The EMBL-EBI Expression Atlas consists of hand-picked high quality datasets from ArrayExpress that have been manually curated and re-analyzed via the Expression Atlas analysis pipeline. The Expression Atlas website allows users to search these datasets for genes and/or experimental conditions, to discover which genes are expressed in which tissues, cell types, developmental stages, and hundreds of other experimental conditions.
The ExpressionAtlas R package allows you to search for and download pre-packaged data from Expression Atlas inside an R session. Raw counts are provided for RNA-seq datasets, while normalized intensities are available for microarray experiments. Protocols describing how the data was generated are contained within the downloaded R objects, with more detailed information available on the Expression Atlas website. Sample annotations are also included in the R object.
You can search for experiments in Atlas using the searchAtlasExperiments() function. This function returns a DataFrame (see S4Vectors) containing the results of your search. The first argument to searchAtlasExperiments() should be a character vector of sample properties, e.g. biological sample attributes and/or experimental treatments. You may also optionally provide a species to limit your search to, as a second argument.
suppressMessages( library( ExpressionAtlas ) )atlasRes <- searchAtlasExperiments( properties = "salt", species = "rice" )
# Searching for Expression Atlas experiments matching your query ...
# Query successful.
# Found 3 experiments matching your query.atlasRes## DataFrame with 3 rows and 4 columns
## Accession Species Type
## <character> <character> <character>
## 1 E-GEOD-11175 Oryza sativa Japonic.. transcription profil..
## 2 E-MTAB-1625 Oryza sativa Japonic.. RNA-seq of coding RNA
## 3 E-MTAB-1624 Oryza sativa Japonic.. transcription profil..
## Title
## <character>
## 1 Transcription profil..
## 2 RNA-seq of coding RN..
## 3 Transcription profil..The Accession column contains the ArrayExpress accession of each dataset – the unique identifier assigned to it. The species, experiment type ( e.g. microarray or RNA-seq), and title of each dataset are also listed.
To download the data for any/all of the experiments in your results, you can use the function getAtlasData(). This function accepts a vector of ArrayExpress accessions. The data is downloaded into a SimpleList object (see package S4Vectors), with one entry per experiment, listed by accession.
For example, to download all the datasets in your results:
allExps <- getAtlasData( atlasRes$Accession )
# Downloading Expression Atlas experiment summary from:
# ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-GEOD-11175/E-GEOD-11175-atlasExperimentSummary.Rdata
# Successfully downloaded experiment summary object for E-GEOD-11175
# Downloading Expression Atlas experiment summary from:
# ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1625/E-MTAB-1625-atlasExperimentSummary.Rdata
# Successfully downloaded experiment summary object for E-MTAB-1625
# Downloading Expression Atlas experiment summary from:
# ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1624/E-MTAB-1624-atlasExperimentSummary.Rdata
# Successfully downloaded experiment summary object for E-MTAB-1624allExps## List of length 3
## names(3): E-GEOD-11175 E-MTAB-1625 E-MTAB-1624To only download the RNA-seq experiment(s):
rnaseqExps <- getAtlasData(
atlasRes$Accession[
grep(
"rna-seq",
atlasRes$Type,
ignore.case = TRUE
)
]
)
# Downloading Expression Atlas experiment summary from:
# ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1625/E-MTAB-1625-atlasExperimentSummary.Rdata
# Successfully downloaded experiment summary object for E-MTAB-1625rnaseqExps## List of length 1
## names(1): E-MTAB-1625To access an experiment summary, use the accession:
mtab1624 <- allExps[[ "E-MTAB-1624" ]]
mtab1625 <- allExps[[ "E-MTAB-1625" ]]Each dataset is also represented by a SimpleList, with one entry per platform used in the experiment. For RNA-seq data there will only ever be one entry, named rnaseq. For microarray data, there is one entry per array design used, listed by ArrayExpress array design accession (see below).
Following on from above, mtab1625 now contains a SimpleList object with a single entry named rnaseq. For RNA-seq experiments, this entry is a RangedSummarizedExperiment object (see package SummarizedExperiment).
sumexp <- mtab1625$rnaseq
sumexp## class: RangedSummarizedExperiment
## dim: 10 18
## metadata(4): pipeline filtering mapping quantification
## assays(1): counts
## rownames(10): EPlOSAG00000000001 EPlOSAG00000000002 ...
## EPlOSAG00000000009 EPlOSAG00000000010
## rowData names(0):
## colnames(18): ERR266221 ERR266222 ... ERR266237 ERR266238
## colData names(9): AtlasAssayGroup organism ... growth_condition
## sampling_timeThe matrix of raw counts for this experiment is stored in the assays slot:
head( assays( sumexp )$counts )## ERR266221 ERR266222 ERR266223 ERR266224 ERR266225 ERR266226
## EPlOSAG00000000001 0 0 0 0 1 0
## EPlOSAG00000000002 0 0 0 0 0 0
## EPlOSAG00000000003 0 0 0 0 0 0
## EPlOSAG00000000004 0 0 0 0 0 0
## EPlOSAG00000000005 0 0 0 0 0 0
## EPlOSAG00000000006 0 0 0 0 0 0
## ERR266227 ERR266228 ERR266229 ERR266230 ERR266231 ERR266232
## EPlOSAG00000000001 0 0 0 1 0 1
## EPlOSAG00000000002 0 0 0 0 0 0
## EPlOSAG00000000003 0 0 0 0 0 0
## EPlOSAG00000000004 0 0 0 0 0 0
## EPlOSAG00000000005 0 0 0 0 0 0
## EPlOSAG00000000006 0 0 0 0 0 0
## ERR266233 ERR266234 ERR266235 ERR266236 ERR266237 ERR266238
## EPlOSAG00000000001 0 1 1 0 0 0
## EPlOSAG00000000002 0 0 0 0 0 0
## EPlOSAG00000000003 0 0 0 0 0 0
## EPlOSAG00000000004 0 0 0 0 0 0
## EPlOSAG00000000005 0 0 0 0 0 0
## EPlOSAG00000000006 0 0 0 0 0 0The sample annotations can be found in the colData slot:
colData( sumexp )## DataFrame with 18 rows and 9 columns
## AtlasAssayGroup organism cultivar
## <character> <character> <character>
## ERR266221 g5 Oryza sativa Japonic.. Nipponbare
## ERR266222 g2 Oryza sativa Japonic.. Nipponbare
## ERR266223 g2 Oryza sativa Japonic.. Nipponbare
## ERR266224 g5 Oryza sativa Japonic.. Nipponbare
## ERR266225 g3 Oryza sativa Japonic.. Nipponbare
## ... ... ... ...
## ERR266234 g3 Oryza sativa Japonic.. Nipponbare
## ERR266235 g4 Oryza sativa Japonic.. Nipponbare
## ERR266236 g4 Oryza sativa Japonic.. Nipponbare
## ERR266237 g4 Oryza sativa Japonic.. Nipponbare
## ERR266238 g6 Oryza sativa Japonic.. Nipponbare
## developmental_stage age time_unit organism_part
## <character> <character> <character> <character>
## ERR266221 seedling, two leaves.. 2 week shoot axis, vascular..
## ERR266222 seedling, two leaves.. 2 week shoot axis, vascular..
## ERR266223 seedling, two leaves.. 2 week shoot axis, vascular..
## ERR266224 seedling, two leaves.. 2 week shoot axis, vascular..
## ERR266225 seedling, two leaves.. 2 week shoot axis, vascular..
## ... ... ... ... ...
## ERR266234 seedling, two leaves.. 2 week shoot axis, vascular..
## ERR266235 seedling, two leaves.. 2 week shoot axis, vascular..
## ERR266236 seedling, two leaves.. 2 week shoot axis, vascular..
## ERR266237 seedling, two leaves.. 2 week shoot axis, vascular..
## ERR266238 seedling, two leaves.. 2 week shoot axis, vascular..
## growth_condition sampling_time
## <character> <character>
## ERR266221 300 millimolar sodiu.. 5
## ERR266222 normal watering 5
## ERR266223 normal watering 5
## ERR266224 300 millimolar sodiu.. 5
## ERR266225 normal watering 24
## ... ... ...
## ERR266234 normal watering 24
## ERR266235 300 millimolar sodiu.. 1
## ERR266236 300 millimolar sodiu.. 1
## ERR266237 300 millimolar sodiu.. 1
## ERR266238 300 millimolar sodiu.. 24Information describing how the raw data files were processed to obtain the raw counts matrix are found in the metadata slot:
metadata( sumexp )## $pipeline
## [1] "iRAP version 0.7.0p1 (http://nunofonseca.github.io/irap/)"
##
## $filtering
## [1] "Discard reads below minimum quality threshold"
## [2] "Check of bacterial contamination; discard offending reads"
## [3] "Discard reads with common uncalled characters (e.g. N)"
## [4] "Remove reads from pair-end libraries that were orphaned by filtering steps 1-3"
##
## $mapping
## [1] "Against genome reference (Ensembl Plants release: 26) tophat2 version: 2.0.12"
##
## $quantification
## [1] "htseq2 version: 0.6.1p1"Data from a single-channel microarray experiment, e.g. E-MTAB-1624, is represented as one or more ExpressionSet object(s) in the SimpleList that is downloaded. ExpressionSet objects are indexed by the ArrayExpress accession(s) of the microarray design(s) used in the original experiment.
names( mtab1624 )## [1] "A-AFFY-126"affy126data <- mtab1624[[ "A-AFFY-126" ]]
affy126data## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 10 features, 18 samples
## element names: exprs
## protocolData: none
## phenoData
## sampleNames: nippon_control_1hr_rep1 nippon_control_1hr_rep2 ...
## nippon_salt_5hr_rep3 (18 total)
## varLabels: AtlasAssayGroup organism ... sampling_time (9 total)
## varMetadata: labelDescription
## featureData
## featureNames: AFFX-BioB-3_at AFFX-BioB-5_at ... AFFX-DapX-3_at (10
## total)
## fvarLabels: probeSets
## fvarMetadata: labelDescription
## experimentData: use 'experimentData(object)'
## Annotation:The matrix of normalized intensity values is in the assayData slot:
head( exprs( affy126data ) )## nippon_control_1hr_rep1 nippon_control_1hr_rep2
## AFFX-BioB-3_at 7.869421 8.365278
## AFFX-BioB-5_at 7.702652 8.020915
## AFFX-BioB-M_at 7.652985 8.156907
## AFFX-BioC-3_at 9.219287 9.556873
## AFFX-BioC-5_at 8.881807 9.186310
## AFFX-BioDn-3_at 11.617725 11.877930
## nippon_control_1hr_rep3 nippon_control_24hr_rep1
## AFFX-BioB-3_at 8.637034 8.403105
## AFFX-BioB-5_at 8.407186 8.150995
## AFFX-BioB-M_at 8.348117 7.998242
## AFFX-BioC-3_at 9.895652 9.598754
## AFFX-BioC-5_at 9.553833 9.354739
## AFFX-BioDn-3_at 12.193324 11.861900
## nippon_control_24hr_rep2 nippon_control_24hr_rep3
## AFFX-BioB-3_at 8.678257 8.456243
## AFFX-BioB-5_at 8.413489 8.227663
## AFFX-BioB-M_at 8.358092 8.111307
## AFFX-BioC-3_at 9.872856 9.699042
## AFFX-BioC-5_at 9.594959 9.383014
## AFFX-BioDn-3_at 12.077460 11.959052
## nippon_control_5hr_rep1 nippon_control_5hr_rep2
## AFFX-BioB-3_at 8.348849 8.643520
## AFFX-BioB-5_at 8.129436 8.374279
## AFFX-BioB-M_at 7.978514 8.285401
## AFFX-BioC-3_at 9.588422 9.828320
## AFFX-BioC-5_at 9.210903 9.512925
## AFFX-BioDn-3_at 11.853478 12.043559
## nippon_control_5hr_rep3 nippon_salt_1hr_rep1
## AFFX-BioB-3_at 8.401530 8.331911
## AFFX-BioB-5_at 8.193307 8.015213
## AFFX-BioB-M_at 8.046037 7.944433
## AFFX-BioC-3_at 9.685030 9.509499
## AFFX-BioC-5_at 9.379879 9.194149
## AFFX-BioDn-3_at 11.952693 11.800154
## nippon_salt_1hr_rep2 nippon_salt_1hr_rep3 nippon_salt_24hr_rep1
## AFFX-BioB-3_at 8.463545 8.901247 8.363449
## AFFX-BioB-5_at 8.290420 8.533720 8.112024
## AFFX-BioB-M_at 8.139875 8.462567 8.115197
## AFFX-BioC-3_at 9.676649 9.950136 9.549797
## AFFX-BioC-5_at 9.343052 9.714590 9.276916
## AFFX-BioDn-3_at 12.043509 12.263983 11.866490
## nippon_salt_24hr_rep2 nippon_salt_24hr_rep3
## AFFX-BioB-3_at 8.185702 8.586542
## AFFX-BioB-5_at 7.828596 8.207703
## AFFX-BioB-M_at 7.775437 8.231843
## AFFX-BioC-3_at 9.300713 9.624600
## AFFX-BioC-5_at 8.916605 9.371714
## AFFX-BioDn-3_at 11.647577 11.908544
## nippon_salt_5hr_rep1 nippon_salt_5hr_rep2 nippon_salt_5hr_rep3
## AFFX-BioB-3_at 8.562492 8.366250 8.499076
## AFFX-BioB-5_at 8.307241 8.275820 8.155382
## AFFX-BioB-M_at 8.078984 8.114156 8.115064
## AFFX-BioC-3_at 9.728441 9.632023 9.531450
## AFFX-BioC-5_at 9.430824 9.358933 9.260982
## AFFX-BioDn-3_at 12.029436 11.832181 11.987857The sample annotations are in the phenoData slot:
pData( affy126data )## AtlasAssayGroup organism cultivar
## nippon_control_1hr_rep1 g1 Oryza sativa Japonica Group Nipponbare
## nippon_control_1hr_rep2 g1 Oryza sativa Japonica Group Nipponbare
## nippon_control_1hr_rep3 g1 Oryza sativa Japonica Group Nipponbare
## nippon_control_24hr_rep1 g3 Oryza sativa Japonica Group Nipponbare
## nippon_control_24hr_rep2 g3 Oryza sativa Japonica Group Nipponbare
## nippon_control_24hr_rep3 g3 Oryza sativa Japonica Group Nipponbare
## nippon_control_5hr_rep1 g2 Oryza sativa Japonica Group Nipponbare
## nippon_control_5hr_rep2 g2 Oryza sativa Japonica Group Nipponbare
## nippon_control_5hr_rep3 g2 Oryza sativa Japonica Group Nipponbare
## nippon_salt_1hr_rep1 g4 Oryza sativa Japonica Group Nipponbare
## nippon_salt_1hr_rep2 g4 Oryza sativa Japonica Group Nipponbare
## nippon_salt_1hr_rep3 g4 Oryza sativa Japonica Group Nipponbare
## nippon_salt_24hr_rep1 g6 Oryza sativa Japonica Group Nipponbare
## nippon_salt_24hr_rep2 g6 Oryza sativa Japonica Group Nipponbare
## nippon_salt_24hr_rep3 g6 Oryza sativa Japonica Group Nipponbare
## nippon_salt_5hr_rep1 g5 Oryza sativa Japonica Group Nipponbare
## nippon_salt_5hr_rep2 g5 Oryza sativa Japonica Group Nipponbare
## nippon_salt_5hr_rep3 g5 Oryza sativa Japonica Group Nipponbare
## developmental_stage age
## nippon_control_1hr_rep1 seedling, two leaves visible, three leaves visible 2
## nippon_control_1hr_rep2 seedling, two leaves visible, three leaves visible 2
## nippon_control_1hr_rep3 seedling, two leaves visible, three leaves visible 2
## nippon_control_24hr_rep1 seedling, two leaves visible, three leaves visible 2
## nippon_control_24hr_rep2 seedling, two leaves visible, three leaves visible 2
## nippon_control_24hr_rep3 seedling, two leaves visible, three leaves visible 2
## nippon_control_5hr_rep1 seedling, two leaves visible, three leaves visible 2
## nippon_control_5hr_rep2 seedling, two leaves visible, three leaves visible 2
## nippon_control_5hr_rep3 seedling, two leaves visible, three leaves visible 2
## nippon_salt_1hr_rep1 seedling, two leaves visible, three leaves visible 2
## nippon_salt_1hr_rep2 seedling, two leaves visible, three leaves visible 2
## nippon_salt_1hr_rep3 seedling, two leaves visible, three leaves visible 2
## nippon_salt_24hr_rep1 seedling, two leaves visible, three leaves visible 2
## nippon_salt_24hr_rep2 seedling, two leaves visible, three leaves visible 2
## nippon_salt_24hr_rep3 seedling, two leaves visible, three leaves visible 2
## nippon_salt_5hr_rep1 seedling, two leaves visible, three leaves visible 2
## nippon_salt_5hr_rep2 seedling, two leaves visible, three leaves visible 2
## nippon_salt_5hr_rep3 seedling, two leaves visible, three leaves visible 2
## time_unit organism_part
## nippon_control_1hr_rep1 week shoot axis, vascular leaf
## nippon_control_1hr_rep2 week shoot axis, vascular leaf
## nippon_control_1hr_rep3 week shoot axis, vascular leaf
## nippon_control_24hr_rep1 week shoot axis, vascular leaf
## nippon_control_24hr_rep2 week shoot axis, vascular leaf
## nippon_control_24hr_rep3 week shoot axis, vascular leaf
## nippon_control_5hr_rep1 week shoot axis, vascular leaf
## nippon_control_5hr_rep2 week shoot axis, vascular leaf
## nippon_control_5hr_rep3 week shoot axis, vascular leaf
## nippon_salt_1hr_rep1 week shoot axis, vascular leaf
## nippon_salt_1hr_rep2 week shoot axis, vascular leaf
## nippon_salt_1hr_rep3 week shoot axis, vascular leaf
## nippon_salt_24hr_rep1 week shoot axis, vascular leaf
## nippon_salt_24hr_rep2 week shoot axis, vascular leaf
## nippon_salt_24hr_rep3 week shoot axis, vascular leaf
## nippon_salt_5hr_rep1 week shoot axis, vascular leaf
## nippon_salt_5hr_rep2 week shoot axis, vascular leaf
## nippon_salt_5hr_rep3 week shoot axis, vascular leaf
## growth_condition sampling_time
## nippon_control_1hr_rep1 normal watering 1
## nippon_control_1hr_rep2 normal watering 1
## nippon_control_1hr_rep3 normal watering 1
## nippon_control_24hr_rep1 normal watering 24
## nippon_control_24hr_rep2 normal watering 24
## nippon_control_24hr_rep3 normal watering 24
## nippon_control_5hr_rep1 normal watering 5
## nippon_control_5hr_rep2 normal watering 5
## nippon_control_5hr_rep3 normal watering 5
## nippon_salt_1hr_rep1 300 millimolar sodium chloride 1
## nippon_salt_1hr_rep2 300 millimolar sodium chloride 1
## nippon_salt_1hr_rep3 300 millimolar sodium chloride 1
## nippon_salt_24hr_rep1 300 millimolar sodium chloride 24
## nippon_salt_24hr_rep2 300 millimolar sodium chloride 24
## nippon_salt_24hr_rep3 300 millimolar sodium chloride 24
## nippon_salt_5hr_rep1 300 millimolar sodium chloride 5
## nippon_salt_5hr_rep2 300 millimolar sodium chloride 5
## nippon_salt_5hr_rep3 300 millimolar sodium chloride 5A brief outline of how the raw data was normalized is in the experimentData slot:
preproc( experimentData( affy126data ) )## $normalization
## [1] "RMA using oligo (http://www.bioconductor.org/packages/release/bioc/html/oligo.html) version 1.24.2"You can also download data for a single Expression Atlas experiment using the getAtlasExperiment() function:
mtab3007 <- getAtlasExperiment( "E-MTAB-3007" )
# Downloading Expression Atlas experiment summary from:
# ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-3007/E-MTAB-3007-atlasExperimentSummary.Rdata
# Successfully downloaded experiment summary object for E-MTAB-3007