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Cancer Informatics

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https://www.readbyqxmd.com/read/27812280/a-modular-repository-based-infrastructure-for-simulation-model-storage-and-execution-support-in-the-context-of-in-silico-oncology-and-in-silico-medicine
#1
Nikolaos A Christodoulou, Nikolaos E Tousert, Eleni Ch Georgiadi, Katerina D Argyri, Fay D Misichroni, Georgios S Stamatakos
The plethora of available disease prediction models and the ongoing process of their application into clinical practice - following their clinical validation - have created new needs regarding their efficient handling and exploitation. Consolidation of software implementations, descriptive information, and supportive tools in a single place, offering persistent storage as well as proper management of execution results, is a priority, especially with respect to the needs of large healthcare providers. At the same time, modelers should be able to access these storage facilities under special rights, in order to upgrade and maintain their work...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27812279/discovering-outliers-of-potential-drug-toxicities-using-a-large-scale-data-driven-approach
#2
Jake Luo, Ron A Cisler
We systematically compared the adverse effects of cancer drugs to detect event outliers across different clinical trials using a data-driven approach. Because many cancer drugs are toxic to patients, better understanding of adverse events of cancer drugs is critical for developing therapies that could minimize the toxic effects. However, due to the large variabilities of adverse events across different cancer drugs, methods to efficiently compare adverse effects across different cancer drugs are lacking. To address this challenge, we present an exploration study that integrates multiple adverse event reports from clinical trials in order to systematically compare adverse events across different cancer drugs...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27812278/cluster-analysis-of-p53-binding-site-sequences-reveals-subsets-with-different-functions
#3
Ji-Hyun Lim, Natasha S Latysheva, Richard D Iggo, Daniel Barker
p53 is an important regulator of cell cycle arrest, senescence, apoptosis and metabolism, and is frequently mutated in tumors. It functions as a tetramer, where each component dimer binds to a decameric DNA region known as a response element. We identify p53 binding site subtypes and examine the functional and evolutionary properties of these subtypes. We start with over 1700 known binding sites and, with no prior labeling, identify two sets of response elements by unsupervised clustering. When combined, they give rise to three types of p53 binding sites...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27773988/a-novel-graph-based-algorithm-to-infer-recurrent-copy-number-variations-in-cancer
#4
Chen Chi, Rasif Ajwad, Qin Kuang, Pingzhao Hu
Many cancers have been linked to copy number variations (CNVs) in the genomic DNA. Although there are existing methods to analyze CNVs from individual samples, cancer-causing genes are more frequently discovered in regions where CNVs are common among tumor samples, also known as recurrent CNVs. Integrating multiple samples and locating recurrent CNV regions remain a challenge, both computationally and conceptually. We propose a new graph-based algorithm for identifying recurrent CNVs using the maximal clique detection technique...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27721651/discovering-microrna-regulatory-modules-in-multi-dimensional-cancer-genomic-data-a-survey-of-computational-methods
#5
Christopher J Walsh, Pingzhao Hu, Jane Batt, Claudia C Dos Santos
MicroRNAs (miRs) are small single-stranded noncoding RNA that function in RNA silencing and post-transcriptional regulation of gene expression. An increasing number of studies have shown that miRs play an important role in tumorigenesis, and understanding the regulatory mechanism of miRs in this gene regulatory network will help elucidate the complex biological processes at play during malignancy. Despite advances, determination of miR-target interactions (MTIs) and identification of functional modules composed of miRs and their specific targets remain a challenge...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27688708/dna-methylation-heterogeneity-patterns-in-breast-cancer-cell-lines
#6
Sunny Tian, Karina Bertelsmann, Linda Yu, Shuying Sun
Heterogeneous DNA methylation patterns are linked to tumor growth. In order to study DNA methylation heterogeneity patterns for breast cancer cell lines, we comparatively study four metrics: variance, I (2) statistic, entropy, and methylation state. Using the categorical metric methylation state, we select the two most heterogeneous states to identify genes that directly affect tumor suppressor genes and high- or moderate-risk breast cancer genes. Utilizing the Gene Set Enrichment Analysis software and the ConsensusPath Database visualization tool, we generate integrated gene networks to study biological relations of heterogeneous genes...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27688707/novel-biomarker-candidates-for-colorectal-cancer-metastasis-a-meta-analysis-of-in-vitro-studies
#7
Nguyen Phuoc Long, Wun Jun Lee, Nguyen Truong Huy, Seul Ji Lee, Jeong Hill Park, Sung Won Kwon
Colorectal cancer (CRC) is one of the most common and lethal cancers. Although numerous studies have evaluated potential biomarkers for early diagnosis, current biomarkers have failed to reach an acceptable level of accuracy for distant metastasis. In this paper, we performed a gene set meta-analysis of in vitro microarray studies and combined the results from this study with previously published proteomic data to validate and suggest prognostic candidates for CRC metastasis. Two microarray data sets included found 21 significant genes...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27688706/identifying-significant-features-in-cancer-methylation-data-using-gene-pathway-segmentation
#8
Zena M Hira, Duncan F Gillies
In order to provide the most effective therapy for cancer, it is important to be able to diagnose whether a patient's cancer will respond to a proposed treatment. Methylation profiling could contain information from which such predictions could be made. Currently, hypothesis testing is used to determine whether possible biomarkers for cancer progression produce statistically significant results. However, this approach requires the identification of individual genes, or sets of genes, as candidate hypotheses, and with the increasing size of modern microarrays, this task is becoming progressively harder...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27679461/overlapping-group-logistic-regression-with-applications-to-genetic-pathway-selection
#9
Yaohui Zeng, Patrick Breheny
Discovering important genes that account for the phenotype of interest has long been a challenge in genome-wide expression analysis. Analyses such as gene set enrichment analysis (GSEA) that incorporate pathway information have become widespread in hypothesis testing, but pathway-based approaches have been largely absent from regression methods due to the challenges of dealing with overlapping pathways and the resulting lack of available software. The R package grpreg is widely used to fit group lasso and other group-penalized regression models; in this study, we develop an extension, grpregOverlap, to allow for overlapping group structure using a latent variable approach...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27625573/biological-networks-for-cancer-candidate-biomarkers-discovery
#10
REVIEW
Wenying Yan, Wenjin Xue, Jiajia Chen, Guang Hu
Due to its extraordinary heterogeneity and complexity, cancer is often proposed as a model case of a systems biology disease or network disease. There is a critical need of effective biomarkers for cancer diagnosis and/or outcome prediction from system level analyses. Methods based on integrating omics data into networks have the potential to revolutionize the identification of cancer biomarkers. Deciphering the biological networks underlying cancer is undoubtedly important for understanding the molecular mechanisms of the disease and identifying effective biomarkers...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27559294/characterization-of-gene-expression-patterns-among-artificially-developed-cancer-stem-cells-using-spherical-self-organizing-map
#11
Akimasa Seno, Tomonari Kasai, Masashi Ikeda, Arun Vaidyanath, Junko Masuda, Akifumi Mizutani, Hiroshi Murakami, Tetsuya Ishikawa, Masaharu Seno
We performed gene expression microarray analysis coupled with spherical self-organizing map (sSOM) for artificially developed cancer stem cells (CSCs). The CSCs were developed from human induced pluripotent stem cells (hiPSCs) with the conditioned media of cancer cell lines, whereas the CSCs were induced from primary cell culture of human cancer tissues with defined factors (OCT3/4, SOX2, and KLF4). These cells commonly expressed human embryonic stem cell (hESC)/hiPSC-specific genes (POU5F1, SOX2, NANOG, LIN28, and SALL4) at a level equivalent to those of control hiPSC 201B7...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27528797/exsurv-a-web-resource-for-prognostic-analyses-of-exons-across-human-cancers-using-clinical-transcriptomes
#12
Seyedsasan Hashemikhabir, Gungor Budak, Sarath Chandra Janga
Survival analysis in biomedical sciences is generally performed by correlating the levels of cellular components with patients' clinical features as a common practice in prognostic biomarker discovery. While the common and primary focus of such analysis in cancer genomics so far has been to identify the potential prognostic genes, alternative splicing - a posttranscriptional regulatory mechanism that affects the functional form of a protein due to inclusion or exclusion of individual exons giving rise to alternative protein products, has increasingly gained attention due to the prevalence of splicing aberrations in cancer transcriptomes...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27486300/recursive-partitioning-method-on-competing-risk-outcomes
#13
Wei Xu, Jiahua Che, Qin Kong
In some cancer clinical studies, researchers have interests to explore the risk factors associated with competing risk outcomes such as recurrence-free survival. We develop a novel recursive partitioning framework on competing risk data for both prognostic and predictive model constructions. We define specific splitting rules, pruning algorithm, and final tree selection algorithm for the competing risk tree models. This methodology is quite flexible that it can corporate both semiparametric method using Cox proportional hazards model and parametric competing risk model...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27486299/pathway-informed-classification-system-pics-for-cancer-analysis-using-gene-expression-data
#14
Michael R Young, David L Craft
We introduce Pathway-Informed Classification System (PICS) for classifying cancers based on tumor sample gene expression levels. PICS is a computational method capable of expeditiously elucidating both known and novel biological pathway involvement specific to various cancers and uses that learned pathway information to separate patients into distinct classes. The method clearly separates a pan-cancer dataset by tissue of origin and also sub-classifies individual cancer datasets into distinct survival classes...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27398021/tmainspiration-decode-interdependencies-in-multifactorial-tissue-microarray-data
#15
Florian Boecker, Horst Buerger, Nikhil V Mallela, Eberhard Korsching
There are no satisfying tools in tissue microarray (TMA) data analysis up to now to analyze the cooperative behavior of all measured markers in a multifactorial TMA approach. The developed tool TMAinspiration is not only offering an analysis option to close this gap but also offering an ecosystem consisting of quality control concepts and supporting scripts to make this approach a platform for informed practice and further research. The TMAinspiration method is specifically focusing on the demands of the TMA analysis by controlling errors and noise by a generalized regression scheme while at the same time avoiding to introduce a priori too many constraints into the analysis of the data...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27385909/an-integrated-approach-for-rna-seq-data-normalization
#16
Shengping Yang, Donald E Mercante, Kun Zhang, Zhide Fang
BACKGROUND: DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27346945/the-melanoma-maicare-framework-a-microsimulation-model-for-the-assessment-of-individualized-cancer-care
#17
Elisabeth van der Meijde, Alfons J M van den Eertwegh, Sabine C Linn, Gerrit A Meijer, Remond J A Fijneman, Veerle M H Coupé
Recently, new but expensive treatments have become available for metastatic melanoma. These improve survival, but in view of the limited funds available, cost-effectiveness needs to be evaluated. Most cancer cost-effectiveness models are based on the observed clinical events such as recurrence- free and overall survival. Times at which events are recorded depend not only on the effectiveness of treatment but also on the timing of examinations and the types of tests performed. Our objective was to construct a microsimulation model framework that describes the melanoma disease process using a description of underlying tumor growth as well as its interaction with diagnostics, treatments, and surveillance...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27330269/multiclust-an-r-package-for-identifying-biologically-relevant-clusters-in-cancer-transcriptome-profiles
#18
REVIEW
Nathan Lawlor, Alec Fabbri, Peiyong Guan, Joshy George, R Krishna Murthy Karuturi
Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27279732/a-novel-approach-to-predict-core-residues-on-cancer-related-dna-binding-domains
#19
Ka-Chun Wong
Protein-DNA interactions are involved in different cancer pathways. In particular, the DNA-binding domains of proteins can determine where and how gene regulatory regions are bound in different cell lines at different stages. Therefore, it is essential to develop a method to predict and locate the core residues on cancer-related DNA-binding domains. In this study, we propose a computational method to predict and locate core residues on DNA-binding domains. In particular, we have selected the cancer-related DNA-binding domains for in-depth studies, namely, winged Helix Turn Helix family, homeodomain family, and basic Helix-Loop-Helix family...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27279731/rational-design-of-peptide-vaccines-against-multiple-types-of-human-papillomavirus
#20
Sumanta Dey, Antara De, Ashesh Nandy
Human papillomavirus (HPV) occurs in many types, some of which cause cervical, genital, and other cancers. While vaccination is available against the major cancer-causing HPV types, many others are not covered by these preventive measures. Herein, we present a bioinformatics study for the designing of multivalent peptide vaccines against multiple HPV types as an alternative strategy to the virus-like particle vaccines being used now. Our technique of rational design of peptide vaccines is expected to ensure stability of the vaccine against many cycles of mutational changes, elicit immune response, and negate autoimmune possibilities...
2016: Cancer Informatics
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