2020
DOI: 10.1002/pmic.202000043
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ProNetView‐ccRCC: A Web‐Based Portal to Interactively Explore Clear Cell Renal Cell Carcinoma Proteogenomics Networks

Abstract: To better understand the molecular basis of cancer, the NCI's Clinical Proteomics Tumor Analysis Consortium (CPTAC) has been performing comprehensive large-scale proteogenomic characterizations of multiple cancer types. Gene and protein regulatory networks are subsequently being derived based on these proteogenomic profiles, which serve as tools to gain systems-level understanding of the molecular regulatory factories underlying these diseases. On the other hand, it remains a challenge to effectively visualize… Show more

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Cited by 7 publications
(13 citation statements)
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“…It was original developed for the development of liver segmentation methods. The CPTAC-CCRCC 16 was introduced by the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) and developed for investigating the clear cell renal cell carcinoma (CCRCC). We utilized the imaging data for CCRCC tumors, containing 242 CT scans for our external testing.…”
Section: Methodsmentioning
confidence: 99%
See 2 more Smart Citations
“…It was original developed for the development of liver segmentation methods. The CPTAC-CCRCC 16 was introduced by the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) and developed for investigating the clear cell renal cell carcinoma (CCRCC). We utilized the imaging data for CCRCC tumors, containing 242 CT scans for our external testing.…”
Section: Methodsmentioning
confidence: 99%
“…As a result, the LiTS 17 dataset has 8 scans of the Arterial phase, and 123 scans of the Venous phase. Meanwhile, the CPTAC-CCRCC 16 contains 57, 69, 53, and 63 scans from 4 categories Non-Contrast, Venous, Arterial, and Others, respectively.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…[13] In the third article, Kalayci et al present a web-based portal called ProNetView-ccRCC, which allows interactive exploration of the phosphopeptide co-expression network inferred from the CPTAC clear cell renal cell carcinoma (ccRCC) phosphoproteomics data. [14] In the fourth article, Odom et al present PathwayPCA, an R package for pathway based integrative analysis of multi-omics data. Modern statistical methodologies including supervised principal component analysis (PCA) and adaptive, elastic-net PCA are used for principal component analysis and gene selection.…”
Section: Bo Wenmentioning
confidence: 99%
“…present a web‐based portal called ProNetView‐ccRCC, which allows interactive exploration of the phosphopeptide co‐expression network inferred from the CPTAC clear cell renal cell carcinoma (ccRCC) phosphoproteomics data. [ 14 ] In the fourth article, Odom et al. present PathwayPCA, an R package for pathway based integrative analysis of multi‐omics data.…”
mentioning
confidence: 99%