ArticleF1000Research2017
A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification.
Article in F1000Research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer.Cancer biology & therapy · 2021Pooled it
- The dark matter in cancer immunology: beyond the visible- unveiling multiomics pathways to breakthrough therapies.Journal of translational medicine · 2025Review
- Impact of Clinical Data Veracity on Cancer Genomic Research.JNCI cancer spectrum · 2022Article
- Organizing training workshops on gene literature retrieval, profiling, and visualization for early career researchers.F1000Research · 2021Article
- Bulk and Single-Cell Profiling of Breast Tumors Identifies TREM-1 as a Dominant Immune Suppressive Marker Associated With Poor Outcomes.Frontiers in oncology · 2021Article
- HLA-G: A New Immune Checkpoint in Cancer?International journal of molecular sciences · 2020Review
- Common data elements of breast cancer for research databases: A systematic review.Journal of family medicine and primary care · 2020Review
- The Paradox of Cancer Immune Exclusion: Immune Oncology Next Frontier.Cancer treatment and research · 2020Article
- Long-Chain Acyl-CoA Synthetase 1 Role in Sepsis and Immunity: Perspectives From a Parallel Review of Public Transcriptome Datasets and of the Literature.Frontiers in immunology · 2019Review
- A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.Database : the journal of biological databases and curation · 2019Article
- Using 'collective omics data' for biomedical research training.Immunology · 2018Review
- The MAPK hypothesis: immune-regulatory effects of MAPK-pathway genetic dysregulations and implications for breast cancer immunotherapy.Emerging topics in life sciences · 2017Article
Corrections and comments
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Authors and funding
22 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increased application of high-throughput approaches in translational research has expanded the number of publicly available data repositories. Gathering additional valuable information contained in the datasets represents a crucial opportunity in the biomedical field. To facilitate and stimulate utilization of these datasets, we have recently developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). In this note, we describe a curated compendium of 13 public datasets on human breast cancer, representing a total of 2142 transcriptome profiles. We classified the samples according to different immune based classification systems and integrated this information into the datasets. Annotated and harmonized datasets were uploaded to GXB. Study samples were categorized in different groups based on their immunologic tumor response profiles, intrinsic molecular subtypes and multiple clinical parameters. Ranked gene lists were generated based on relevant group comparisons. In this data note, we demonstrate the utility of GXB to evaluate the expression of a gene of interest, find differential gene expression between groups and investigate potential associations between variables with a specific focus on immunologic classification in breast cancer. This interactive resource is publicly available online at: http://breastcancer.gxbsidra.org/dm3/geneBrowser/list.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.