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Frequently asked questions about the Gene Expression Atlas
Questions
- What can I query the genes on?
- What can I query the experiments on?
- Why are there fewer experiments listed as being in the Atlas when I query the archive compared to the number listed on the Atlas home page?
- Can I link directly to the Atlas gene pages/heat maps using a gene identifier?
Answers
- What can I query the genes on?
The following fields/identifiers are indexed for all genes in the Gene Expression Atlas. These can be typed directly into the web interface. For web service index please see the Atlas programmatic access documentation:
(identifier fields)
- EMBL e.g. AC000015
- Ensembl Gene e.g. ENSG00000171658
- Ensembl Protein e.g. ENSP00000000233
- Ensembl Transcript e.g. ENST00000000233
- Gene Ontology e.g. GO:0008134
- Interpro IPR017892
- OMIM e.g. 120290
- RefSeq e.g. NM_212505
- UniProt e.g. Q8T3U2
- Human Metabolome Data Base e.g. HMDB00060
- UniProt Metabolic Enzyme e.g. O15269
(text fields)
- gene or protein name e.g. WNT1 or Wnt-1
- disease e.g. "Osteogenesis imperfecta
- goterm e.g. transcription factor binding
- interproterm e.g. HLH_basic
- keyword e.g. transcription
- synonym e.g. SCA1
- What can I query the experiments on?
The following assay/sample attribute categories are indexed for experiments in the Gene Expression Atlas (where available):
- Cell Line e.g. HeLa
- Cell Type e.g. epithelial
- Clinical History e.g. inherited mutation
- Clinical Information e.g. smoker
- Clinical Treatment e.g. aortic banding
- Compound e.g. dexamethasone
- Developmental Stage e.g. adult
- Disease Location e.g. thoracic
- Disease Staging e.g. T4aN1
- Disease State e.g. breast cancer
- Dose e.g. 10 mg/kg
- Ecotype e.g. Col
- Genetic modification e.g. gene_knock_out
- Genotype e.g. wild type
- Histology e.g. well differentiated
- Individual e.g. CEPH pedigree 1463
- Initial Time e.g. birth
- Light e.g. ultraviolet light
- Organism e.g. Capra hircus
- Organism Part e.g. liver
- Phenotype e.g. cognitively impaired
- Sex e.g. male
- Strain or Line e.g. BALB/c
- Target Cell Type e.g. epithelial
- Temperature e.g. 39 degree_C
- Time e.g. 1 d
- Tumor Grading e.g. grade II
- Vehicle e.g. DMSO
Additionally, all experiments have a descriptive one-sentence description and accession numbers, which are indexed as well.
- Why are there fewer experiments listed as being in the Atlas when I query the archive compared to the number listed on the Atlas home page?
If you browse the ArrayExpress Archive and check the box to select only experiments that are also in the Atlas, the total number of experiments returned is less that the total number of experiments in the Atlas because only experiments where at least one gene shows signficant differential expression are listed in the Archive query.
- Can I link directly to the Atlas gene pages/heat maps using a gene identifier?
Yes, you can include a gene identifier in a URL to link directly to the Atlas gene page (if there is only one match) or heat map (if there is a match to more than one gene). See the linking to Atlas page for more information.
Additional resources:
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