ggorilla_homolog_dn dN
1865 ggorilla_homolog_ds dS
2577 go_id GO ID
2578 quick_go Quick GO ID
2707 go_id GO Term Accession
2710 go_linkage_type GO Term Evidence Code
2712 goslim_goa_accession GOSlim GOA Accession(s)
2713 goslim_goa_description GOSlim GOA Description
3190 ggorilla_homolog_ensembl_gene Gorilla Ensembl Gene ID
3191 ggorilla_homolog_canomical_transcript_protein Canonical Protein or Transcript ID
3192 ggorilla_homolog_ensembl_peptide Gorilla Ensembl Protein ID
3193 ggorilla_homolog_chromosome Gorilla Chromosome Name
3194 ggorilla_homolog_chrom_start Gorilla Chromosome Start (bp)
3195 ggorilla_homolog_chrom_end Gorilla Chromosome End (bp)
3196 ggorilla_homolog_orthology_type Homology Type
3197 ggorilla_homolog_subtype Ancestor
3198 ggorilla_homolog_orthology_confidence Orthology confidence [0 low, 1 high]
3199 ggorilla_homolog_perc_id % Identity with respect to query gene
3200 ggorilla_homolog_perc_id_r1 % Identity with respect to Gorilla gene
3201 ggorilla_homolog_dn dN
3202 ggorilla_homolog_ds dS
3914 go_id GO ID
3915 quick_go Quick GO ID
dataset mart
33 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
36 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
38 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
39 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
516 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
517 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
518 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
519 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
520 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
521 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
522 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
523 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
524 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
525 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
526 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
527 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
528 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1240 drerio_gene_vega ENSEMBL_MART_ENSEMBL
1241 drerio_gene_vega ENSEMBL_MART_ENSEMBL
1370 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1373 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1375 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1376 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1853 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1854 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1855 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1856 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1857 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1858 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1859 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1860 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1861 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1862 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1863 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1864 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
1865 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
2577 drerio_gene_vega ENSEMBL_MART_ENSEMBL
2578 drerio_gene_vega ENSEMBL_MART_ENSEMBL
2707 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
2710 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
2712 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
2713 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3190 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3191 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3192 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3193 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3194 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3195 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3196 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3197 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3198 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3199 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3200 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3201 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3202 drerio_gene_ensembl ENSEMBL_MART_ENSEMBL
3914 drerio_gene_vega ENSEMBL_MART_ENSEMBL
3915 drerio_gene_vega ENSEMBL_MART_ENSEMBLNow users can specify the filter zfin_id and attribute go_id to retrieve the GO terms of corresponding gene ids (Please note that this will take some time).
# retrieve GO terms of D. rerio brain genes originating in PS5
GO_tbl.BrainGenes <- biomart(genes = unlist(BrainGenes.PS5[ , "ZFIN_ID"]),
mart = "ENSEMBL_MART_ENSEMBL",
dataset = "drerio_gene_ensembl",
attributes = "go_id",
filters = "zfin_id")
head(GO_tbl.BrainGenes) zfin_id go_id
1 ZDB-GENE-000210-6 GO:0060037
2 ZDB-GENE-000210-6 GO:0046983
3 ZDB-GENE-000210-7 GO:0046983
4 ZDB-GENE-000328-4 GO:0007275
5 ZDB-GENE-000328-4 GO:0007166
6 ZDB-GENE-000328-4 GO:0035567