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n3:pmcid: PMC0
bibo:doi: 10.1038%2Fsrep02652
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dc:title: results
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rdf:value: Compared to the other cancers within TCGA, AML is a distinct, relatively homogenous group, yet it can be further divided into subtypes by clustering genomic data such as miRNA expression>>4<< or DNA methylation (Peter Laird, Personal communication) (Figure 1b).
n3:mentions: n2:23634996

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rdf:value: The double cluster 5 shows relatively few mutations and is strongly enriched for samples with favorable cytogenetic risk>>4<<. The UCSC Cancer Genomics Browser's dynamic Kaplan-Meier plot confirms this by demonstrating that the samples in miRNA cluster 5 show a substantial advantage in overall survival (Figure 1c). Altogether, this analysis connects cancer
n3:mentions: n2:23634996

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rdf:value: The TCGA Pan-Cancer analysis revealed that tumor samples cluster largely by their tissue of origin>>5<<. For example, lung squamous cell carcinoma (LUSC) clusters with other squamous cell carcinomas such as head and neck (HNSC) and some bladder urothelial carcinoma (BLCA) samples, while lung adenocarcinoma (LUAD) falls into a distinct
n3:mentions: n2:24071849

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rdf:value: This is not too surprising, since LUAD and LUSC are difficult to distinguish histologically, with as much as 40% disagreement between pathologists>>6<<. Misdiagnosis is potentially fatal: Bevacizumab (Avastin) is the recommended chemotherapy for LUAD, but can lead to a life-threatening hemorrhage in LUSC patients7. A user-defined custom annotation column divides the samples into three
n3:mentions: n2:16476504

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rdf:value: Misdiagnosis is potentially fatal: Bevacizumab (Avastin) is the recommended chemotherapy for LUAD, but can lead to a life-threatening hemorrhage in LUSC patients>>7<<. A user-defined custom annotation column divides the samples into three categories: LUAD, discordant LUSC (those for which the RNA subtype is inconsistent with the cohort), and concordant LUSC (for which the RNA subtype and cohort are
n3:mentions: n2:19349493

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rdf:value: Many of these discordant LUSC samples lack the 3q26 amplification commonly seen in LUSC and other squamous cell carcinomas, where PIK3CA and ECT2 are located>>8<< (Figure 3).
n3:mentions: n2:19896966

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rdf:value: We further analyzed the discordant samples against the Shedden gene expression signature where a high signature value predicts poor overall survival in LUAD>>9<<. We are able to confirm the Shedden signature in TCGA LUAD data in terms of both overall and recurrence free survival (Figure 4). The Shedden signature value is high for the discordant LUSC samples, suggesting that if they are
n3:mentions: n2:18641660

Subject Item: _:vb25477875
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rdf:value: Pan-Cancer subtypes are defined by the Pan-Cancer working group using gene expression, copy number, DNA methylation, protein expression, or somatic mutation data individually, or integratively by iCluster>>10<<, PARADIGM pathway inference11, Cluster of Clusters and SuperCluster method5 are available.
n3:mentions: n2:19759197

Subject Item: _:vb25477876
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rdf:value: Pan-Cancer subtypes are defined by the Pan-Cancer working group using gene expression, copy number, DNA methylation, protein expression, or somatic mutation data individually, or integratively by iCluster10, PARADIGM pathway inference>>11<<, Cluster of Clusters and SuperCluster method5 are available.
n3:mentions: n2:20529912

Subject Item: _:vb25477877
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rdf:value: working group using gene expression, copy number, DNA methylation, protein expression, or somatic mutation data individually, or integratively by iCluster10, PARADIGM pathway inference11, Cluster of Clusters and SuperCluster method>>5<< are available.
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dc:title: methods
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rdf:value: Public datasets include TCGA, Cancer Cell Line Encyclopedia>>12<<, and the Stand Up To Cancer (SU2C) Breast Cancer Dream Team13 as well as other datasets from the literature.
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rdf:value: Public datasets include TCGA, Cancer Cell Line Encyclopedia12, and the Stand Up To Cancer (SU2C) Breast Cancer Dream Team>>13<< as well as other datasets from the literature.
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