# Accessing curated gene expression data with gemma.R

Javier Castillo-Arnemann1, Jordan Sicherman1 and B. Ogan Mancarci1

1Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

#### 29 October 2024

#### Package

gemma.R 3.2.0

# Contents

    library(gemma.R)
    library(data.table)
    library(dplyr)
    library(ggplot2)
    library(ggrepel)
    library(SummarizedExperiment)
    library(pheatmap)
    library(viridis)
    library(listviewer)

# 1 About Gemma

Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Every dataset in Gemma has passed a rigorous curation process that re-annotates the expression platform at the sequence level, which allows for more consistent cross-platform comparisons and meta-analyses.

For detailed information on the curation process, read this page or the latest publication.

# 2 Package cheat sheet

# 3 Installation instructions

## 3.1 Bioconductor

You can install `gemma.R` through Bioconductor with the following code:

    if (!require("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

    BiocManager::install("gemma.R")

# 4 Searching for datasets of interest in Gemma

Using the `get_datasets` function, datasets fitting various criteria can be accessed.

    # accessing all mouse and human datasets
    get_datasets(taxa = c('mouse','human')) %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE2018 | Human Lung Transplant - BAL | Bronchoalveolar lavage samp… | human
GSE4523 | Expression Studies of Melan… | Melanotransferrin (MTf) or … | mouse
GSE4036 | perro-affy-human-186940 | Our laboratory has develope… | human
GSE4034 | palme-affy-mouse-198967 | Fear conditioning (FC) is a… | mouse
GSE2866 | Donarum-3R01NS040270-03S1 | Succinate semialdehyde dehy… | mouse
GSE3253 | Exaggerated neuroinflammati… | Acute cognitive impairment … | mouse

    # accessing human datasets with the word "bipolar"
    get_datasets(query = 'bipolar',taxa = 'human') %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE5389 | Adult postmortem brain tiss… | Bipolar affective disorder … | human
GSE4030 | bunge-affy-arabi-162779 | Schwann cells, expanded in … | human
GSE5388 | Adult postmortem brain tiss… | Bipolar affective disorder … | human
GSE7036 | Expression profiling in mon… | To identify genes dysregula… | human
McLean Hippocampus | McLean Hippocampus | Hippocampus of schizophreni… | human
McLean_PFC | McLean_PFC | Prefrontal cortex of schizo… | human

    # access human datasets that were annotated with the ontology term for the
    # bipolar disorder
    # use search_annotations function to search for available annotation terms
    get_datasets(taxa ='human',
                 uris = 'http://purl.obolibrary.org/obo/MONDO_0004985') %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE5389 | Adult postmortem brain tiss… | Bipolar affective disorder … | human
GSE5388 | Adult postmortem brain tiss… | Bipolar affective disorder … | human
GSE7036 | Expression profiling in mon… | To identify genes dysregula… | human
McLean Hippocampus | McLean Hippocampus | Hippocampus of schizophreni… | human
McLean_PFC | McLean_PFC | Prefrontal cortex of schizo… | human
stanley_feinberg | Stanley consortium collecti… | 50 samples of individuals f… | human

`get_dataset` function also includes a `filter` parameter that allows filtering for datasets with specific properties in a more structured manner. A list of the available properties can be accessed using `filter_properties`

    filter_properties()$dataset %>% head %>% gemma_kable()

properties | type | description
--- | --- | ---
accession.accession | string | NA
accession.accessionVersion | string | NA
accession.externalDatabase…. | string | NA
accession.externalDatabase.id | integer | NA
accession.externalDatabase…. | string | NA
accession.externalDatabase…. | string | NA

These properties can be used together to fine tune your results

    # access human datasets that has bipolar disorder as an experimental factor
    get_datasets(taxa = 'human',
                 filter = "experimentalDesign.experimentalFactors.factorValues.characteristics.valueUri = http://purl.obolibrary.org/obo/MONDO_0004985")  %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE5389 | Adult postmortem brain tiss… | Bipolar affective disorder … | human
GSE5388 | Adult postmortem brain tiss… | Bipolar affective disorder … | human
GSE7036 | Expression profiling in mon… | To identify genes dysregula… | human
McLean_PFC | McLean_PFC | Prefrontal cortex of schizo… | human
stanley_feinberg | Stanley consortium collecti… | 50 samples of individuals f… | human
stanley_kato | Stanley array collection DL… | 102 samples of individuals … | human

    # all datasets with more than 4 samples annotated for any disease
    get_datasets(filter = 'bioAssayCount > 4 and allCharacteristics.category = disease') %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE2018 | Human Lung Transplant - BAL | Bronchoalveolar lavage samp… | human
GSE4036 | perro-affy-human-186940 | Our laboratory has develope… | human
GSE2866 | Donarum-3R01NS040270-03S1 | Succinate semialdehyde dehy… | mouse
GSE2426 | Pre-Neoplastic Stage of Med… | SUMMARY Medulloblastoma is… | mouse
GSE2867 | Zoghbi-5R01NS027699-14 | A number of human neurodege… | mouse
GSE3489 | Patterns of gene dysregulat… | The neurodegenerative proce… | human

    # all datasets with ontology terms for Alzheimer's disease and Parkinson's disease
    # this is equivalent to using the uris parameter
    get_datasets(filter = 'allCharacteristics.valueUri in (http://purl.obolibrary.org/obo/MONDO_0004975,http://purl.obolibrary.org/obo/MONDO_0005180
    )')  %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE1555 | Vehicle and sAPPalpha-treat… | Gene expression changes ind… | mouse
GSE4757 | Rogers-3U24NS043571-01S1 | Alzheimer’s Disease (AD) is… | human
GSE6613 | Parkinson’s disease vs. con… | Parkinson?s disease (PD) pr… | human
GSE12685 | Expression of mRNAs Regulat… | In Alzheimer’s disease (AD)… | human
GSE14499 | Effect of BDNF on the APP t… | We examined transgenic (TG)… | mouse
GSE10908 | Differential gene expressio… | In a transgenic mouse model… | mouse

Note that a single call of these functions will only return 20 results by default and a 100 results maximum, controlled by the `limit` argument. In order to get all available results, use `get_all_pages` function on the output of the function

    get_datasets(taxa = 'human') %>%
        get_all_pages() %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE2018 | Human Lung Transplant - BAL | Bronchoalveolar lavage samp… | human
GSE4036 | perro-affy-human-186940 | Our laboratory has develope… | human
GSE3489 | Patterns of gene dysregulat… | The neurodegenerative proce… | human
GSE1923 | Identification of PDGF-depe… | Overall study: Identificati… | human
GSE361 | Mammary epithelial cell tra… | Analysis of gene expression… | human
GSE492 | Effect of prostaglandin ana… | The purpose of this study i… | human

See larger queries section for more details. To keep this vignette simpler we will keep using the first 20 results returned by default in examples below.

Dataset information provided by `get_datasets` also includes some quality information that can be used to determine the suitability of any given experiment. For instance `experiment.batchEffect` column will be set to -1 if Gemma’s preprocessing has detected batch effects that were unable to be resolved by batch correction. More information about these and other fields can be found at the function documentation.

    get_datasets(taxa = 'human', filter = 'bioAssayCount > 4') %>%
         filter(experiment.batchEffect !=-1) %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE2018 | Human Lung Transplant - BAL | Bronchoalveolar lavage samp… | human
GSE4036 | perro-affy-human-186940 | Our laboratory has develope… | human
GSE3489 | Patterns of gene dysregulat… | The neurodegenerative proce… | human
GSE1923 | Identification of PDGF-depe… | Overall study: Identificati… | human
GSE361 | Mammary epithelial cell tra… | Analysis of gene expression… | human
GSE492 | Effect of prostaglandin ana… | The purpose of this study i… | human

Gemma uses multiple ontologies when annotating datasets and using the term URIs instead of free text to search can lead to more specific results. `search_annotations` function allows searching for annotation terms that might be relevant to your query.

    search_annotations('bipolar') %>%
        head %>% gemma_kable()

category.name | category.URI | value.name | value.URI
--- | --- | --- | ---
NA | NA | bipolar i disorder | http://www.ebi…/EFO_0009963
NA | NA | bipolar ii disorder | http://www.ebi…/EFO_0009964
NA | NA | bipolar disorder | http://purl.obolibrary…/MONDO_0004985
NA | NA | bipolar affective disorder | http://purl.obolibrary…/HP_0007302
NA | NA | bipolar neuron | http://purl.obolibrary…/CL_0000103
NA | NA | bipolar i disorder | http://purl.obolibrary…/MONDO_0001866

# 5 Downloading expression data

Upon identifying datasets of interest, more information about specific ones can be requested. In this example we will be using GSE46416 which includes samples taken from healthy donors along with manic/euthymic phase bipolar disorder patients.

The data associated with specific experiments can be accessed by using `get_datasets_by_ids`

    get_datasets_by_ids("GSE46416") %>%
        select(experiment.shortName, experiment.name,
               experiment.description,taxon.name) %>%
        head %>% gemma_kable

experiment.shortName | experiment.name | experiment.description | taxon.name
--- | --- | --- | ---
GSE46416 | State- and trait-specific g… | Gene expression profiles of… | human

To access the expression data in a convenient form, you can use `get_dataset_object`. It is a high-level wrapper that combines various endpoint calls to return lists of annotated `SummarizedExperiment` or `ExpressionSet` objects that are compatible with other Bioconductor packages or a tidyverse-friendly long form tibble for downstream analyses. These include the expression matrix along with the experimental design, and ensure the sample names match between both when transforming/subsetting data.

    dat <- get_dataset_object("GSE46416",
                              type = 'se') # SummarizedExperiment is the default output type

Note that the tidy format is less memory efficient but allows easy visualization and exploration with ggplot2 and the rest of the tidyverse.

To show how subsetting works, we’ll keep the “manic phase” data and the `reference_subject_role`s, which refers to the control samples in Gemma datasets.

    # Check the levels of the disease factor
    dat[[1]]$disease %>% unique()

    [1] "bipolar disorder has_modifier euthymic phase"
    [2] "reference subject role"
    [3] "bipolar disorder has_modifier manic phase"

    # Subset patients during manic phase and controls
    manic <- dat[[1]][, dat[[1]]$disease == "bipolar disorder has_modifier manic phase" |
            dat[[1]]$disease == "reference subject role"]
    manic

    class: SummarizedExperiment
    dim: 18758 21
    metadata(8): title abstract ... gemmaSuitabilityScore taxon
    assays(1): counts
    rownames(18758): 2315430 2315554 ... 7385683 7385696
    rowData names(4): Probe GeneSymbol GeneName NCBIid
    colnames(21): Control, 12 Control, 1_DE50 ... Bipolar disorder patient
      manic phase, 21 Bipolar disorder patient manic phase, 16
    colData names(3): factorValues block disease

Let’s take a look at sample to sample correlation in our subset.

    # Get Expression matrix
    manicExpr <- assay(manic, "counts")

    manicExpr %>%
        cor %>%
        pheatmap(col =viridis(10),border_color = NA,angle_col = 45,fontsize = 7)

Figure 1: Sample to sample correlations of bipolar patients during manic phase and controls

You can also use `get_dataset_processed_expression` to only get the expression matrix, `get_dataset_samples` to get the metadata information. The output of this function includes some additional details about a sample such as the original accession ID or whether or not it was determined to be an outlier but it can be simplified to match the design table included in the output of `get_dataset_object` by using `make_design` on the output.

    get_dataset_samples('GSE46416') %>% make_design('text') %>% select(-factorValues) %>%  head %>%
        gemma_kable()

| block | disease
--- | --- | ---
Bipolar disorder patient euthymic phase, 11 | Batch_02_26/11/09 | bipolar disorder has_modifi…
Bipolar disorder patient euthymic phase, 17 | Batch_02_26/11/09 | bipolar disorder has_modifi…
Control, 12 | Batch_02_26/11/09 | reference subject role
Control, 1_DE50 | Batch_05_24/11/10 | reference subject role
Bipolar disorder patient euthymic phase, 19 | Batch_03_27/11/09 | bipolar disorder has_modifi…
Control, 9 | Batch_01_25/11/09 | reference subject role

# 6 Platform Annotations

Expression data in Gemma comes with annotations for the gene each expression profile corresponds to. Using the `get_platform_annotations` function, these annotations can be retrieved independently of the expression data, along with additional annotations such as Gene Ontology terms.

Examples:

    head(get_platform_annotations('GPL96') %>% select(-GOTerms))

       ElementName   GeneSymbols                                     GeneNames
            <char>        <char>                                        <char>
    1: 211750_x_at TUBA1C|TUBA1A             tubulin alpha 1c|tubulin alpha 1a
    2:   216678_at
    3:   216345_at        ZSWIM8            zinc finger SWIM-type containing 8
    4:   207273_at
    5: 216025_x_at        CYP2C9 cytochrome P450 family 2 subfamily C member 9
    6: 218191_s_at        LMBRD1                     LMBR1 domain containing 1
            GemmaIDs    NCBIids
              <char>     <char>
    1: 360802|172797 84790|7846
    2:
    3:        235733      23053
    4:
    5:         32964       1559
    6:        303717      55788

    head(get_platform_annotations('Generic_human_ncbiIds') %>% select(-GOTerms))

       ElementName  GeneSymbols
             <int>       <char>
    1:       55236         UBA6
    2:       79664         ICE2
    3:   100126270     FMR1-AS1
    4:   105373684    LINC01818
    5:   124900245 LOC124900245
    6:   102725051 LOC102725051
                                                   GeneNames GemmaIDs   NCBIids
                                                      <char>    <int>     <int>
    1:           ubiquitin like modifier activating enzyme 6   295849     55236
    2: interactor of little elongation complex ELL subunit 2   336840     79664
    3:                                  FMR1 antisense RNA 1  3157248 100126270
    4:           long intergenic non-protein coding RNA 1818  9235895 105373684
    5:                           small nucleolar RNA SNORA40 10578422 124900245
    6:                          uncharacterized LOC102725051  9008981 102725051

If you are interested in a particular gene, you can see which platforms include it using `get_gene_probes`. Note that functions to search gene work best with unambigious identifiers rather than symbols.

    # lists genes in gemma matching the symbol or identifier
    get_genes('Eno2') %>% gemma_kable()

gene.symbol | gene.ensembl | gene.NCBI | gene.name | gene.aliases | gene.MFX.rank | taxon.name | taxon.scientific | taxon.ID | taxon.NCBI | taxon.database.name | taxon.database.ID
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ENO2 | ENSG00000111674 | 2026 | enolase 2 | HEL-S-27…. | 0.8776645 | human | Homo sapiens | 1 | 9606 | hg38 | 87
Eno2 | ENSMUSG00000004267 | 13807 | enolase 2, gamma neuronal | D6Ertd37…. | 0.8794051 | mouse | Mus musculus | 2 | 10090 | mm10 | 81
Eno2 | ENSRNOG00000013141 | 24334 | enolase 2 | NSE, RNEN3 | 0.8187614 | rat | Rattus norvegicus | 3 | 10116 | rn6 | 86

    # ncbi id for human ENO2
    probes <- get_gene_probes(2026)

    # remove the description for brevity of output
    head(probes[,.SD, .SDcols = !colnames(probes) %in% c('mapping.Description','platform.Description')]) %>%
        gemma_kable()

element.name | element.description | platform.shortName | platform.name | platform.ID | platform.type | platform.description | platform.troubled | taxon.name | taxon.scientific | taxon.ID | taxon.NCBI | taxon.database.name | taxon.database.ID
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
201313_at | enolase 2 (gamma, neuronal) | GPL96 | Affymetrix GeneChip Human G… | 1 | ONECOLOR | The U133 set includes 2 ar… | FALSE | human | Homo sapiens | 1 | 9606 | hg38 | 87
201313_at | enolase 2 (gamma, neuronal) | GPL570 | Affymetrix GeneChip Human G… | 4 | ONECOLOR | Complete coverage of the H… | FALSE | human | Homo sapiens | 1 | 9606 | hg38 | 87
40193_at | enolase 2 (gamma, neuronal) | GPL91 | Affymetrix GeneChip Human G… | 8 | ONECOLOR | The Human Genome U95 (HG-U… | FALSE | human | Homo sapiens | 1 | 9606 | hg38 | 87
1639 | NA | GPL962 | CHUGAI 41K | 36 | TWOCOLOR | Patients and Sample Prepar… | FALSE | human | Homo sapiens | 1 | 9606 | hg38 | 87
6621 | NA | GPL230 | UP_5Ka | 38 | TWOCOLOR | A cDNA microarray with ~50… | FALSE | human | Homo sapiens | 1 | 9606 | hg38 | 87
861 | NA | GPL230 | UP_5Ka | 38 | TWOCOLOR | A cDNA microarray with ~50… | FALSE | human | Homo sapiens | 1 | 9606 | hg38 | 87

# 7 Differential expression analyses

Gemma contains precomputed differential expression analyses for most of its datasets. Analyses can involve more than one factor, such as “sex” as well as “disease”. Some datasets contain more than one analysis to account for different factors and their interactions. The results are stored as resultSets, each corresponding to one factor (or their interaction). You can access them using `get_differential_expression_values`. From here on, we can explore and visualize the data to find the most differentially-expressed genes

Note that `get_differential_expression_values` can return multiple differentials per study if a study has multiple factors to contrast. Since GSE46416 only has one extracting the first element of the returned list is all we need.

    dif_exp <- get_differential_expression_values('GSE46416')
    dif_exp[[1]] %>% head %>% gemma_kable()

Probe | NCBIid | GeneSymbol | GeneName | pvalue | corrected_pvalue | rank | contrast_113004_coefficient | contrast_113004_log2fc | contrast_113004_tstat | contrast_113004_pvalue | contrast_113005_coefficient | contrast_113005_log2fc | contrast_113005_tstat | contrast_113005_pvalue
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3563604 | 283551 | LINC01588 | long intergenic non-protein… | 9.0e-07 | 0.0028 | 3.00e-04 | -0.5543 | -0.5543 | -5.7640 | 2.10e-06 | -0.5617 | -0.5617 | -5.8407 | 1.7e-06
3361181 | 387751 | GVINP1 | GTPase, very large interfer… | 9.0e-07 | 0.0028 | 2.00e-04 | -0.5702 | -0.5702 | -4.0491 | 3.00e-04 | -0.9326 | -0.9326 | -6.6228 | 2.0e-07
2362351 | 149628 | PYHIN1 | pyrin and HIN domain family… | 5.0e-07 | 0.0028 | 1.00e-04 | -0.7474 | -0.7474 | -5.3795 | 6.40e-06 | -0.8938 | -0.8938 | -6.4326 | 3.0e-07
3328214 | 221120 | ALKBH3 | alkB homolog 3, alpha-ketog… | 4.0e-07 | 0.0028 | 9.11e-05 | -0.2252 | -0.2252 | -4.0499 | 3.00e-04 | -0.3849 | -0.3849 | -6.9210 | 1.0e-07
3918696 | 6651 | SON | SON DNA and RNA binding pro… | 6.0e-07 | 0.0028 | 2.00e-04 | -0.2222 | -0.2222 | -4.1695 | 2.00e-04 | -0.3588 | -0.3588 | -6.7310 | 1.0e-07
3406015 | 55729 | ATF7IP | activating transcription fa… | 1.1e-06 | 0.0031 | 4.00e-04 | -0.3672 | -0.3672 | -4.5202 | 7.86e-05 | -0.5220 | -0.5220 | -6.4259 | 3.0e-07

By default the columns names of the output correspond to contrast IDs. To see what conditions these IDs correspond to we can either use `get_dataset_differential_expression_analyses` to get the metadata about differentials of a given dataset, or set `readableContrasts` argument of `get_differential_expression_values` to `TRUE`. The former approach is usually better for a large scale systematic analysis while the latter is easier to read in an interactive session.

`get_dataset_differential_expression_analyses` function returns structured metadata about the differentials.

    contrasts <- get_dataset_differential_expression_analyses('GSE46416')
    contrasts %>% gemma_kable()

result.ID | contrast.ID | experiment.ID | factor.category | factor.category.URI | factor.ID | baseline.factors | experimental.factors | isSubset | subsetFactor | probes.analyzed | genes.analyzed
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
550248 | 113004 | 8997 | disease | http://www.ebi…/EFO_0000408 | 19134 | disease,…. | disease,…. | FALSE | logical(…. | 21961 | 18959
550248 | 113005 | 8997 | disease | http://www.ebi…/EFO_0000408 | 19134 | disease,…. | disease,…. | FALSE | logical(…. | 21961 | 18959

`contrast.ID` column corresponds to the column names in the output of `get_differential_expression_values` while `result.ID` corresponds to the name of the differential in the output object. Using them together will let one to access differentially expressed gene counts for each condition contrast

    # using result.ID and contrast.ID of the output above, we can access specific
    # results. Note that one study may have multiple contrast objects
    seq_len(nrow(contrasts)) %>% sapply(function(i){
        result_set = dif_exp[[as.character(contrasts[i,]$result.ID)]]
        p_values = result_set[[glue::glue("contrast_{contrasts[i,]$contrast.ID}_pvalue")]]

        # multiple testing correction
        sum(p.adjust(p_values,method = 'BH') < 0.05)
    }) -> dif_exp_genes

    contrasts <- data.table(result.ID = contrasts$result.ID,
                            contrast.id = contrasts$contrast.ID,
                            baseline.factorValue = contrasts$baseline.factors,
                            experimental.factorValue = contrasts$experimental.factors,
                            n_diff = dif_exp_genes)

    contrasts %>% gemma_kable()

result.ID | contrast.id | baseline.factorValue | experimental.factorValue | n_diff
--- | --- | --- | --- | ---
550248 | 113004 | disease,…. | disease,…. | 1
550248 | 113005 | disease,…. | disease,…. | 1294

    contrasts$baseline.factors

    NULL

    contrasts$experimental.factors

    NULL

Alternatively we, since we are only looking at one dataset and one contrast manually, we can simply use `readableContrasts`.

    de <- get_differential_expression_values("GSE46416",readableContrasts = TRUE)[[1]]
    de %>% head %>% gemma_kable

Probe

NCBIid

GeneSymbol

GeneName

pvalue

corrected_pvalue

rank

contrast_bipolar disorder has_modifier manic phase_coefficient

contrast_bipolar disorder has_modifier manic phase_logFoldChange

contrast_bipolar disorder has_modifier manic phase_tstat

contrast_bipolar disorder has_modifier manic phase_pvalue

contrast_bipolar disorder has_modifier euthymic phase_coefficient

contrast_bipolar disorder has_modifier euthymic phase_logFoldChange

contrast_bipolar disorder has_modifier euthymic phase_tstat

contrast_bipolar disorder has_modifier euthymic phase_pvalue

3563604 | 283551 | LINC01588 | long intergenic non-protein… | 9.0e-07 | 0.0028 | 3.00e-04 | -0.5543 | -0.5543 | -5.7640 | 2.10e-06 | -0.5617 | -0.5617 | -5.8407 | 1.7e-06
3361181 | 387751 | GVINP1 | GTPase, very large interfer… | 9.0e-07 | 0.0028 | 2.00e-04 | -0.5702 | -0.5702 | -4.0491 | 3.00e-04 | -0.9326 | -0.9326 | -6.6228 | 2.0e-07
2362351 | 149628 | PYHIN1 | pyrin and HIN domain family… | 5.0e-07 | 0.0028 | 1.00e-04 | -0.7474 | -0.7474 | -5.3795 | 6.40e-06 | -0.8938 | -0.8938 | -6.4326 | 3.0e-07
3328214 | 221120 | ALKBH3 | alkB homolog 3, alpha-ketog… | 4.0e-07 | 0.0028 | 9.11e-05 | -0.2252 | -0.2252 | -4.0499 | 3.00e-04 | -0.3849 | -0.3849 | -6.9210 | 1.0e-07
3918696 | 6651 | SON | SON DNA and RNA binding pro… | 6.0e-07 | 0.0028 | 2.00e-04 | -0.2222 | -0.2222 | -4.1695 | 2.00e-04 | -0.3588 | -0.3588 | -6.7310 | 1.0e-07
3406015 | 55729 | ATF7IP | activating transcription fa… | 1.1e-06 | 0.0031 | 4.00e-04 | -0.3672 | -0.3672 | -4.5202 | 7.86e-05 | -0.5220 | -0.5220 | -6.4259 | 3.0e-07

    # Classify probes for plotting
    de$diffexpr <- "No"
    de$diffexpr[de$`contrast_bipolar disorder has_modifier manic phase_logFoldChange` > 1.0 &
            de$`contrast_bipolar disorder has_modifier manic phase_pvalue` < 0.05] <- "Up"
    de$diffexpr[de$`contrast_bipolar disorder has_modifier manic phase_logFoldChange` < -1.0 &
            de$`contrast_bipolar disorder has_modifier manic phase_pvalue` < 0.05] <- "Down"

    # Upregulated probes
    filter(de, diffexpr == "Up") %>%
        arrange(`contrast_bipolar disorder has_modifier manic phase_pvalue`) %>%
        select(Probe, GeneSymbol, `contrast_bipolar disorder has_modifier manic phase_pvalue`,
            `contrast_bipolar disorder has_modifier manic phase_logFoldChange`) %>%
        head(10) %>% gemma_kable()

Probe | GeneSymbol | contrast_bipolar disorder has_modifier manic phase_pvalue | contrast_bipolar disorder has_modifier manic phase_logFoldChange
--- | --- | --- | ---
2319550 | RBP7 | 8.61e-05 | 1.0740
2548699 | CYP1B1 | 1.00e-04 | 1.3225
3907190 | SLPI | 3.00e-04 | 1.0558
3629103 | PCLAF | 5.00e-04 | 1.2783
3545525 | SLIRP | 6.00e-04 | 1.3490
3146433 | COX6C | 9.00e-04 | 1.4670
2899102 | H3C3 | 1.30e-03 | 1.0260
3635198 | BCL2A1 | 1.80e-03 | 1.0798
2633191 | GPR15 | 2.40e-03 | 1.2046
3518169 | COMMD6 | 2.50e-03 | 1.3763

    # Downregulated probes
    filter(de, diffexpr == "Down") %>%
        arrange(`contrast_bipolar disorder has_modifier manic phase_pvalue`) %>%
        select(Probe, GeneSymbol, `contrast_bipolar disorder has_modifier manic phase_pvalue`,
            `contrast_bipolar disorder has_modifier manic phase_logFoldChange`) %>%
        head(10) %>% gemma_kable()

Probe | GeneSymbol | contrast_bipolar disorder has_modifier manic phase_pvalue | contrast_bipolar disorder has_modifier manic phase_logFoldChange
--- | --- | --- | ---
3245871 | WDFY4 | 0.0002 | -1.1569
3022689 | SND1-IT1 | 0.0002 | -1.2199
3384417 | ANKRD42-DT | 0.0004 | -1.0030
3930525 | RUNX1-IT1 | 0.0004 | -1.5169
3336402 | RBM14 | 0.0004 | -1.0711
3652609 | SMG1P2 | 0.0005 | -1.2544
2663083 | TAMM41 | 0.0005 | -1.3056
3404030 | KLRG1 | 0.0007 | -1.0949
3041550 | TRA2A | 0.0008 | -1.0496
3526425 | PCID2 | 0.0011 | -1.0719

    # Add gene symbols as labels to DE genes
    de$delabel <- ""
    de$delabel[de$diffexpr != "No"] <- de$GeneSymbol[de$diffexpr != "No"]

    # Volcano plot for bipolar patients vs controls
    ggplot(
        data = de,
        aes(
            x = `contrast_bipolar disorder has_modifier manic phase_logFoldChange`,
            y = -log10(`contrast_bipolar disorder has_modifier manic phase_pvalue`),
            color = diffexpr,
            label = delabel
        )
    ) +
        geom_point() +
        geom_hline(yintercept = -log10(0.05), col = "gray45", linetype = "dashed") +
        geom_vline(xintercept = c(-1.0, 1.0), col = "gray45", linetype = "dashed") +
        labs(x = "log2(FoldChange)", y = "-log10(p-value)") +
        scale_color_manual(values = c("blue", "black", "red")) +
        geom_text_repel(show.legend = FALSE) +
        theme_minimal()

Figure 2: Differentially-expressed genes in bipolar patients during manic phase versus controls

# 8 Larger queries

To query large amounts of data, the API has a pagination system which uses the `limit` and `offset` parameters. To avoid overloading the server, calls are limited to a maximum of 100 entries, so the offset allows you to get the next batch of entries in the next call(s).

To simplify the process of accessing all available data, gemma.R includes the `get_all_pages` function which can use the output from one page to make all the follow up requests

    get_platforms_by_ids() %>%
        get_all_pages() %>% head %>% gemma_kable()

platform.ID | platform.shortName | platform.name | platform.description | platform.troubled | platform.experimentCount | platform.type | taxon.name | taxon.scientific | taxon.ID | taxon.NCBI | taxon.database.name | taxon.database.ID
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | GPL96 | Affymetrix GeneChip Human G… | The U133 set includes 2 ar… | FALSE | 400 | ONECOLOR | human | Homo sapiens | 1 | 9606 | hg38 | 87
2 | GPL1355 | Affymetrix GeneChip Rat Gen… | The GeneChip Rat Genome 23… | FALSE | 296 | ONECOLOR | rat | Rattus norvegicus | 3 | 10116 | rn6 | 86
3 | GPL1261 | Affymetrix GeneChip Mouse G… | All probe sets represented… | FALSE | 1303 | ONECOLOR | mouse | Mus musculus | 2 | 10090 | mm10 | 81
4 | GPL570 | Affymetrix GeneChip Human G… | Complete coverage of the H… | FALSE | 1554 | ONECOLOR | human | Homo sapiens | 1 | 9606 | hg38 | 87
5 | GPL81 | Affymetrix GeneChip Murine … | The MG-U74 set includes 3 … | FALSE | 193 | ONECOLOR | mouse | Mus musculus | 2 | 10090 | mm10 | 81
6 | GPL85 | Affymetrix GeneChip Rat Gen… | The RG-U34 set includes 3 … | FALSE | 86 | ONECOLOR | rat | Rattus norvegicus | 3 | 10116 | rn6 | 86

Alternative way to access all pages is to do so manually. To see how many available results are there, you can look at the attributes of the output objects where additional information from the API response is appended.

    platform_count = attributes(get_platforms_by_ids(limit = 1))$totalElements
    print(platform_count)

    [1] 634

After which you can use `offset` to access all available platforms.

    lapply(seq(0,platform_count,100), function(offset){
        get_platforms_by_ids(limit = 100, offset = offset) %>%
            select(platform.ID, platform.shortName, taxon.name)
    }) %>% do.call(rbind,.) %>%
        head %>% gemma_kable()

platform.ID | platform.shortName | taxon.name
--- | --- | ---
1 | GPL96 | human
2 | GPL1355 | rat
3 | GPL1261 | mouse
4 | GPL570 | human
5 | GPL81 | mouse
6 | GPL85 | rat

Many endpoints only support a single identifier:

    get_dataset_annotations(c("GSE35974", "GSE46416"))

    Error: Please specify one valid identifier for dataset.

In these cases, you will have to loop over all the identifiers you wish to query and send separate requests.

    lapply(c("GSE35974", "GSE12649"), function(dataset) {
        get_dataset_annotations(dataset) %>%
            mutate(experiment.shortName = dataset) %>%
            select(experiment.shortName, class.name, term.name)
    }) %>% do.call(rbind,.) %>% gemma_kable()

experiment.shortName | class.name | term.name
--- | --- | ---
GSE35974 | biological sex | female
GSE35974 | disease | depressive disorder
GSE35974 | disease | bipolar disorder
GSE35974 | biological sex | male
GSE35974 | labelling | biotin
GSE35974 | disease | schizophrenia
GSE35974 | organism part | cerebellum
GSE12649 | disease | schizophrenia
GSE12649 | labelling | biotin
GSE12649 | disease | bipolar disorder
GSE12649 | organism part | prefrontal cortex

# 9 Output options

## 9.1 Raw data

By default, Gemma API does some parsing on the raw API results to make it easier to work with inside of R. In the process, it drops some typically unused values. If you wish to fetch everything, use `raw = TRUE`. Instead of a data table, you’ll usually be served a list that represents the underlying JSON response.

    get_gene_locations("DYRK1A") %>% gemma_kable()

chromosome | strand | nucleotide | length | taxon.name | taxon.scientific | taxon.ID | taxon.NCBI | taxon.database.name | taxon.database.ID
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---

11

33890705

118714

rat

Rattus norvegicus

3

10116

rn6

86

21

37365572

160785

human

Homo sapiens

1

9606

hg38

87

16

94370769

125608

mouse

Mus musculus

2

10090

mm10

81

    get_gene_locations("DYRK1A", raw = TRUE) %>% jsonedit()

## 9.2 File outputs

Sometimes, you may wish to save results to a file for future inspection. You can do this simply by providing a filename to the `file` parameter. The extension for this file will be one of three options:

1. `.json`, if you requested results with `raw=TRUE`
2. `.csv` if the results have no nested data tables
3. `.rds` otherwise

You can also specify whether or not the new fetched results are allowed to overwrite an existing file by specifying the `overwrite = TRUE` parameter.

## 9.3 Memoise data

To speed up results, you can remember past results so future queries can proceed virtually instantly. This is enabled through the `memoise` package. To enable memoisation, simply set `memoised = TRUE` in the function call whenever you want to refer to the cache, both to save data for future calls and use the saved data for repeated calls. By default this will create a cache in your local filesystem.

If you wish to change where the cache is stored or change the default behaviour to make sure you always use the cache without relying on the `memoised` argument, use `gemma_memoised`.

    # use memoisation by default using the default cache
    gemma_memoised(TRUE)

    # set an altnernate cache path
    gemma_memoised(TRUE,"path/to/cache_directory")

    # cache in memory of the R session
    # this cache will not be preserved between sessions
    gemma_memoised(TRUE,"cache_in_memory")

If you’re done with your fetching and want to ensure no space is being used for cached results, or if you just want to ensure you’re getting up-to-date data from Gemma, you can clear the cache using `forget_gemma_memoised`.

## 9.4 Changing defaults

We’ve seen how to change `raw = TRUE`, `overwrite = TRUE` and `memoised = TRUE` in individual function calls. It’s possible that you want to always use the functions these ways without specifying the option every time. You can do this by simply changing the default, which is visible in the function definition. See below for examples.

    options(gemma.memoised = TRUE) # always refer to cache. this is redundant with gemma_memoised function
    options(gemma.overwrite = TRUE) # always overwrite when saving files
    options(gemma.raw = TRUE) # always receive results as-is from Gemma

# 10 Session info

    sessionInfo()

    R version 4.4.1 (2024-06-14)
    Platform: x86_64-pc-linux-gnu
    Running under: Ubuntu 24.04.1 LTS

    Matrix products: default
    BLAS:   /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
    LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0

    locale:
     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
     [3] LC_TIME=en_GB              LC_COLLATE=C
     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
     [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
     [9] LC_ADDRESS=C               LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

    time zone: America/New_York
    tzcode source: system (glibc)

    attached base packages:
    [1] stats4    stats     graphics  grDevices utils     datasets  methods
    [8] base

    other attached packages:
     [1] listviewer_4.0.0            viridis_0.6.5
     [3] viridisLite_0.4.2           pheatmap_1.0.12
     [5] SummarizedExperiment_1.36.0 Biobase_2.66.0
     [7] GenomicRanges_1.58.0        GenomeInfoDb_1.42.0
     [9] IRanges_2.40.0              S4Vectors_0.44.0
    [11] BiocGenerics_0.52.0         MatrixGenerics_1.18.0
    [13] matrixStats_1.4.1           ggrepel_0.9.6
    [15] ggplot2_3.5.1               dplyr_1.1.4
    [17] data.table_1.16.2           gemma.R_3.2.0
    [19] BiocStyle_2.34.0

    loaded via a namespace (and not attached):
     [1] tidyselect_1.2.1        farver_2.1.2            fastmap_1.2.0
     [4] digest_0.6.37           timechange_0.3.0        lifecycle_1.0.4
     [7] magrittr_2.0.3          compiler_4.4.1          rlang_1.1.4
    [10] sass_0.4.9              tools_4.4.1             utf8_1.2.4
    [13] yaml_2.3.10             knitr_1.48              labeling_0.4.3
    [16] S4Arrays_1.6.0          htmlwidgets_1.6.4       bit_4.5.0
    [19] curl_5.2.3              DelayedArray_0.32.0     xml2_1.3.6
    [22] RColorBrewer_1.1-3      abind_1.4-8             withr_3.0.2
    [25] purrr_1.0.2             grid_4.4.1              fansi_1.0.6
    [28] colorspace_2.1-1        scales_1.3.0            tinytex_0.53
    [31] cli_3.6.3               rmarkdown_2.28          crayon_1.5.3
    [34] generics_0.1.3          rstudioapi_0.17.1       httr_1.4.7
    [37] cachem_1.1.0            stringr_1.5.1           zlibbioc_1.52.0
    [40] assertthat_0.2.1        BiocManager_1.30.25     XVector_0.46.0
    [43] vctrs_0.6.5             Matrix_1.7-1            jsonlite_1.8.9
    [46] bookdown_0.41           bit64_4.5.2             magick_2.8.5
    [49] systemfonts_1.1.0       jquerylib_0.1.4         glue_1.8.0
    [52] lubridate_1.9.3         stringi_1.8.4           gtable_0.3.6
    [55] UCSC.utils_1.2.0        munsell_0.5.1           tibble_3.2.1
    [58] pillar_1.9.0            rappdirs_0.3.3          htmltools_0.5.8.1
    [61] GenomeInfoDbData_1.2.13 R6_2.5.1                evaluate_1.0.1
    [64] kableExtra_1.4.0        lattice_0.22-6          highr_0.11
    [67] memoise_2.0.1           bslib_0.8.0             Rcpp_1.0.13
    [70] svglite_2.1.3           gridExtra_2.3           SparseArray_1.6.0
    [73] xfun_0.48               pkgconfig_2.0.3