Q (sonnet):
How does ESR1 mRNA expression differ between PAM50 subtypes in TCGA breast cancer?
In Breast Invasive Carcinoma (TCGA, PanCancer Atlas), ESR1 mRNA is highest in Luminal A and Luminal B tumors, intermediate in Normal-like and HER2-enriched, and lowest in Basal-like tumors. You can see the distribution here:
[ESR1 expression by subtype](https://www.cbioportal.org/results/plots?cancer_study_list=brca_tcga_pan_can_atlas_2018&gene_list=ESR1)
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Can you do this with METABRIC instead?
▶ resolve_and_route
{
"studyKeywords": [
"METABRIC",
"breast"
]
}
◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"brca_metabric","name":"Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)","sampleCount":2509,"studyViewUrl":"https://www.cbioportal.org/study?id=brca_metabric","metadata":{"clinicalAttributeIds":["AGE_AT_DIAGNOSIS","BREAST_SURGERY","CANCER_TYPE","CANCER_TYPE_DETAILED","CELLULARITY","CHEMOTHERAPY","CLAUDIN_SUBTYPE","COHORT","ER_IHC","ER_STATUS","GRADE","HER2_SNP6","HER2_STATUS","HISTOLOGICAL_SUBTYPE","HORMONE_THERAPY","INFERRED_MENOPAUSAL_STATE","INTCLUST","LATERALITY","LYMPH_NODES_EXAMINED_POSITIVE","MUTATION_COUNT","NPI","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","PR_STATUS","RADIO_THERAPY","RFS_MONTHS","RFS_STATUS","SAMPLE_COUNT","SAMPLE_TYPE","SEX","THREEGENE","TMB_NONSYNONYMOUS","TUMOR_SIZE","TUMOR_STAGE","VITAL_STATUS"],"molecularProfileIds":["brca_metabric_cna","brca_metabric_methylation_promoters_rrbs","brca_metabric_mrna","brca_metabric_mrna_median_all_sample_Zscores","brca_metabric_mutations"],"heatmapProfileIds":["brca_metabric_methylation_promoters_rrbs","brca_metabric_mrna_median_all_sample_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna","dna_methylation"]}}]}}
▶ get_studyviewfilter_options
{
"studyId": "brca_metabric",
"attributeIds": [
"CLAUDIN_SUBTYPE"
]
}
◀ result
{"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"brca_metabric","attributes":[{"attributeId":"CLAUDIN_SUBTYPE","displayName":"Pam50 + Claudin-low subtype","description":"Pam50 + Claudin-low subtype","datatype":"STRING","values":["Basal","NA","NC","claudin-low","LumA","LumB","Normal","Her2"]}]}}
▶ navigate_to_group_comparison
{
"studyIds": [
"brca_metabric"
],
"tab": "mrna",
"groups": [
{
"name": "LumA",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "CLAUDIN_SUBTYPE",
"values": [
{
"value": "LumA"
}
]
}
]
}
},
{
"name": "LumB",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "CLAUDIN_SUBTYPE",
"values": [
{
"value": "LumB"
}
]
}
]
}
},
{
"name": "Her2",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "CLAUDIN_SUBTYPE",
"values": [
{
"value": "Her2"
}
]
}
]
}
},
{
"name": "Basal",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "CLAUDIN_SUBTYPE",
"values": [
{
"value": "Basal"
}
]
}
]
}
},
{
"name": "Normal",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "CLAUDIN_SUBTYPE",
"values": [
{
"value": "Normal"
}
]
}
]
}
},
{
"name": "claudin-low",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "CLAUDIN_SUBTYPE",
"values": [
{
"value": "claudin-low"
}
]
}
]
}
}
],
"selectedGene": "ESR1"
}
◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/comparison/mrna?comparisonId=6ab8224ce497aad53593c5cb&selectedGene=ESR1","url":"https://www.cbioportal.org/comparison/mrna?comparisonId=6ab8224ce497aad53593c5cb&selectedGene=ESR1","data":{"description":"Group comparison (6 custom groups)","studies":["brca_metabric"],"totalGroups":6,"groups":[{"name":"LumA","sampleCount":700},{"name":"LumB","sampleCount":475},{"name":"Her2","sampleCount":224},{"name":"Basal","sampleCount":209},{"name":"Normal","sampleCount":148},{"name":"claudin-low","sampleCount":218}],"studyViewUrl":"https://www.cbioportal.org/study?id=brca_metabric","groupUrls":[{"groupName":"LumA","url":"https://www.cbioportal.org/study?id=brca_metabric#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CLAUDIN_SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22LumA%22%7D%5D%7D%5D%7D"},{"groupName":"LumB","url":"https://www.cbioportal.org/study?id=brca_metabric#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CLAUDIN_SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22LumB%22%7D%5D%7D%5D%7D"},{"groupName":"Her2","url":"https://www.cbioportal.org/study?id=brca_metabric#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CLAUDIN_SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Her2%22%7D%5D%7D%5D%7D"},{"groupName":"Basal","url":"https://www.cbioportal.org/study?id=brca_metabric#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CLAUDIN_SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Basal%22%7D%5D%7D%5D%7D"},{"groupName":"Normal","url":"https://www.cbioportal.org/study?id=brca_metabric#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CLAUDIN_SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Normal%22%7D%5D%7D%5D%7D"},{"groupName":"claudin-low","url":"https://www.cbioportal.org/study?id=brca_metabric#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CLAUDIN_SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22claudin-low%22%7D%5D%7D%5D%7D"}],"pageDescription":"mRNA expression for all genes compared across LumA (700) vs LumB (475) vs Her2 (224) vs Basal (209) vs Normal (148) vs claudin-low (218)."}}
═ answer (success)
Yes — in [Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)](https://www.cbioportal.org/study?id=brca_metabric), the intrinsic subtype field is called **CLAUDIN_SUBTYPE** (PAM50 + claudin-low classification), rather than a plain "PAM50" attribute. It includes six groups:
| Subtype | Samples |
|---|---|
| Luminal A (LumA) | 700 |
| Luminal B (LumB) | 475 |
| HER2-enriched (Her2) | 224 |
| Basal-like | 209 |
| Normal-like | 148 |
| Claudin-low | 218 |
I've set up a group comparison across all six subtypes on the mRNA expression tab, pre-selecting ESR1:
[ESR1 mRNA expression by CLAUDIN_SUBTYPE — METABRIC](https://www.cbioportal.org/comparison/mrna?comparisonId=6ab8224ce497aad53593c5cb&selectedGene=ESR1)
This will let you view box plots of ESR1 z-scores across the six groups directly (METABRIC uses microarray-based mRNA z-scores rather than RNA-seq). Based on prior TCGA findings, you'd generally expect Luminal A/B tumors to show the highest ESR1 expression, with Basal-like and claudin-low tumors showing the lowest — but please confirm the actual distribution and any statistical comparison (ANOVA/Kruskal-Wallis) using the plot linked above, since I have not run that test myself.
If you'd rather browse the underlying cohort first, here's the [study overview](https://www.cbioportal.org/study?id=brca_metabric).