Embedded Files
Code
Code
HER2-low: https://github.com/AndresBedoyaPhD/HER2-low-project
Code used for the analyses performed during the study of "Epigenetic determinants of an immune-evasive phenotype in HER2-low triple-negative breast cancer".
Publication (Gold Open Access): https://www.nature.com/articles/s41698-025-01023-3
TNBC-ICI: https://github.com/CancerEpigeneticsLab/TNBC-ICI
Code used to identify a minimum signature that can predict response to immunotherapy in triple-negative breast cancer patients. The resources also include a methodology to test new samples.
Publication (Pre-Print, accepted at Communications Medicine): https://www.researchsquare.com/article/rs-2284514/v1
cGSCs: https://github.com/CancerEpigeneticsLab/cGSCs
Scripts employed for the discovery of a Glioma Stem Cell (GSC) population called core-GSC (c-GSC) with embryonic-like features and immune-evasive phenotype, and for the validation of the model of induced-cGSCs (ic-GSCs)
Publication (Gold Open Access): https://www.mdpi.com/2072-6694/14/9/2070
iGlioSub: https://github.com/CancerEpigeneticsLab/iGlioSub
Methodology used for the creation of iGlioSub, a machine learning-based classifier (Random Forest and Nearest Shrunken Centroid) which uses transcriptomic and epigenomic features to stratify GBM subtypes.
Publication (Gold Open Access): https://biodatamining.biomedcentral.com/articles/10.1186/s13040-021-00273-8
EpiLN: https://github.com/CancerEpigeneticsLab/EpiLN
Methodology used for the creation of EpiLN, a machine learning-based classifier which employs DNA methylation features to identify breast cancer patients with lymph node metastasis.
Data
Data
Methylation profiling by array of TNBC xenografts, comparing primary tumors and distant metastases (lymph node and lung).
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE305869 (EPIC microarray data)
RNA-seq of wildtype and PTBP1-KO TNBC cell line (MDA-MB-231)
E-MTAB-15284 (private, manuscript under consideration)
Methylation profiling by array of TNBC patients with variable HER2 expression
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE291237 (EPIC microarray data)
RNA-seq, ATAC-seq and Hi-C data of TNBC cell lines
https://identifiers.org/arrayexpress:E‐MTAB‐12821 https://identifiers.org/arrayexpress:E‐MTAB‐12825 https://identifiers.org/arrayexpress:E‐MTAB‐12823
Transcriptomic and epigenomic data of ic-GSCs and GBM-DCs
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10977/ (RNA-seq data)
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10978/ (EPIC microarray data)
Protocols
Protocols
Tumor microdissection protocol
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