Month: November 2015

Cancer RNA-Seq Nexus

[PMID:26602695] [Nucleic Acids Research]

Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells

“features: (i) large-scale and comprehensive data archives and analyses, including coding-transcript profiling, long non-coding RNA (lncRNA) profiling and coexpression networks; (ii) phenotype-oriented data organization and searching and (iii) the visualization of expression profiles, differential expression and regulatory networks.”



[PMID:26600239] [PLoS Computational Biology]

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

“The pipeline supports the analysis for: 1) the distinction and identification of major cell types; 2) the identification of cell type specific gene signatures; and 3) the determination of driving forces of given cell types.”


TSGene 2.0

[PMID:26590405] [Nucleic Acids Research]

TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes

“the current TSGene 2.0 contains 1217 human TSGs (1018 protein-coding and 199 non-coding genes) curated from over 9000 articles. Additionally, TSGene 2.0 provides thousands of expression and mutation patterns derived from pan-cancer data of The Cancer Genome Atlas.”


Germline Findings in Tumor-Only Sequencing

[PMID:26590952] [Journal of National Cancer Institute]

Germline Findings in Tumor-Only Sequencing: Points to Consider for Clinicians and Laboratories

“Analysis of the cancer genome is most informative when paired with germline genomic DNA to delineate inherited and somatic variants. Although tumor-only analysis remains the most common methodology for numerous reasons, it holds the potential to identify clinically significant germline variants.”


Cancer Noncoding Mutation Prioritization

[PMID:26588488] [PLoS Computational Biology]

A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events

“cancer-specific mutational patterns can be used to predict non-coding regions that are preserved from mutations and may thus be important for cancer cell survival.”



[PMID:26512062] [Human Molecular Genetics]

Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation

“whole-genome bisulfite sequencing from 10 diverse human tissues to identify a comprehensive, experimentally obtained, single-base resolution CGI catalog.”