BRCA1 expression in TCGA breast cancer samples

Browse datasets

datamonger:brca1@1 · Registry 1.2.0. Default version in this registry.

Prepared directly from official TCGA Agilent Level 3 measurements hosted by the NCI GDC. Contains 533 primary tumors, three metastatic tumors, 17,322 complete gene expression predictors, and response y (BRCA1 expression). Values are log2 lowess-normalized Cy5/Cy3 ratios collapsed by gene symbol. Retains official precision, gene symbols, and sample identifiers, with no extra centering or imputation. Samples and predictors are sorted lexicographically. The public sample_id is metadata excluded from model features. Iowa's added gene annotations are omitted.

Dimensions and tasks

Task

Type

Split

Samples

Predictors

default

regression

—

536

17,322

Predictor counts follow each task's feature selection and exclude targets and identifiers. Sample counts are reported separately for each split.

Retrieve

These examples pin both the dataset version and the registry's exact index. An uncached dataset requires network access to its source. The CLI retrieves verified artifacts. The language clients also decode them.

Python

from datamonger import Registry, fetch_data

registry = Registry(
    release="1.2.0",
    index_sha256="4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21",
    index_url="https://github.com/jolars/datamonger/releases/download/registry-v1.2.0/index.json",
)
data = fetch_data("datamonger:brca1@1", registry=registry)

R

library(datamonger)

registry <- registry_selector(
  release = "1.2.0",
  index_sha256 = "4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21",
  index_url = "https://github.com/jolars/datamonger/releases/download/registry-v1.2.0/index.json"
)
data <- fetch_data("datamonger:brca1@1", registry = registry)

Julia

using Datamonger

registry = registry_selector(
    "1.2.0",
    "4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21",
    "https://github.com/jolars/datamonger/releases/download/registry-v1.2.0/index.json",
)
data = fetch_data("datamonger:brca1@1"; registry=registry)

CLI

cat > datamonger-registry.json <<'JSON'
{
  "index_sha256": "4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21",
  "index_url": "https://github.com/jolars/datamonger/releases/download/registry-v1.2.0/index.json",
  "release": "1.2.0",
  "schema_version": 1
}
JSON
datamonger --selector datamonger-registry.json fetch 'datamonger:brca1@1'

Representation and variables

Tabular data with a dense representation. Decoder: delimited-text version 1.

Component

Kind

Type

Shape

sample_id

vector

string

536

15E1.2

vector

float64

536

2'-PDE

vector

float64

536

7A5

vector

float64

536

A1BG

vector

float64

536

A2BP1

vector

float64

536

A2M

vector

float64

536

A2ML1

vector

float64

536

A3GALT2

vector

float64

536

A4GALT

vector

float64

536

A4GNT

vector

float64

536

AAAS

vector

float64

536

AACS

vector

float64

536

AADAC

vector

float64

536

AADACL1

vector

float64

536

AADACL2

vector

float64

536

AADACL3

vector

float64

536

AADAT

vector

float64

536

AAK1

vector

float64

536

AAMP

vector

float64

536

AANAT

vector

float64

536

AARS

vector

float64

536

AARS2

vector

float64

536

AARSD1

vector

float64

536

AASDH

vector

float64

536

AASDHPPT

vector

float64

536

AASS

vector

float64

536

AATF

vector

float64

536

AATK

vector

float64

536

ABAT

vector

float64

536

Showing 30 of 17,324 components. The complete registry record contains every variable name and task binding.

Preprocessing

Preprocessing history is not recorded in this registry release.

Provenance and citation

Provider: Datamonger; derived from official TCGA data at the NCI GDC. Upstream name: TCGA BRCA Agilent G4502A-07-3 Level 3. Retrieved: 2026-10-16.

Original source

Authors: The Cancer Genome Atlas Network, University of North Carolina Cancer Genomic Characterization Center.

The Cancer Genome Atlas Network (2012). Comprehensive molecular portraits of human breast tumours. Nature 490:61-70. https://doi.org/10.1038/nature11412. Underlying TCGA Level 3 gene expression archive at the NCI GDC: f0b74706-6b9e-4430-931d-9f233b4ac67c. Datamonger portable representation, version 1: https://doi.org/10.5281/zenodo.23418110.

License

Known (see terms)

License information

Official TCGA open-access Agilent Level 3 measurements, retrieved from the NCI GDC publication archive. GDC policies permit analysis and publication of open-access data, require attribution, and prohibit attempts to reidentify participants. This automated review treats publishing the portable numeric extract as publication under those source policies. No SPDX license or public-domain dedication is inferred. Iowa's RDS and added annotations are not preparation inputs.

Artifacts

Total download: 35.5 MiB. Sizes describe the distributed files, including any compression.

Artifact

Format

Compression

Size

Distribution

Preservation

data

csv

gzip

35.5 MiB

mirror

durable

data: mirror

Preservation deposit

Versions in this registry

1 (default)

Registry record

Download the complete registry record, registry selector, or full registry index.

Index SHA-256: 4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21.