Unsupervised Single-Cell Clustering with Asymmetric Within-Sample Transformation and Per-Cluster Supervised Features Selection.

This chapter shows applying the Asymmetric Within-Sample Transformation to single-cell RNA-Seq data matched with a previous dropout imputation. The asymmetric transformation is a special winsorization that flattens low-expressed intensities and preserves highly expressed gene levels. Before a standard hierarchical clustering algorithm, an intermediate step removes noninformative genes according to a threshold applied to a per-gene entropy estimate.

massiveGST: A Mann-Whitney-Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis.

Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space's statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted to global tests, in contrast to competitive methods that have been largely ignored, although they appear more flexible because they are independent from the source of gene-profiles.

Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles.

Motivation: Data transformations are an important step in the analysis of RNA-seq data. Nonetheless, the impact of transformation on the outcome of unsupervised clustering procedures is still unclear.

Results: Here, we present an Asymmetric Winsorization per-Sample Transformation (AWST), which is robust to data perturbations and removes the need for selecting the most informative genes prior to sample clustering.

The Tomb of the Diver and the frescoed tombs in Paestum (southern Italy): New insights from a comparative archaeometric study.

The Tomb of the Diver has been subject for many decades of fierce debate among archaeologists and classicists. Since its discovery in 1968, some scholars have considered it a unique example of the lost tradition of Greek painting, others have emphasized Etruscan or Italic parallels. More recently, a possible local production has been suggested.

A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas.

Chordoid glioma (ChG) is a characteristic, slow growing, and well-circumscribed diencephalic tumor, whose mutational landscape is unknown. Here we report the analysis of 16 ChG by whole-exome and RNA-sequencing. We found that 15 ChG harbor the same PRKCA mutation.

Comparison between invasive breast cancer with extensive peritumoral vascular invasion and inflammatory breast carcinoma: a clinicopathologic study of 161 cases.

Objectives: Extensive peritumoral neoplastic lymphovascular invasion (ePVI) is a marker of aggressiveness in invasive breast carcinoma (BC).

Methods: We explored the impact of ePVI on different BC subtypes. In a total of 2,116 BCs, 91 ePVI-BCs, 70 inflammatory breast carcinomas (IBCs), and 114 casual BCs as a control group (CG-BC) were recruited.

Ensemble of gene signatures identifies novel biomarkers in colorectal cancer activated through PPARγ and TNFα signaling.

We describe a novel bioinformatic and translational pathology approach, gene Signature Finder Algorithm (gSFA) to identify biomarkers associated with Colorectal Cancer (CRC) survival. Here a robust set of CRC markers is selected by an ensemble method. By using a dataset of 232 gene expression profiles, gSFA discovers 16 highly significant small gene signatures.

Finding recurrent copy number alterations preserving within-sample homogeneity.

Motivation: Copy number alterations (CNAs) represent an important component of genetic variation and play a significant role in many human diseases. Development of array comparative genomic hybridization (aCGH) technology has made it possible to identify CNAs. Identification of recurrent CNAs represents the first fundamental step to provide a list of genomic regions which form the basis for further biological investigations.