Month: May 2016
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IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC.
Abstract: Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) expression correlates with malignancy, but its role(s) in pathogenesis remains enigmatic. We interrogated the IGF2BP3-RNA interaction network in pancreatic ductal adenocarcinoma (PDAC) cells. Using a combination of genome-wide approaches, we have identified 164 direct mRNA targets of IGF2BP3. These transcripts encode proteins enriched for functions…
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Effects of Prolonged Media Usage and Long-term Planning on Archival Systems
Abstract: In archival systems, storage media are often replaced much earlier than their expected service life in exchange for other benefits of new media, such as higher capacity, bandwidth, and input/output operations per second, or lower costs. In an era of decreasing media density growth rates, retiring media early by considering only short-term benefits while…
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New book by UCSC biologist highlights efforts to save Hawaiian monk seals
By Tim Stephens, UCSC Public Information Office In 2009, federal officials monitoring the endangered Hawaiian monk seal population asked marine biologist Terrie Williams if she could care for an orphaned pup at her lab at the University of California, Santa Cruz. Williams, a professor of ecology and evolutionary biology, jumped at the opportunity to study…
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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
Abstract: To compare lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SqCC) and to identify new drivers of lung carcinogenesis, we examined the exome sequences and copy number profiles of 660 lung ADC and 484 lung SqCC tumor-normal pairs. Recurrent alterations in lung SqCCs were more similar to those of other squamous carcinomas than to…
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Facilitating a culture of responsible and effective sharing of cancer genome data.
Rapid and affordable tumor molecular profiling has led to an explosion of clinical and genomic data poised to enhance the diagnosis, prognostication and treatment of cancer. A critical point has now been reached at which the analysis and storage of annotated clinical and genomic information in unconnected silos will stall the advancement of precision cancer…
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TNF-α modulates genome-wide redistribution of ΔNp63α/TAp73 and NF-κB cREL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer.
Abstract: The Cancer Genome Atlas (TCGA) network study of 12 cancer types (PanCancer 12) revealed frequent mutation of TP53, and amplification and expression of related TP63 isoform ΔNp63 in squamous cancers. Further, aberrant expression of inflammatory genes and TP53/p63/p73 targets were detected in the PanCancer 12 project, reminiscent of gene programs comodulated by cREL/ΔNp63/TAp73 transcription…
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UCSC Data Integrator and Variant Annotation Integrator
Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user’s own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other…