Author: Maria Keays
Date: 2025-10-31

# ExpressionAtlas package vignette

#### Maria Keays

#### 2025-10-31

# Expression Atlas

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. Since October 2022, ArrayExpress is a collection of functional genomics data in [BioStudies] (https://www.ebi.ac.uk/biostudies). 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.

# Searching and downloading Expression Atlas data

## Searching

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 = "oryza" )
    # Searching for Expression Atlas experiments matching your query ...
    # Query successful.
    # Found 16 experiments matching your query.

We will proceed with a subset of three accessions:

    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.

## Downloading the data

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-1624

    allExps

    ## List of length 3
    ## names(3): E-GEOD-11175 E-MTAB-1625 E-MTAB-1624

To 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-1625

    rnaseqExps

    ## List of length 1
    ## names(1): E-MTAB-1625

To 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).

### RNA-seq experiment summaries

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_time

The 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         0

The 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..            24

Information 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"

### Single-channel microarray experiments

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            11.987857

The 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             5

A 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"

# Downloading a single Expression Atlas experiment summary

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