Frenkel-Morgenstern, M. | Search bioRxiv

bioRxiv2018

A Comprehensive Approach Characterizing Fusion Proteins and Their Interactions Using Biomedical Literature

Todays increase in scientific literature requires the efficient methods of data mining for improving the extraction of the useful information from texts. In this manuscript, we used a data and text mining method to identify fusions and their protein-protein interactions from published biomedical text. The extracted fusion proteins and their protein-protein interactions are used as a training set for a Naive Bayes classifier that is further used for final identification of testing dataset, consisting of 1817 fusions. Our method has a literature corpus, text and annotation mappers; keywords, rule bases, negative tokens, and pattern extractor; synonym tagger, normalization, regular expression mapper; and Naive Bayes classifier. We classified 1817 unique fusion proteins and their corresponding 2908 protein-protein interactions for 18 cancer types. Therefore, it can be used for screening literature for identifying mentions unique cases of fusions that can be further used for downstream analysis. It is available at http://protfus.md.biu.ac.il/.

bioinformatics↗

bioRxiv2017

Pan-cancer study of heterogeneous RNA aberrations

We present the most comprehensive catalogue of cancer-associated gene alterations through characterization of tumor transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes project. Using matched whole-genome sequencing data, we attributed RNA alterations to germline and somatic DNA alterations, revealing likely genetic mechanisms. We identified 444 associations of gene expression with somatic non-coding single-nucleotide variants. We found 1,872 splicing alterations associated with somatic mutation in intronic regions, including novel exonization events associated with Alu elements. Somatic copy number alterations were the major driver of total gene and allele-specific expression (ASE) variation. Additionally, 82% of gene fusions had structural variant support, including 75 of a novel class called \"bridged\" fusions, in which a third genomic location bridged two different genes. Globally, we observe transcriptomic alteration signatures that differ between cancer types and have associations with DNA mutational signatures. Given this unique dataset of RNA alterations, we also identified 1,012 genes significantly altered through both DNA and RNA mechanisms. Our study represents an extensive catalog of RNA alterations and reveals new insights into the heterogeneous molecular mechanisms of cancer gene alterations.

genomics↗