Gene expression and relative ovarian xenograft tumor volume

Browse datasets

datamonger:koussounadis2014@1 · Registry 1.3.0. Default version in this registry.

Prepared from the authors' GSE49577 processed expression matrix and phenodata, with GPL10558 internal gene identifiers. Contains 101 ovarian cancer xenografts, 34,694 expression predictors obtained by averaging probes with the same ILMN_Gene label, and response y (log2 relative tumor volume). Preserves GEO sample order and numeric precision, with labels sorted by ASCII bytes. Retains sample_id, tumor_id, Treatment, Day, CellLine, and untransformed RTV as metadata excluded from model features. No additional normalization, filtering, imputation, or repair of historical gene labels is applied.

Dimensions and tasks

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.

from datamonger import Registry, fetch_data

registry = Registry(
    release="1.3.0",
    index_sha256="94639f8d711d64895689d6da87add0f0f56574070262ec2a04f1f1ad43279f85",
    index_url="https://github.com/jolars/datamonger/releases/download/registry-v1.3.0/index.json",
)
data = fetch_data("datamonger:koussounadis2014@1", registry=registry)

library(datamonger)

registry <- registry_selector(
  release = "1.3.0",
  index_sha256 = "94639f8d711d64895689d6da87add0f0f56574070262ec2a04f1f1ad43279f85",
  index_url = "https://github.com/jolars/datamonger/releases/download/registry-v1.3.0/index.json"
)
data <- fetch_data("datamonger:koussounadis2014@1", registry = registry)

using Datamonger

registry = registry_selector(
    "1.3.0",
    "94639f8d711d64895689d6da87add0f0f56574070262ec2a04f1f1ad43279f85",
    "https://github.com/jolars/datamonger/releases/download/registry-v1.3.0/index.json",
)
data = fetch_data("datamonger:koussounadis2014@1"; registry=registry)

cat > datamonger-registry.json <<'JSON'
{
  "index_sha256": "94639f8d711d64895689d6da87add0f0f56574070262ec2a04f1f1ad43279f85",
  "index_url": "https://github.com/jolars/datamonger/releases/download/registry-v1.3.0/index.json",
  "release": "1.3.0",
  "schema_version": 1
}
JSON
datamonger --selector datamonger-registry.json fetch 'datamonger:koussounadis2014@1'

Representation and variables

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

Showing 30 of 34,701 components. The complete registry record contains every variable name and task binding.

Preprocessing

Upstream

Status: documented.

normalization. The submitted expression values include background correction, variance stabilization, and robust spline normalization with Bioconductor lumi.

Parameters: method: lumi robust spline normalization.

Evidence: curation/koussounadis2014/1/DATASET.md, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49577

Datamonger

Status: documented.

No additional expression normalization, probe filtering, standardization, or gene-label repair is applied.

aggregation. For each sample, average probes sharing the GPL10558 ILMN_Gene label using the arithmetic mean, producing 34,694 features.

Parameters: group_by: GPL10558 ILMN_Gene; method: R arithmetic mean.

response-transformation. Compute the response y as log2 of relative tumor volume from the original phenodata.

Parameters: base: 2; input: RTV; method: R log2; output: y.

Evidence: curation/koussounadis2014/1/DATASET.md, curation/koussounadis2014/1/read_source.R

Provenance and citation

Provider: Datamonger; derived from Koussounadis et al. at NCBI GEO. Upstream name: Chemotherapy induced dynamic gene expression changes in vivo are prognostic in ovarian cancer. Retrieved: 2026-10-19.

Original source

Authors: Antonis Koussounadis, Simon P. Langdon, David J. Harrison, V. Anne Smith.

Koussounadis A, Langdon SP, Harrison DJ, and Smith VA (2014). Chemotherapy-induced dynamic gene expression changes in vivo are prognostic in ovarian cancer. British Journal of Cancer 110:2975-2984. https://doi.org/10.1038/bjc.2014.258. GEO accession GSE49577, platform GPL10558. Datamonger portable representation, version 1: https://doi.org/10.5281/zenodo.23468640.

License

Known (see terms)

License information

GEO places no restrictions on use or distribution of submitted data, while warning that submitters may retain intellectual property rights. No additional data-specific restriction was found in GSE49577, GSM1202097, or GPL10558. This automated review treats GEO's source terms as the redistribution basis for this numeric extract and its identifiers, retaining attribution. No SPDX license or public-domain dedication is inferred. The article's CC BY-NC-SA 3.0 license is not assumed to license the separate GEO deposit. Iowa's RDS and code are not preparation inputs.

Artifacts

Total download: 21.8 MiB. Sizes describe the distributed files, including any compression.

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: 94639f8d711d64895689d6da87add0f0f56574070262ec2a04f1f1ad43279f85.