The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal

UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses.

https://bradleybiology.org/papers/pdf/2015/RobinsonEtAl2015.pdf

Integrative clinical genomics of advanced prostate cancer

The Cancer Genome Atlas (TCGA) is a public funded project that aims to catalogue and discover major cancer-causing genomic alterations to create a comprehensive "atlas" of cancer genomic profiles. So far, TCGA researchers have analysed large cohorts of over 30 human tumours through large-scale genome sequencing and integrated multi-dimensional analyses. Studies of individual cancer types, as well as comprehensive pan-cancer analyses have extended current knowledge of tumorigenesis. A major goal of the project was to provide publicly available datasets to help improve diagnostic methods, treatment standards, and finally to prevent cancer. This review discusses the current status of TCGA Research Network structure, purpose, and achievements.

https://www.termedia.pl/Journal/-77/pdf-24047-10?filename=The Cancer Genome Atlas.pdf

The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63∆N transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.

Genomic analyses identify molecular subtypes of pancreatic cancer

The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications.

/pdf/the-cbio-cancer-genomics-portal-an-open-platform-for-4kclcxogdw.pdf

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data

Australia's international education serves as public diplomacy, essentially engaging and influencing public audiences in ways that progress Australian foreign policy priorities and national interests. The multidimensional and increasingly globalised nature of international education presents enormous opportunity for vital exchange and interactions between and with students, academics and communities via onshore and offshore modes of delivery. Positive experiences of student mobility and the development of intellectual, commercial and social relationships can build upon a nation's reputation, and enhance the ability of that nation to participate in and influence regional or global outcomes. This is ultimately the essence of soft power. While Australia has made significant commercial gains through international education, it has fallen short of realising the soft power potential inherent in the volume and depth of interactions, relationships and achievements resulting from it, particularly in the Asian regi...

Realising Australia's international education as public diplomacy

The New Colombo Plan (NCP), a key plank in the Australian government’s foreign policy agenda, leverages student mobility as public diplomacy to improve Australia’s standing and influence within the...

Australia's New Colombo Plan: Enhancing regional soft power through student mobility

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Public Diplomacy in an Australian Context : a Policy-based Framework to Enhance Understanding and Practice

SummaryPublic diplomacy’s scholarship and practice are evolving and seeking to adapt to the expanding interests, expectations, connectivity and mobility of the publics that have come to define the field in an organic fashion. The characteristic distinction between international and domestic publics as the key to defining the practice of public diplomacy is increasingly challenged by public audiences that are no longer constrained by such traditional delineations. The attention on the involvement of domestic publics in public diplomacy, or its domestic dimension, has to be understood within this context. This article aims to cast further light on public diplomacy’s domestic dimension, with Canada and Australia — two countries that have much in common — as the launch pads for discussion. The article’s first section investigates the approach and development of public diplomacy’s domestic dimension in both countries and draws out the similarities and differences. The second section identifies the opportunities, challenges and tendencies in its practice as well as the conceptual implications. The article finds that while differences in approach remain, Canada and Australia have more in common than not when it comes to involving domestic audiences in international policy, especially in recent years. Their practice of public diplomacy’s domestic dimension appears to be resilient and adaptive in nature, although it has been subject to fluctuations resulting from changes in the political climate, leadership styles and governmental preferences, and resource availability. Additionally, reconceptualizing public diplomacy with a domestic dimension and constructivist underpinnings opens the window on norms that are taken for granted in diplomacy and offers the potential for a more inclusive view and practice — a better fit for its time.

Caitlin Byrne

Papers

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data

Realising Australia's international education as public diplomacy

Australia's New Colombo Plan: Enhancing regional soft power through student mobility

Public Diplomacy in an Australian Context : a Policy-based Framework to Enhance Understanding and Practice

Opening the windows on diplomacy: A comparison of the domestic dimension of public diplomacy in Canada and Australia