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BACKGROUND Tumor classification is inexact and largely dependent on the qualitative pathological examination of the images of the tumor tissue slides. In this study, our aim was to develop an automated computational method to classify Hematoxylin and Eosin (H&E) stained tissue sections based on cancer tissue texture features. METHODS Image processing of(More)
Grading of breast cancer and the subsequent treatment options are largely dependent on the pathological examination of the histology slides from the tumor tissue. Tumor grading is currently based on the spatial organization of the tissue, including the distribution of cancer cells, the morphological properties of their nuclei and the presence/absence of(More)
BACKGROUND Much of the public access cancer microarray data is asymmetric, belonging to datasets containing no samples from normal tissue. Asymmetric data cannot be used in standard meta-analysis approaches (such as the inverse variance method) to obtain large sample sizes for statistical power enrichment. Noting that plenty of normal tissue microarray(More)
BACKGROUND Recent research with tissue microarrays led to a rapid progress toward quantifying the expressions of large sets of biomarkers in normal and diseased tissue. However, standard procedures for sampling tissue for molecular profiling have not yet been established. METHODS This study presents a high throughput analysis of texture heterogeneity on(More)
BACKGROUND Independently derived expression profiles of the same biological condition often have few genes in common. In this study, we created populations of expression profiles from publicly available microarray datasets of cancer (breast, lymphoma and renal) samples linked to clinical information with an iterative machine learning algorithm. ROC curves(More)
BACKGROUND Three-dimensional in vitro culture of cancer cells are used to predict the effects of prospective anti-cancer drugs in vivo. In this study, we present an automated image analysis protocol for detailed morphological protein marker profiling of tumoroid cross section images. METHODS Histologic cross sections of breast tumoroids developed in(More)
BACKGROUND Large-scale compilation of gene expression microarray datasets across diverse biological phenotypes provided a means of gathering a priori knowledge in the form of identification and annotation of bimodal genes in the human and mouse genomes. These switch-like genes consist of 15% of known human genes, and are enriched with genes coding for(More)
BACKGROUND Phosphorylation events direct the flow of signals and metabolites along cellular protein networks. Current annotations of kinase-substrate binding events are far from complete. In this study, we scanned the entire human protein sequences using the PROSITE domain annotation tool to identify patterns of domain composition in kinases and their(More)
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