keyword
MENU ▼
Read by QxMD icon Read
search

Tcga kidney

keyword
https://www.readbyqxmd.com/read/29915691/establishment-of-a-12-gene-expression-signature-to-predict-colon-cancer-prognosis
#1
Dalong Sun, Jing Chen, Longzi Liu, Guangxi Zhao, Pingping Dong, Bingrui Wu, Jun Wang, Ling Dong
A robust and accurate gene expression signature is essential to assist oncologists to determine which subset of patients at similar Tumor-Lymph Node-Metastasis (TNM) stage has high recurrence risk and could benefit from adjuvant therapies. Here we applied a two-step supervised machine-learning method and established a 12-gene expression signature to precisely predict colon adenocarcinoma (COAD) prognosis by using COAD RNA-seq transcriptome data from The Cancer Genome Atlas (TCGA). The predictive performance of the 12-gene signature was validated with two independent gene expression microarray datasets: GSE39582 includes 566 COAD cases for the development of six molecular subtypes with distinct clinical, molecular and survival characteristics; GSE17538 is a dataset containing 232 colon cancer patients for the generation of a metastasis gene expression profile to predict recurrence and death in COAD patients...
2018: PeerJ
https://www.readbyqxmd.com/read/29912290/accounting-for-differential-variability-in-detecting-differentially-methylated-regions
#2
Ya Wang, Andrew E Teschendorff, Martin Widschwendter, Shuang Wang
DNA methylation plays an essential role in cancer. Differential variability (DV) in cancer was recently observed that contributes to cancer heterogeneity and has been shown to be crucial in detecting epigenetic field defects, DNA methylation alterations happening early in carcinogenesis. As neighboring CpG sites are highly correlated, here, we present a new method to detect differentially methylated regions (DMRs) that uses combined signals from differential methylation and DV between sample groups. We demonstrated in simulation studies the superior performance of the new method than existing methods that use only one type of signals when true DMRs have both...
August 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29850911/a-graph-embedded-deep-feedforward-network-for-disease-outcome-classification-and-feature-selection-using-gene-expression-data
#3
Yunchuan Kong, Tianwei Yu
Motivation: Gene expression data represents a unique challenge in predictive model building, because of the small number of samples (n) compared to the huge amount of features (p). This "n = p" property has hampered application of deep learning techniques for disease outcome classification. Sparse learning by incorporating external gene network information could be a potential solution to this issue. Still, the problem is very challenging because (1) there are tens of thousands of features and only hundreds of training samples, (2) the scale-free structure of the gene network is unfriendly to the setup of convolutional neural networks...
May 29, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29843367/prognostic-value-of-rnaseh2a-cdk1-and-cd151-related-pathway-gene-profiling-for-kidney-cancers
#4
Chin-An Yang, Hsi-Yuan Huang, Ju-Chen Yen, Jan-Gowth Chang
The nucleotide degrading enzyme gene RNASEH2A (ribonuclease H2 subunit A) has been found to be overexpressed in cancers. Our aim was to understand the role of RNASEH2A in cancer prognostication and to establish a scoring system based on the expressions of genes interacting with RNASEH2A. We screened the nucleotide degrading enzyme gene expression in RNAseq data of 14 cancer types derived from The Cancer Genome Atlas (TCGA) and found that RNASEH2A overexpression was associated with poor patient survival only in renal cell carcinomas (RCCs)...
May 28, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29773494/plin3-is-up-regulated-and-correlates-with-poor-prognosis-in-clear-cell-renal-cell-carcinoma
#5
Keshan Wang, HaiLong Ruan, ZhengShuai Song, Qi Cao, Lin Bao, Di Liu, TianBo Xu, HaiBing Xiao, Cheng Wang, Gong Cheng, JunWei Tong, XianGui Meng, HongMei Yang, Ke Chen, XiaoPing Zhang
BACKGROUND: PLIN3, one of the members of the perilipin family, has been reported to be involved in the formation and accumulation of lipid droplets. However, the expression levels and diagnostic and prognostic value of PLIN3 in renal cell carcinoma (RCC) remain unclear. METHODS: Bioinformatic analysis was used to assess the levels of PLIN3 and the correlation between PLIN3 levels and clinicopathological parameters in renal cancer. The expression levels of PLIN3 were determined in human RCC tissues and cell lines by western blot, immunofluorescence and immunohistochemistry assays...
May 14, 2018: Urologic Oncology
https://www.readbyqxmd.com/read/29720944/identification-of-biomarkers-associated-with-pathological-stage-and-prognosis-of-clear-cell-renal-cell-carcinoma-by-co-expression-network-analysis
#6
Liang Chen, Lushun Yuan, Kaiyu Qian, Guofeng Qian, Yuan Zhu, Chin-Lee Wu, Han C Dan, Yu Xiao, Xinghuan Wang
Clear cell renal cell carcinoma (ccRCC) is the most common subtype among renal cancer whose prognostic is affected by the tumor progression associated with complex gene interactions. However, there is currently no available molecular markers associated with ccRCC progression and used or clinical application. In our study, microarray data of 101 ccRCC samples and 95 normal kidney samples were analyzed and 2,425 differentially expressed genes (DEGs) were screened. Weighted gene co-expression network analysis (WGCNA) was then conducted and 11 co-expressed gene modules were identified...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29625048/cell-of-origin-patterns-dominate-the-molecular-classification-of-10-000-tumors-from-33-types-of-cancer
#7
Katherine A Hoadley, Christina Yau, Toshinori Hinoue, Denise M Wolf, Alexander J Lazar, Esther Drill, Ronglai Shen, Alison M Taylor, Andrew D Cherniack, Vésteinn Thorsson, Rehan Akbani, Reanne Bowlby, Christopher K Wong, Maciej Wiznerowicz, Francisco Sanchez-Vega, A Gordon Robertson, Barbara G Schneider, Michael S Lawrence, Houtan Noushmehr, Tathiane M Malta, Joshua M Stuart, Christopher C Benz, Peter W Laird
We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation...
April 5, 2018: Cell
https://www.readbyqxmd.com/read/29618931/upregulated-vegfa-and-dll4-act-as-potential-prognostic-genes-for-clear-cell-renal-cell-carcinoma
#8
Xilong Wang, Jun Zhang, Yangyun Wang, Minqi Tu, Ying Wang, Guowei Shi
Purpose: As a typical hypervascular tumor, clear cell renal cell carcinoma (ccRCC) is the most common type of RCC. This study was aimed to explore the prognostic genes for ccRCC, focusing on the roles of vascular endothelial growth factor A ( VEGFA ) and Delta-like ligand 4 ( DLL4 ) in the disease. Materials and methods: The mRNA-sequencing data of kidney renal clear cell carcinoma (KIRC) were obtained from The Cancer Genome Atlas (TCGA) database, including 469 tumor samples and 68 adjacent normal samples...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29515971/the-expression-and-prognostic-impact-of-immune-cytolytic-activity-related-markers-in-human-malignancies-a-comprehensive-meta-analysis
#9
Constantinos Roufas, Dimitrios Chasiotis, Anestis Makris, Christodoulos Efstathiades, Christos Dimopoulos, Apostolos Zaravinos
Background: Recently, immune-checkpoint blockade has shown striking clinical results in different cancer patients. However, a significant inter-individual and inter-tumor variability exists among different cancers. The expression of the toxins granzyme A (GZMA) and perforin 1 (PRF1), secreted by effector cytotoxic T cells and natural killer (NK) cells, were recently used as a denominator of the intratumoral immune cytolytic activity (CYT). These levels are significantly elevated upon CD8+ T-cell activation as well as during a productive clinical response against immune-checkpoint blockade therapies...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29504244/distinct-chromatin-signatures-of-dna-hypomethylation-in-aging-and-cancer
#10
Raúl F Pérez, Juan Ramón Tejedor, Gustavo F Bayón, Agustín F Fernández, Mario F Fraga
Cancer is an aging-associated disease, but the underlying molecular links between these processes are still largely unknown. Gene promoters that become hypermethylated in aging and cancer share a common chromatin signature in ES cells. In addition, there is also global DNA hypomethylation in both processes. However, the similarity of the regions where this loss of DNA methylation occurs is currently not well characterized, and it is unknown if such regions also share a common chromatin signature in aging and cancer...
June 2018: Aging Cell
https://www.readbyqxmd.com/read/29440068/molecular-characterization-of-renal-cell-carcinoma-a-potential-three-microrna-prognostic-signature
#11
Soum D Lokeshwar, Asif Talukder, Travis J Yates, Martin J P Hennig, Michael Garcia-Roig, Sarrah S Lahorewala, Naureen N Mullani, Zachary Klaassen, Bruce R Kava, Murugesan Manoharan, Mark S Soloway, Vinata B Lokeshwar
Background: Aberrantly expressed miRNAs promote renal cell carcinoma (RCC) growth and metastasis and are potentially useful biomarkers for metastatic disease. However, a consensus clinically significant miRNA signature has not been identified. To identify an miRNA signature for predicting clinical outcome in RCC patients, we used a four-pronged interconnected approach. Methods: Differentially expressed miRNAs were identified and analyzed in 113 specimens (normal kidney: 59; tumor: 54). miRNA profiling was performed in matched normal and tumor specimens from 8 patients and extended to 32 specimens...
April 2018: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/29340018/survival-prediction-of-kidney-renal-papillary-cell-carcinoma-by-comprehensive-lncrna-characterization
#12
Huihua Lan, Jianghui Zeng, Gang Chen, Huayi Huang
Kidney renal papillary cell carcinoma (KIRP) accounts for 10%-15% of renal cell carcinoma (RCC), patients with KIRP tend to have a poor prognosis, and there was a lack of effective prognostic indicators for this type of cancer. Currently, owing to the availability of The Cancer Genome Atlas (TCGA), long non-coding RNAs (LncRNAs) have been discovered to indicate a prognostic value in some tumors. In that regard, we analyzed lncRNA-sequencing data of KIRP in TCGA, and among 780 differentially-expressed lncRNAs, we selected 37 lncRNAs which were able to assist the prognosis...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29332336/downregulation-of-guanine-nucleotide-binding-protein-beta-1-gnb1-is-associated-with-worsened-prognosis-of-clearcell-renal-cell-carcinoma-and-is-related-to-vegf-signaling-pathway
#13
C Chen, H Chi, L Min, Z Junhua
PURPOSE: Clear-cell renal cell carcinoma (ccRCC) is characterized by genetic abnormalities, while the role of Guanine Nucleotide-Binding Protein Beta 1 (GNB1) in ccRCC has not been studied. We thus aimed to evaluate the expression and prognostic value of GNB1 in ccRCC. METHODS: A two-stage study (exploration and validation) was conducted using in silico and immunohistochemical (IHC) scoring of ccRCC samples from our institute, to evaluate the association between GNB1 expression and clinicopathological parameters of ccRCC patients...
November 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29299153/identify-clear-cell-renal-cell-carcinoma-related-genes-by-gene-network
#14
Fangrong Yan, Yue Wang, Chunhui Liu, Huiling Zhao, Liya Zhang, Xiaofan Lu, Chen Chen, Yaoyan Wang, Tao Lu, Fei Wang
Clear cell renal cell carcinoma (ccRCC) is the most prominent type of kidney cancer in adults. The patients within metastatic ccRCC have a poor 5-year survival rate that is less than 10%. It is essential to identify ccRCC -related genes to help with the understanding of molecular mechanism of ccRCC. In this literature, we aim to identify genes related to ccRCC based on a gene network. We collected gene expression level data of ccRCC from the Cancer Genome Atlas (TCGA) for our analysis. We constructed a co-expression gene network as the first step of our study...
December 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/29192325/downregulation-of-microrna-1274a-induces-cell-apoptosis-through-regulation-of-bmpr1b-in-clear-cell-renal-cell-carcinoma
#15
Hirofumi Yoshino, Tomokazu Yonezawa, Masaya Yonemori, Kazutaka Miyamoto, Takashi Sakaguchi, Satoru Sugita, Youichi Osako, Shuichi Tatarano, Masayuki Nakagawa, Hideki Enokida
Our previous studies of the microRNA (miRNA) expression signature in clear cell renal cell carcinoma (ccRCC) indicated that miRNA-1274a (miR-1274a) was significantly upregulated in clinical specimens, suggesting that miR-1274a may act as an oncogenic miRNA in ccRCC. The aim of this study was to investigate the functional roles of miR-1274a and identify downstream tumor-suppressive targets regulated by miR‑1274a in ccRCC cells. Functional studies of miR-1274a were carried out by anti-miRNA to investigate cell proliferation and apoptosis using the A498, ACHN and Caki1 ccRCC cell lines...
January 2018: Oncology Reports
https://www.readbyqxmd.com/read/29176561/hif-drives-lipid-deposition-and-cancer-in-ccrcc-via-repression-of-fatty-acid-metabolism
#16
Weinan Du, Luchang Zhang, Adina Brett-Morris, Brittany Aguila, Janos Kerner, Charles L Hoppel, Michelle Puchowicz, Dolors Serra, Laura Herrero, Brian I Rini, Steven Campbell, Scott M Welford
Clear cell renal cell carcinoma (ccRCC) is histologically defined by its lipid and glycogen-rich cytoplasmic deposits. Alterations in the VHL tumor suppressor stabilizing the hypoxia-inducible factors (HIFs) are the most prevalent molecular features of clear cell tumors. The significance of lipid deposition remains undefined. We describe the mechanism of lipid deposition in ccRCC by identifying the rate-limiting component of mitochondrial fatty acid transport, carnitine palmitoyltransferase 1A (CPT1A), as a direct HIF target gene...
November 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/29158991/ndufa4l2-is-associated-with-clear-cell-renal-cell-carcinoma-malignancy-and-is-regulated-by-elk1
#17
Lei Wang, Zhiqiang Peng, Kaizhen Wang, Yijun Qi, Ying Yang, Yue Zhang, Xinyuan An, Shudong Luo, Junfang Zheng
Background: Clear cell renal cell carcinoma (ccRCC) is the most common and lethal cancer of the adult kidney. However, its pathogenesis has not been fully understood till now, which hinders the therapeutic development of ccRCC. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) was found to be upregulated and play an important role in ccRCC. We aimed to further investigate the underlying mechanisms by which NDUFA4L2 exerted function and its expression level was upregulated...
2017: PeerJ
https://www.readbyqxmd.com/read/29104463/plasma-levels-of-endothelial-cell-specific-molecule-1-as-a-potential-biomarker-of-oral-cancer-progression
#18
Wei-En Yang, Ming-Ju Hsieh, Chiao-Wen Lin, Chun-Ying Kuo, Shun-Fa Yang, Chun-Yi Chuang, Mu-Kuan Chen
In Taiwan, oral cancer is the fourth most common cancer and the most common malignancy with a poor prognosis. Endothelial cell-specific molecule-1 (ESM-1) is secreted by vascular endothelial cells in the liver, lungs, kidneys, and gastrointestinal tract. ESM-1 expression is associated with tumor prognosis, metastasis, and angiogenesis in many cancers. However, few studies have examined the association of plasma ESM-1 levels with oral squamous cell carcinoma (OSCC) progression. We measured the plasma ESM-1 levels of 438 male OSCC patients through a commercial enzyme-linked immunosorbent assay...
2017: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/29073199/reduced-expression-of-iqgap2-and-higher-expression-of-iqgap3-correlates-with-poor-prognosis-in-cancers
#19
Dinesh Kumar, Md Khurshidul Hassan, Niharika Pattnaik, Nachiketa Mohapatra, Manjusha Dixit
IQGAPs is a family of proteins which comprises three members, in humans. The expression pattern and role of IQGAP1 has been well established in many cancers, whereas those of IQGAP2 and IQGAP3, have mostly remained unexplored. We used available large datasets, to explore the pan-cancer status of these two genes in-silico. Here we have analysed their mRNA expression and correlation with survivability in eight different cancers, including lung, breast, gastric, brain, colorectal, prostate, liver and kidney cancers and, their subtypes...
2017: PloS One
https://www.readbyqxmd.com/read/29036190/clusternomics-integrative-context-dependent-clustering-for-heterogeneous-datasets
#20
Evelina Gabasova, John Reid, Lorenz Wernisch
Integrative clustering is used to identify groups of samples by jointly analysing multiple datasets describing the same set of biological samples, such as gene expression, copy number, methylation etc. Most existing algorithms for integrative clustering assume that there is a shared consistent set of clusters across all datasets, and most of the data samples follow this structure. However in practice, the structure across heterogeneous datasets can be more varied, with clusters being joined in some datasets and separated in others...
October 2017: PLoS Computational Biology
keyword
keyword
71088
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"