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Pan-urologic cancer genomic subtypes that transcend tissue of origin
2017
Nature Communications
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., ,"Pan-urologic cancer genomic subtypes that transcend tissue of origin. ...
copy number, and RNA and protein expression). ...
Analysis of external multi-cancer data set. ...
doi:10.1038/s41467-017-00289-x
pmid:28775315
pmcid:PMC5543131
fatcat:5xdmfiq2yvhg7iky3f64f4r3oi
Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype
2015
Epigenetics & Chromatin
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With a minimal set of 89 discriminative loci, we demonstrate accurate pan-cancer separation of the 12 CIMP+/− subpopulations, based on their average levels of methylation. ...
Even though there have been numerous studies of CIMP in individual cancer types, a uniform analysis across tissues is still lacking. ...
Acknowledgement This work was supported by the Intramural Program of the National Human Genome Research Institute, National Institutes of Health. ...
doi:10.1186/s13072-015-0007-7
pmid:25960768
pmcid:PMC4424513
fatcat:ryrlnqpelzd4dcm2iowlmx7mqe
The UCSC Cancer Genomics Browser: update 2015
2014
Nucleic Acids Research
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Users can download and upload clinical data, generate Kaplan-Meier plots dynamically, export data directly to Galaxy for analysis, plus generate URL bookmarks of specific views of the data to share with ...
The Cancer Genomics Browser currently hosts 575 public datasets from genome-wide analyses of over 227 000 samples, including datasets from TCGA, CCLE, Connectivity Map and TARGET. ...
In addition to the efforts of the TCGA Pan-Cancer Analysis Working Group, we also have assembled gene-level copy number and gene expression across all 31 TCGA cancer types. ...
doi:10.1093/nar/gku1073
pmid:25392408
pmcid:PMC4383911
fatcat:engeo7umabdqrdqupnemmwgucu
Assessing the clinical utility of cancer genomic and proteomic data across tumor types
2014
Nature Biotechnology
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Here we retrospectively predict patient survival using diverse molecular data (somatic copy-number alteration, DNA methylation and mRNA, miRNA and protein expression) from 953 samples of four cancer types ...
In clinically relevant genes, we identified 10,281 somatic alterations across 12 cancer types in 2,928 of 3,277 patients (89.4%), many of which would not be revealed in single-tumor analyses. ...
We obtained the clinical variables from TCGA Data Portal (https://tcga-data.nci.nih.gov/tcga/) and the molecular data (including DNA methylation, mRNA, miRNA and protein expression) from the Pan-cancer ...
doi:10.1038/nbt.2940
pmid:24952901
pmcid:PMC4102885
fatcat:nvu2cvkfcbg4lfg3nvyebkagp4
Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer
2018
Cell
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Highlights d An integrative data clustering method is applied to reclassify human tumors d Cell-of-origin influences, but does not fully determine, tumor classification d Immune features and copy-number ...
aberrations define the most mixed tumor groups d Multi-cancer groups reveal new features with potential clinical utility ...
TCGA RNA-seq values from the PanCancer Atlas normalized gene expression matrix were scored for each of the 160 identified gene expression signatures using single-sample gene set enrichment (ssGSEA) analysis ...
doi:10.1016/j.cell.2018.03.022
pmid:29625048
pmcid:PMC5957518
fatcat:mb7h6nnkordonoalcs754havi4
Comparison of gene expression patterns across 12 tumor types identifies a cancer supercluster characterized by TP53 mutations and cell cycle defects
2014
Oncogene
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and similarities in gene expression. ...
of DNA double strand breaks and high expression of cyclin B1 protein. ...
National Cancer Institute (NCI; MD Anderson TCGA Genome Data Analysis Center) grant numbers CA143883 and CA083639, and MD Anderson Cancer Center Support Grant P30 CA016672. ...
doi:10.1038/onc.2014.216
pmid:25088195
pmcid:PMC4317393
fatcat:3xkht4dorvbm5i2k7voe75sf34
Wx: a neural network-based feature selection algorithm for next-generation sequencing data
[article]
2017
bioRxiv
pre-print
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We applied the Wx algorithm to a TCGA pan-cancer gene-expression cohort to identify an optimal set of gene-expression biomarker (universal gene-expression biomarkers) candidates that can distinguish cancer ...
With a gene list ranked by DI score, researchers can institutively select the optimal set of genes from the highest-ranking ones. ...
Funding This study was supported by a grant from the National R&D Program for Cancer Control, Ministry of Health & Welfare, Republic of Korea(1720100). ...
doi:10.1101/221911
fatcat:2f6zfjrpjreznlgemwqc7vdjne
Wx: a neural network-based feature selection algorithm for transcriptomic data
2019
Scientific Reports
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We applied the Wx algorithm to a TCGA pan-cancer gene-expression cohort to identify an optimal set of gene-expression biomarker candidates that can distinguish cancer samples from normal samples for 12 ...
different types of cancer. ...
This study was supported by a grant from the National R&D Program for Cancer Control, Ministry of Health & Welfare, Republic of Korea (1720100). ...
doi:10.1038/s41598-019-47016-8
pmid:31324856
pmcid:PMC6642261
fatcat:jtgnopdnyjezdg34atifdrpgui
Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types
2014
Nature Communications
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Here we examined their properties in gene co-expression networks for four cancer types using data from 'The Cancer Genome Atlas'. ...
In contrast, the prognostic genes are enriched in modules (a group of highly interconnected genes), especially in module genes conserved across different cancer co-expression networks. ...
The TCGA Pan-Cancer Analysis Working Group is coordinated by J.M. Stuart ...
doi:10.1038/ncomms4231
pmid:24488081
pmcid:PMC3951205
fatcat:d6yikb7g7zecfbiemxiuf67h4e
Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types
2019
Nature Communications
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We perform correlation analysis and gene set enrichment analysis to understand the differences between cell lines and primary tumors. ...
Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia to evaluate cell lines as models of primary tumors ...
We would also like to thank researchers at the Broad Institute and The Cancer Genome Atlas Consortium who released data to the public. ...
doi:10.1038/s41467-019-11415-2
pmid:31395879
pmcid:PMC6687785
fatcat:pjkmtto4z5e55npsephqgmzmba
Transcriptional response profiles of paired tumor-normal samples offer novel perspectives in pan-cancer analysis
2017
OncoTarget
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Our results suggest that transcriptional response profiles of paired tumor-normal tissues can provide novel perspectives in pan-cancer analysis. ...
Transcriptional response profiles represent the changes of gene expression levels between paired tumor and adjacent normal tissues. ...
RESULTS
Transcriptional response profile-based pancancer clustering We collected gene expression profiles of 633 paired tumor-normal samples from 13 TCGA cancer data sets [6-9, [22] [23] [24] [25] [ ...
doi:10.18632/oncotarget.17295
pmid:28489584
pmcid:PMC5522216
fatcat:vy72hiibefcp3ftz55kle4f2ge
Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin
2014
Cell
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From these, we identified gene programs as those whose genes have mRNA-seq signatures of high mutual correlation across the Pan-Cancer-12 data set. ...
Genes were then identified as those predicted to be targeted by a differentially expressed miRNA that was also anticorrelated across the Pan-Cancer-12 data set. ...
doi:10.1016/j.cell.2014.06.049
pmid:25109877
pmcid:PMC4152462
fatcat:ft7riwvnb5egvlowairhf7ej6a
Identification of HOXB9 to predict prognosis of endometrial cancer based on comprehensive bioinformatics analysis
2023
European Journal of Medical Research
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Methods We used multiple bioinformatics tools to explore the role of HOXB9 in EC. Results The expression of HOXB9 was significantly upregulated in pan-cancer, including EC (P < 0.05). ...
Background The HOXB9 gene, which plays a key role in embryonic development, is also involved in the regulation of various human cancers. ...
In our pan-cancer analysis, we found HOXB9 expression was elevated in these cancers, with roughly the same results. ...
doi:10.1186/s40001-022-00979-3
pmid:36803556
pmcid:PMC9936693
fatcat:ambdje4m4beind2fi2uknvs6xe
Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple Cancers
2021
Cancers
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In this study, the human kinome's DNA methylation and gene expression patterns were analyzed using the level-3 TCGA data for 32 cancers. ...
DNA methylation is one of the key epigenetic regulators that modulate gene expression. ...
The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. ...
doi:10.3390/cancers13061189
pmid:33801837
pmcid:PMC8001681
fatcat:rg6bznlvvvgtloquttadq2c5s4
Comprehensive Characterization of Molecular Differences in Cancer between Male and Female Patients
2016
Cancer Cell
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Graphical Abstract Highlights d A rigorous, pan-cancer analysis of sex effects on molecular profiles of patients d Two sex-effect cancer groups showing distinct incidence and mortality profiles d Extensive ...
sex-biased gene expression signatures in some cancer types d A considerable number of clinically actionable genes with sex-biased signatures SUMMARY An individual's sex has been long recognized as a key ...
ACKNOWLEDGMENTS We gratefully acknowledge contributions from TCGA Research Network and TCGA Pan-Cancer Analysis Working Group. This study was supported by the NIH (CA175486 and CCSG . ...
doi:10.1016/j.ccell.2016.04.001
pmid:27165743
pmcid:PMC4864951
fatcat:ruwf6llwqrfehbkimgn467ivyq
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