Prognostically relevant gene signatures of high-grade serous ovarian carcinoma.
By R. Verhaak, Pablo Tamayo, Ji-Yeon Yang, D. Hubbard, Hailei Zhang, Chad Creighton, S. Fereday, M. Lawrence, Scott L. Carter, Craig H. Mermel and 31 more. Journal of Clinical Investigation, 2012
595 citations recorded by the source corpus.
Subfields: Cancer Research, Molecular Biology, Reproductive Medicine
View Paper: https://www.semanticscholar.org/paper/e35bd4b47b48c663393bbdfaa46b41452d51cd87
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In Cancer Research
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- G. Way
- Casey S. Greene
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- Trey Ideker
- Aaron M. Newman
- Matan Hofree
- Hannah Carter
- Andrew M. Gross
Citations in the corpus
- Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage (2019, unknown): “To address this question, we performed single-sample gene set enrichment analysis (ssGSEA) 31 to quantify the expression of human orthologues of genes of interest in a published microarray dataset of 167 lung samples from patients with lung fibrosis and 50 healthy controls 32 .”
- Dimension reduction techniques for the integrative analysis of multi-omics data (2016, background): “Overlapping clusters have been identified in many tumors including glioblastoma and serous ovarian cancer [6, 7].”
- Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses (2015, unknown): “Cell 162, 974–986, August 27, 2015 ª2015 Elsevier Inc. 981 Indeed, basal levels of our viral defense gene transcripts divide EOC, and other major cancer types in TCGA, into low and high expression subgroups.”
- Evaluating deep variational autoencoders trained on pan-cancer gene expression (2017, methodology): “Using original TCGA subtype labels [23], we calculated mean HGSC subtype vector representations for the mesenchymal and immunoreactive subtypes with the latent space representation from each dimensionality reduction algorithm.”
- Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients (2014, unknown): “To compute the EMT score of a sample, we adopted a similar approach to that used in ssGSEA (Verhaak et al , 2013) The paper explained Problem During epithelial-mesenchymal transition (EMT), epithelial cells lose polarity and acquire migratory properties reminiscent of mesenchymal cells.”
- Profiling tumor infiltrating immune cells with CIBERSORT (2018, background): “Although previous studies of bulk tumor samples revealed a number of immune-enriched gene signatures with prognostic significance [7,8], linking these signatures to specific TIL phenotypes has been challenging [9–13].”
- Network-based stratification of tumor mutations (2013, methodology): “Next, we divided the patient cohort randomly into four equal-sized subtypes (four was selected as reasonable owing to the four expression-based subtypes that have been identified for glioblastoma, ovarian and breast cancers 2,18,60,62 ).”