OncoMap RESEARCH EXPLORER LOCAL ONLY

EDUCATIONAL BIOINFORMATICS PROJECT

OncoMap

Breast Cancer Bioinformatics Explorer

A focused view of public breast-tissue gene-expression data, with probe-level results kept visible for careful interpretation.

GEO SERIES GSE42568 ARRAY PLATFORM GPL570
TOTAL SAMPLES 121 GEO sample records
BREAST CANCER 104 tumour tissue samples
NORMAL BREAST 17 normal tissue samples
RESEARCH GENES 08 selected for exploration
TARGET PANEL BRCA1BRCA2TP53ERBB2 PIK3CAESR1PTENEGFR
RESEARCH QUESTION

How do selected breast cancer-associated gene-expression probes differ between normal breast tissue and breast cancer tissue?

BIOLOGICAL CONTEXT

Why This Research Matters

The selected genes connect to several themes often studied in breast cancer. These are useful ways to organize the question, not claims that one expression measurement explains a tumour.

01 / GENOME MAINTENANCE

DNA repair

BRCA1 and BRCA2 are associated with repairing damaged DNA and maintaining genome stability.

02 / SIGNAL TRANSDUCTION

Cell growth signalling

ERBB2, PIK3CA and EGFR are linked to pathways that transmit signals involved in cell growth and survival.

03 / CELL-CYCLE CONTROL

Tumour suppression

TP53 and PTEN are associated with cellular controls that can limit abnormal growth.

04 / HORMONE RESPONSE

Hormone receptor signalling

ESR1 encodes the estrogen receptor alpha, which is involved in hormone-responsive signalling.

PROJECT WORKFLOW

Project journey

  1. 01Public dataset selection
  2. 02Data inspection
  3. 03Probe annotation
  4. 04Gene selection
  5. 05Differential-expression analysis
  6. 06Scientific visualisation
  7. 07Interactive exploration

INTERACTIVE TABLE

Gene explorer

01
LOCAL FILE / GEO2R

Load differential-expression results

Select Data/processed/GSE42568.top.table.tsv from your computer. The file is read in this browser only.

No file loaded yet. Choose the GEO2R TSV to view real probe-level results.

0 matching probes

Upload the GEO2R table to explore its measured probes. This dashboard does not invent or pre-fill result rows.

DIFFERENTIAL EXPRESSION

Volcano plot

02
GSE42568 / GEO2R
ADJUSTED P < 0.05Open full-size figure

Wide figure: scroll horizontally to inspect the details.

Volcano plot of GEO2R differential expression results. Points show log fold change and adjusted P-value; target probes are highlighted.
Each dot represents a probe. Color indicates logFC direction for probes passing the adjusted P-value threshold. Target probes are outlined and significant target probes are labeled.

SAMPLE-LEVEL PATTERNS

Gene-expression heatmap

03
38 PROBES / 121 SAMPLES
ROW-WISE Z-SCOREOpen full-size figure

Wide figure: scroll horizontally to inspect the details.

Heatmap of row-wise standardized expression for 38 individual target probes across normal breast and breast cancer samples.
Each row is a separate array probe. Blue indicates values below that probe's average, white is near average, and red is above average. This view is descriptive and keeps probes separate.

EXPLORATORY SUMMARY

Research findings

04

These observations come from the supplied GEO2R table for the eight selected genes. They describe individual probe rows, not combined gene-level measurements.

18 significant probes / 38
adj. P-value < 0.05
14 / 38

Significant probes with negative logFC

For the cancer-versus-normal contrast, these probes have lower reported measurements in cancer. This includes all 3 PIK3CA probes, 6 of 8 PTEN probes, and 5 of 9 EGFR probes.

4 / 38

Significant probes with positive logFC

One probe each for BRCA2, TP53, ERBB2, and ESR1 has positive logFC. The other probes for those genes do not pass the threshold.

20 / 38

Selected probes not below the threshold

These probes have adjusted P-values of 0.05 or higher. Their direction alone should not be described as a statistically significant difference.

STUDY CONTEXT

Methodology & limitations

05
DATASET

Public microarray study

NCBI GEO Series GSE42568, measured with the Affymetrix Human Genome U133 Plus 2.0 Array (GPL570). The series contains 121 samples: 104 breast cancer and 17 normal breast tissue samples.

PROCESSING

Processed measurements

The GEO2R results are based on GC-RMA processed array measurements. The table remains probe-level; the annotation file provides probe-to-symbol mappings, including some one-to-many mappings.

STATISTICS

GEO2R / limma

GEO2R uses the limma framework to estimate differential expression. Adjusted P-values use the Benjamini-Hochberg procedure to account for testing many probes. The dashboard displays the supplied results and does not rerun this model.

LIMITATIONS

Use as an exploration, not a conclusion

The groups are imbalanced, and clinical or technical factors may affect measurements. Multiple probes can represent a gene, annotations can be ambiguous, and these results need independent validation. No diagnostic or treatment decisions should be made from this project.

OFFICIAL SOURCES NCBI GEO Series GSE42568 NCBI GEO Platform GPL570