Abstract 923: The cBioPortal for Cancer Genomics: An intuitive open-source platform for exploration, analysis and visualization of cancer genomics data

Gao, Jianjiong; Mazor, Tali; Ciftci, Ersin; Raman, Pichai; Lukasse, Pieter; Bahceci, Istemi; Sigaras, Alexandros; Abeshouse, Adam; Bruijn, Ino de; Groß, Benjamin; Kundra, Ritika; Lisman, Aaron; Ochoa, Angelica; Sheridan, Robert P.; Su, Jing; Sumer, S. Onur; Sun, Yichao; Wang, Avery; Wang, Jiaojiao; Wilson, Manda; Kumari, Priti; Lindsay, James; Kalletla, Karthik; Zhu, Kelsey; Plantalech, Oleguer; Schaeffer, Fedde; Tan, Sander; Zaal, Dionne; Hagen, Sjoerd van; Bochove, Kees van; Doğrusöz, Uğur; Pugh, Trevor J.; Resnick, Adam; Sander, Chris; Schultz, Nikolaus; Cerami, Ethan

doi:10.1158/1538-7445.am2018-923

Cited by 9 publications

(3 citation statements)

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“…TUBB6 mutation analysis was produced by COSMIC database (Tate et al, 2019) and characterized in a pie chart. The frequency of TUBB6 mutations in GBM was tested by cBioPortal (Gao et al, 2018).…”

Section: Identification Of Prognostic Demfgs and Construction Of The mentioning

confidence: 99%

Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma

et al. 2020

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Glioblastoma (GBM) has long been a major clinical research challenge to scientists. The pivotal role of the mitochondria related gene family in the promotion of GBM tumorigenesis is not clear. We detected that microtubular tubulin beta 6 class V (TUBB6) was one of 33 differentially expressed mitochondrial-focused genes (DEMFGs) in GBM, and considered that TUBB6 is a potential therapeutic target in GBM. TUBB6 was vital for GBM and marked as the key prognostic gene in primary GBM. Mutations of TUBB6 in GBM were rare. Only four TUBB6 co-expressed hub genes (ANXA2, S100A11, FLNA, and MSN) exhibited poorer overall survival rates in higher expression groups (p-value < 0.05). We have confirmed the up-regulation of TUBB6 and its partners, ANXA2 and S100A11 in GBM and validated their importance as prognostic factors in primary GBM. TUBB6 was significantly correlated with stromal score in GBM samples (p-value = 6.99E-04). This study aimed to assess the importance of novel hub genes by analyzing the expression, potential function and prognostic impact of TUBB6 in human primary GBM cancer.

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Section: Identification Of Prognostic Demfgs and Construction Of The mentioning

confidence: 99%

Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma

et al. 2020

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“…27 Therefore, we analyzed the frequency of mutations in the genes encoding receptors and ligands from the Wnt, Notch, Hedgehog, and TGFb pathways, using the mutational data from cBioPortal as an interface for TCGA data. 28 We found that mutational burden, even in survival-significant receptors or ligands, such as FZD2, WNT7A, NOTCH2, ACVRL1, and BMP2, was low, with mutations present at very low frequency compared to the frequency in commonly mutated genes, such as TP53, KRAS, or PTEN (Fig. S1).…”

Section: Enrichment Of Developmental Signaling Pathwaysmentioning

confidence: 87%

Pan-cancer analysis of the developmental pathways reveals non-canonical wnt signaling as a driver of mesenchymal-type tumors

Xue

Chan

Gujral

2020

Translational Research

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The processes of angiogenesis, cell proliferation, invasion, and migration, and the signaling pathways that drive these events, are activated in both cancer and during embryonic development. Here, we systematically assessed how the activity of major developmental signaling pathways, represented by the expression of genes encoding components of the pathways, correlated with patient survival in »8000 patients across 17 cancer types. We also compared the expressed genes enriched in developmental pathways with those associated with epithelial-mesenchymal transition (EMT) both in a cancer cohort and in mice during embryonic development. We found that EMT and gene expression profiles consistent with high activity of several developmental pathways, including the TGFβ, Notch, and non-canonical Wnt pathways, significantly correlated with poor patient survival in multiple cancer types. We investigated individual components of these pathways and found that expression of the gene encoding the non-canonical Wnt receptor, frizzled 2 (FZD2), is highly correlated with both poor patient survival and gene expression indicating EMT in the tumors. Further mechanistic studies and pathway analyses revealed that FZD2-regulated genes in cancer cells in culture or FZD2-regulated gene sets from the TCGA data or FZD2-regulated genes involved in mouse organogenesis converged in EMT-associated biological processes, suggesting that FZD2 is a key driver of mesenchymal-like cell state and thus, a contributor to cancer progression and metastasis.

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“…To validate our pipeline, we used gene fusions covering the genes ERG , ETV1 , ETV4 , and FLI1 reported by the TCGA consortium for the TCGA_PRAD cohort as a reference. The annotated data from the TCGA consortium was provided by the cBioPortal for Cancer Genomics database [ 31 ] in the Prostate Adenocarcinoma study (TCGA, Cell 2015). We compared the samples carrying an ERG -fusion as published by the TCGA consortium with those for which we detected an ERG -fusion in TCGA_PRAD with the Arriba pipeline one-to-one and created contingency tables of the results.…”

Section: Methodsmentioning

confidence: 99%

Characterization and evaluation of gene fusions as a measure of genetic instability and disease prognosis in prostate cancer

et al. 2023

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Background Prostate cancer (PCa) is one of the most prevalent cancers worldwide. The clinical manifestations and molecular characteristics of PCa are highly variable. Aggressive types require radical treatment, whereas indolent ones may be suitable for active surveillance or organ-preserving focal therapies. Patient stratification by clinical or pathological risk categories still lacks sufficient precision. Incorporating molecular biomarkers, such as transcriptome-wide expression signatures, improves patient stratification but so far excludes chromosomal rearrangements. In this study, we investigated gene fusions in PCa, characterized potential novel candidates, and explored their role as prognostic markers for PCa progression. Methods We analyzed 630 patients in four cohorts with varying traits regarding sequencing protocols, sample conservation, and PCa risk group. The datasets included transcriptome-wide expression and matched clinical follow-up data to detect and characterize gene fusions in PCa. With the fusion calling software Arriba, we computationally predicted gene fusions. Following detection, we annotated the gene fusions using published databases for gene fusions in cancer. To relate the occurrence of gene fusions to Gleason Grading Groups and disease prognosis, we performed survival analyses using the Kaplan–Meier estimator, log-rank test, and Cox regression. Results Our analyses identified two potential novel gene fusions, MBTTPS2,L0XNC01::SMS and AMACR::AMACR. These fusions were detected in all four studied cohorts, providing compelling evidence for the validity of these fusions and their relevance in PCa. We also found that the number of gene fusions detected in a patient sample was significantly associated with the time to biochemical recurrence in two of the four cohorts (log-rank test, p-value < 0.05 for both cohorts). This was also confirmed after adjusting the prognostic model for Gleason Grading Groups (Cox regression, p-values < 0.05). Conclusions Our gene fusion characterization workflow revealed two potential novel fusions specific for PCa. We found evidence that the number of gene fusions was associated with the prognosis of PCa. However, as the quantitative correlations were only moderately strong, further validation and assessment of clinical value is required before potential application.

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Abstract 923: The cBioPortal for Cancer Genomics: An intuitive open-source platform for exploration, analysis and visualization of cancer genomics data

Cited by 9 publications

References 0 publications

Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma

Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma

Pan-cancer analysis of the developmental pathways reveals non-canonical wnt signaling as a driver of mesenchymal-type tumors

Characterization and evaluation of gene fusions as a measure of genetic instability and disease prognosis in prostate cancer

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