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Integrative genomics cancer

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https://www.readbyqxmd.com/read/29227715/human-papillomavirus-genome-integration-and-head-and-neck-cancer
#1
L M Pinatti, H M Walline, T E Carey
We conducted a critical review of human papillomavirus (HPV) integration into the host genome in oral/oropharyngeal cancer, reviewed the literature for HPV-induced cancers, and obtained current data for HPV-related oral and oropharyngeal cancers. In addition, we performed studies to identify HPV integration sites and the relationship of integration to viral-host fusion transcripts and whether integration is required for HPV-associated oncogenesis. Viral integration of HPV into the host genome is not required for the viral life cycle and might not be necessary for cellular transformation, yet HPV integration is frequently reported in cervical and head and neck cancer specimens...
December 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/29227586/identification-of-potential-crucial-genes-associated-with-carcinogenesis-of-clear-cell-renal-cell-carcinoma
#2
Erlin Song, Wenting Song, Minghua Ren, Li Xing, Wenjun Ni, Yongxiang Li, Mancheng Gong, Mingbo Zhao, Xin Ma, Xu Zhang, Ruihua An
Clear cell renal cell carcinoma (ccRCC) is a common genitourinary malignancy with high mortality. However, the molecular pathogenesis of ccRCC remains unclear and effective biomarkers for daily practice are still limited. Thus, we aimed to identify the potential crucial genes and pathways associated with carcinogenesis of ccRCC and further analyze the molecular mechanisms implicated in tumorigenesis. In the present study, expression profiles GSE 66270, GSE 53757, GSE 36895 and GSE 76351 were downloaded from GEO database, including 244 matched primary and adjacent normal tissues, furthermore, the level 3 RNAseq dataset (RNAseqV2 RSEM) of KIRC was also downloaded from The Cancer Genome Atlas (TCGA), which consist of 529 ccRCC tumors and 72 normal tissues...
December 11, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29226853/clinical-and-rna-expression-integrated-signature-for-urothelial-bladder-cancer-prognosis
#3
Jie Xiong, Ke Xiong, Zhitong Bing
BACKGROUND: Accumulating evidence shows that clinical factors alone are not adequate for predicting the survival of patients with urothelial bladder cancer (UBC), and many genes have been found to be associated with UBC prognosis. PURPOSE: The objective of this study is to develop a signature which integrates clinical and molecular information to predict the overall survival of UBC patients more accurate. MATERIALS AND METHODS: We integrated messenger RNA (mRNA) and microRNA (miRNA) expression profiles and the corresponding clinical data of 402 UBC patients and 19 normal controls from The Cancer Genome Atlas...
November 25, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/29221171/proteogenomic-analysis-prioritises-functional-single-nucleotide-variants-in-cancer-samples
#4
Shiyong Ma, Ranjeeta Menon, Rebecca C Poulos, Jason W H Wong
Massively parallel DNA sequencing enables the detection of thousands of germline and somatic single nucleotide variants (SNVs) in cancer samples. The functional analysis of these mutations is often carried out through in silico predictions, with further downstream experimental validation rarely performed. Here, we examine the potential of using mass spectrometry-based proteomics data to further annotate the function of SNVs in cancer samples. RNA-seq and whole genome sequencing (WGS) data from Jurkat cells were used to construct a custom database of single amino acid variant (SAAV) containing peptides and identified over 1,000 such peptides in two Jurkat proteomics datasets...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220513/integrating-5hmc-and-gene-expression-data-to-infer-regulatory-mechanisms
#5
Cristina Mitrea, Priyanga Wijesinghe, Greg Dyson, Adéle Kruger, Douglas M Ruden, Sorin Draghici, Aliccia Bollig-Fischer
Motivation: Epigenetic mechanisms are known to play a major role in breast cancer. However, the role of 5-hydroxymethylcytosine (5hmC) remains understudied. We hypothesize that 5hmC mediates redox regulation of gene expression in an aggressive subtype known as triple negative breast cancer (TNBC). To address this, our objective was to highlight genes that may be the target of this process by identifying redox-regulated, antioxidant-sensitive, gene-localized 5hmC changes associated with mRNA changes in TNBC cells...
December 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29218918/annotating-gene-sets-by-mining-large-literature-collections-with-protein-networks
#6
Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W Huang, Jiawei Han, Jian Peng, Trey Ideker
Analysis of patient genomes and transcriptomes routinely recognizes new gene sets associated with human disease. Here we present an integrative natural language processing system which infers common functions for a gene set through automatic mining of the scientific literature with biological networks. This system links genes with associated literature phrases and combines these links with protein interactions in a single heterogeneous network. Multiscale functional annotations are inferred based on network distances between phrases and genes and then visualized as an ontology of biological concepts...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218912/network-analysis-of-pseudogene-gene-relationships-from-pseudogene-evolution-to-their-functional-potentials
#7
Travis S Johnson, Sihong Li, Jonathan R Kho, Kun Huang, Yan Zhang
Pseudogenes are fossil relatives of genes. Pseudogenes have long been thought of as "junk DNAs", since they do not code proteins in normal tissues. Although most of the human pseudogenes do not have noticeable functions, ∼20% of them exhibit transcriptional activity. There has been evidence showing that some pseudogenes adopted functions as lncRNAs and work as regulators of gene expression. Furthermore, pseudogenes can even be "reactivated" in some conditions, such as cancer initiation. Some pseudogenes are transcribed in specific cancer types, and some are even translated into proteins as observed in several cancer cell lines...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218909/reading-between-the-genes-computational-models-to-discover-function-from-noncoding-dna
#8
Yves A Lussier, Joanne Berghout, Francesca Vitali, Kenneth S Ramos, Maricel Kann, Jason H Moore
Noncoding DNA - once called "junk" has revealed itself to be full of function. Technology development has allowed researchers to gather genome-scale data pointing towards complex regulatory regions, expression and function of noncoding RNA genes, and conserved elements. Variation in these regions has been tied to variation in biological function and human disease. This PSB session tackles the problem of handling, analyzing and interpreting the data relating to variation in and interactions between noncoding regions through computational biology...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218893/discriminative-bag-of-cells-for-imaging-genomics
#9
Benjamin Chidester, Minh N Do, Jian Ma
Connecting genotypes to image phenotypes is crucial for a comprehensive understanding of cancer. To learn such connections, new machine learning approaches must be developed for the better integration of imaging and genomic data. Here we propose a novel approach called Discriminative Bag-of-Cells (DBC) for predicting genomic markers using imaging features, which addresses the challenge of summarizing histopathological images by representing cells with learned discriminative types, or codewords. We also developed a reliable and efficient patch-based nuclear segmentation scheme using convolutional neural networks from which nuclear and cellular features are extracted...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#10
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29212479/a-pilot-systematic-genomic-comparison-of-recurrence-risks-of-hepatitis-b-virus-associated-hepatocellular-carcinoma-with-low-and-high-degree-liver-fibrosis
#11
Seungyeul Yoo, Wenhui Wang, Qin Wang, M Isabel Fiel, Eunjee Lee, Spiros P Hiotis, Jun Zhu
BACKGROUND: Chronic hepatitis B virus (HBV) infection leads to liver fibrosis, which is a major risk factor in hepatocellular carcinoma (HCC) and an independent risk factor of recurrence after HCC tumor resection. The HBV genome can be inserted into the human genome, and chronic inflammation may trigger somatic mutations. However, how HBV integration and other genomic changes contribute to the risk of tumor recurrence with regards to the different degree of liver fibrosis is not clearly understood...
December 7, 2017: BMC Medicine
https://www.readbyqxmd.com/read/29212152/prpf8-is-important-for-brca1-mediated-homologous-recombination
#12
David O Onyango, Gabriella Lee, Jeremy M Stark
Disruption of RNA splicing causes genome instability, which could contribute to cancer etiology. Furthermore, RNA splicing is an emerging anti-cancer target. Thus, we have evaluated the influence of the spliceosome factor PRPF8 and the splicing inhibitor Pladienolide B (PlaB) on homologous recombination (HR). We find that PRPF8 depletion and PlaB treatment cause a specific defect in homology-directed repair (HDR), and single strand annealing (SSA), which share end resection as a common intermediate, and BRCA1 as a required factor...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29209625/prediction-and-validation-of-hub-genes-associated-with-colorectal-cancer-by-integrating-ppi-network-and-gene-expression-data
#13
Yongfu Xiong, Wenxian You, Rong Wang, Linglong Peng, Zhongxue Fu
Although hundreds of colorectal cancer- (CRC-) related genes have been screened, the significant hub genes still need to be further identified. The aim of this study was to identify the hub genes based on protein-protein interaction network and uncover their clinical value. Firstly, 645 CRC patients' data from the Tumor Cancer Genome Atlas were downloaded and analyzed to screen the differential expression genes (DEGs). And then, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed, and PPI network of the DEGs was constructed by Cytoscape software...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29209147/transcriptome-integration-analysis-in-hepatocellular-carcinoma-reveals-discordant-intronic-mirna-host-gene-pairs-in-expression
#14
Yulin Sun, Fubo Ji, Mia R Kumar, Xin Zheng, Yi Xiao, Niya Liu, Jiong Shi, Linda Wong, Marshonna Forgues, Lun-Xiu Qin, Zhao-You Tang, Xiaohang Zhao, Xin Wei Wang, Junfang Ji
Intronic miRNAs, residing in intronic regions of host genes, are thought to be co-transcribed from their host genes and present consistent expression patterns with host genes. Recent studies reported a few intronic miRNAs with discordant expression with their host genes. We therefore aimed to understand the expression pattern of intronic miRNAs and their host genes in hepatocellular carcinoma (HCC) and reveal possible associated molecular mechanisms. Our genome wide integration analysis of miRNA and mRNA transcriptomes, in three dataset from 550 patients with HCC, found that a large amount of miRNA-host gene pairs were discordantly expressed...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29209073/integrating-clinical-and-multiple-omics-data-for-prognostic-assessment-across-human-cancers
#15
Bin Zhu, Nan Song, Ronglai Shen, Arshi Arora, Mitchell J Machiela, Lei Song, Maria Teresa Landi, Debashis Ghosh, Nilanjan Chatterjee, Veera Baladandayuthapani, Hongyu Zhao
Multiple omic profiles have been generated for many cancer types; however, comprehensive assessment of their prognostic values across cancers is limited. We conducted a pan-cancer prognostic assessment and presented a multi-omic kernel machine learning method to systematically quantify the prognostic values of high-throughput genomic, epigenomic, and transcriptomic profiles individually, integratively, and in combination with clinical factors for 3,382 samples across 14 cancer types. We found that the prognostic performance varied substantially across cancer types...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208983/comprehensive-statistical-inference-of-the-clonal-structure-of-cancer-from-multiple-biopsies
#16
Jie Liu, John T Halloran, Jeffrey A Bilmes, Riza M Daza, Choli Lee, Elisabeth M Mahen, Donna Prunkard, Chaozhong Song, Sibel Blau, Michael O Dorschner, Vijayakrishna K Gadi, Jay Shendure, C Anthony Blau, William S Noble
A comprehensive characterization of tumor genetic heterogeneity is critical for understanding how cancers evolve and escape treatment. Although many algorithms have been developed for capturing tumor heterogeneity, they are designed for analyzing either a single type of genomic aberration or individual biopsies. Here we present THEMIS (Tumor Heterogeneity Extensible Modeling via an Integrative System), which allows for the joint analysis of different types of genomic aberrations from multiple biopsies taken from the same patient, using a dynamic graphical model...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208897/network-dynamics-based-cancer-panel-stratification-for-systemic-prediction-of-anticancer-drug-response
#17
Minsoo Choi, Jue Shi, Yanting Zhu, Ruizhen Yang, Kwang-Hyun Cho
Cancer is a complex disease involving multiple genomic alterations that disrupt the dynamic response of signaling networks. The heterogeneous nature of cancer, which results in highly variable drug response, is a major obstacle to developing effective cancer therapy. Previous studies of cancer therapeutic response mostly focus on static analysis of genome-wide alterations, thus they are unable to unravel the dynamic, network-specific origin of variation. Here we present a network dynamics-based approach to integrate cancer genomics with dynamics of biological network for drug response prediction and design of drug combination...
December 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/29208006/identification-and-validation-of-a-44-gene-expression-signature-for-the-classification-of-renal-cell-carcinomas
#18
Qifeng Wang, Hualei Gan, Chengshu Chen, Yifeng Sun, Jinying Chen, Midie Xu, Weiwei Weng, Liyu Cao, Qinghua Xu, Jian Wang
BACKGROUND: Renal cancers account for more than 3% of all adult malignancies and cause more than 23,400 deaths per year in China alone. The four most common types of kidney tumours include clear cell, papillary, chromophobe and benign oncocytoma. These histological subtypes vary in their clinical course and prognosis, and different clinical strategies have been developed for their management. Some kidney tumours can be very difficult to distinguish based on the pathological assessment of morphology and immunohistochemistry...
December 6, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29207666/integrative-analysis-to-identify-oncogenic-gene-expression-changes-associated-with-copy-number-variations-of-enhancer-in-ovarian-cancer
#19
Xiaoyan Li, Yining Liu, Jiachun Lu, Min Zhao
Enhancers are short regulatory regions (50-1500 bp) of DNA that control the tissue-specific activation of gene expression by long distance interaction with targeting gene regions. Recently, genome-wide identification of enhancers in diverse tissues and cell lines was achieved using high-throughput sequencing. Enhancers have been associated with malfunctions in cancer development resulting from point mutations in regulatory regions. However, the potential impact of copy number variations (CNVs) on enhancer regions is unknown...
October 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/29207133/potential-role-of-microrna%C3%A2-223%C3%A2-3p-in-the-tumorigenesis-of-hepatocellular-carcinoma-a-comprehensive-study-based-on-data-mining-and-bioinformatics
#20
Rui Zhang, Li-Jie Zhang, Mei-Ling Yang, Lan-Shan Huang, Gang Chen, Zhen-Bo Feng
The aims of the present study were to examine the potential role of microRNA‑233‑3p (miR)‑223‑3p in the tumorigenesis of hepatocellular carcinoma (HCC), and to investigate its diagnostic accuracy and potential molecular mechanisms. The expression data of miR‑223‑3p in HCC were obtained from the Gene Expression Omnibus (GEO). Data for the precursor miR‑223 were obtained from The Cancer Genome Atlas (TCGA). The diagnostic role of miR‑223‑3p was identified by the receiver operating curve (ROC), and the diagnostic value of miR‑223‑3p in HCC was calculated from qualified reports in the literature...
November 27, 2017: Molecular Medicine Reports
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