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Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification
BackgroundIn recent years, researchers have made significant strides in understanding the heterogeneity of breast cancer and its various subtypes....
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Feature-specific quantile normalization and feature-specific mean–variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data
BackgroundCross-platform normalization seeks to minimize technological bias between microarray and RNAseq whole-transcriptome data. Incorporating...
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classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes
BackgroundTranscriptionally informed predictions are increasingly important for sub-ty** cancer patients, understanding underlying biology and to...
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Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series
BackgroundFull RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in...
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Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities
Molecular profiling guides precision treatment of breast cancer; however, Asian patients are underrepresented in publicly available large-scale...
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N-of-one differential gene expression without control samples using a deep generative model
Differential analysis of bulk RNA-seq data often suffers from lack of good controls. Here, we present a generative model that replaces controls,...
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SPACA6P-AS: a trailblazer in breast cancer pathobiology and therapeutics
ObjectiveThe primary objective of this investigation is to delve into the involvement of the long noncoding RNA (lncRNA) SPACA6P-AS in breast cancer...
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How to Compare Various Clustering Outcomes? Metrices to Investigate Breast Cancer Patient Subpopulations Based on Proteomic Profiles
Breast cancer is a highly diverse disease. With the state-of-the-art methods of molecular studies, novel subgroups of breast cancer can be revealed....
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Lactadherin immunoblockade in small extracellular vesicles inhibits sEV-mediated increase of pro-metastatic capacities
BackgroundTumor-derived small extracellular vesicles (sEVs) can promote tumorigenic and metastatic capacities in less aggressive recipient cells...
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TMO-Net: an explainable pretrained multi-omics model for multi-task learning in oncology
Cancer is a complex disease composing systemic alterations in multiple scales. In this study, we develop the Tumor Multi-Omics pre-trained Network...
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Removing unwanted variation from large-scale RNA sequencing data with PRPS
Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from RNA sequencing...
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Transcriptome profiling and network enrichment analyses identify subtype-specific therapeutic gene targets for breast cancer and their microRNA regulatory networks
Previous studies have suggested that breast cancer (BC) from the Middle East and North Africa (MENA) is presented at younger age with advanced tumor...
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Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data
BackgroundSingle-cell RNA sequencing (sc-RNASeq) data illuminate transcriptomic heterogeneity but also possess a high level of noise, abundant...
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Glycolysis-related lncRNA TMEM105 upregulates LDHA to facilitate breast cancer liver metastasis via sponging miR-1208
Increased glycolysis is one of the key metabolic hallmarks of cancer cells. However, the roles of lncRNAs in energy metabolism and cancer metastasis...
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Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis
The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with...
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Multiomics-Based Tensor Decomposition for Characterizing Breast Cancer Heterogeneity
Breast cancer is heterogeneous and consists of intrinsic components with various alterations. Combining multiple genomic sources to identify the...
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A primary luminal/HER2 negative breast cancer patient with mismatch repair deficiency
Here, we present the case of a 47-year-old woman diagnosed with luminal B breast cancer subtype and provide an in-depth analysis of her gene...
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moBRCA-net: a breast cancer subtype classification framework based on multi-omics attention neural networks
BackgroundBreast cancer is a highly heterogeneous disease that comprises multiple biological components. Owing its diversity, patients have different...
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PD-L1 blockade in combination with carboplatin as immune induction in metastatic lobular breast cancer: the GELATO trial
Invasive lobular breast cancer (ILC) is the second most common histological breast cancer subtype, but ILC-specific trials are lacking. Translational...
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The prognostic value of arachidonic acid metabolism in breast cancer by integrated bioinformatics
BackgroundAs the second cause of cancer death in women, breast cancer has become a worldwide priority. Previous studies based on tumour cell lines...
