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TCGA data

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7 papers 0 to 25 followers
Maria Vila-Casadesús, Meritxell Gironella, Juan José Lozano
MicroRNAs (miRNAs) are small RNAs that regulate the expression of target mRNAs by specific binding on the mRNA 3'UTR and promoting mRNA degradation in the majority of cases. It is often of interest to know the specific targets of a miRNA in order to study them in a particular disease context. In that sense, some databases have been designed to predict potential miRNA-mRNA interactions based on hybridization sequences. However, one of the main limitations is that these databases have too many false positives and do not take into account disease-specific interactions...
2016: PloS One
George S Krasnov, Alexey A Dmitriev, Nataliya V Melnikova, Andrew R Zaretsky, Tatiana V Nasedkina, Alexander S Zasedatelev, Vera N Senchenko, Anna V Kudryavtseva
The contribution of different mechanisms to the regulation of gene expression varies for different tissues and tumors. Complementation of predicted mRNA-miRNA and gene-transcription factor (TF) relationships with the results of expression correlation analyses derived for specific tumor types outlines the interactions with functional impact in the current biomaterial. We developed CrossHub software, which enables two-way identification of most possible TF-gene interactions: on the basis of ENCODE ChIP-Seq binding evidence or Jaspar prediction and co-expression according to the data of The Cancer Genome Atlas (TCGA) project, the largest cancer omics resource...
April 20, 2016: Nucleic Acids Research
Antonio Colaprico, Tiago C Silva, Catharina Olsen, Luciano Garofano, Claudia Cava, Davide Garolini, Thais S Sabedot, Tathiane M Malta, Stefano M Pagnotta, Isabella Castiglioni, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr
The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers...
May 5, 2016: Nucleic Acids Research
Daniel Wai-Hung Ho, Alan Ka-Lun Kai, Irene Oi-Lin Ng
This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding nontumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs...
September 2015: Frontiers of Medicine
Yitan Zhu, Yanxun Xu, Donald L Helseth, Kamalakar Gulukota, Shengjie Yang, Lorenzo L Pesce, Riten Mitra, Peter Müller, Subhajit Sengupta, Wentian Guo, Jonathan C Silverstein, Ian Foster, Nigel Parsad, Kevin P White, Yuan Ji
BACKGROUND: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. METHODS: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data...
August 2015: Journal of the National Cancer Institute
Joseph D Khoury, Nizar M Tannir, Michelle D Williams, Yunxin Chen, Hui Yao, Jianping Zhang, Erika J Thompson, Funda Meric-Bernstam, L Jeffrey Medeiros, John N Weinstein, Xiaoping Su
Elucidation of tumor-DNA virus associations in many cancer types has enhanced our knowledge of fundamental oncogenesis mechanisms and provided a basis for cancer prevention initiatives. RNA-Seq is a novel tool to comprehensively assess such associations. We interrogated RNA-Seq data from 3,775 malignant neoplasms in The Cancer Genome Atlas database for the presence of viral sequences. Viral integration sites were also detected in expressed transcripts using a novel approach. The detection capacity of RNA-Seq was compared to available clinical laboratory data...
August 2013: Journal of Virology
Yong-Wan Kim, Dimpy Koul, Se Hoon Kim, Agda Karina Lucio-Eterovic, Pablo R Freire, Jun Yao, Jing Wang, Jonas S Almeida, Ken Aldape, W K Alfred Yung
BACKGROUND: The Cancer Genome Atlas (TCGA) project is a large-scale effort with the goal of identifying novel molecular aberrations in glioblastoma (GBM). METHODS: Here, we describe an in-depth analysis of gene expression data and copy number aberration (CNA) data to classify GBMs into prognostic groups to determine correlates of subtypes that may be biologically significant. RESULTS: To identify predictive survival models, we searched TCGA in 173 patients and identified 42 probe sets (P = ...
July 2013: Neuro-oncology
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