scholarly journals A robust Correntropy-based method for analyzing multisample aCGH data

Genomics ◽  
2015 ◽  
Vol 106 (5) ◽  
pp. 257-264 ◽  
Author(s):  
Majid Mohammadi ◽  
Ghosheh Abed Hodtani ◽  
Maryam Yassi
Keyword(s):  
PLoS ONE ◽  
2011 ◽  
Vol 6 (10) ◽  
pp. e26975 ◽  
Author(s):  
Chihyun Park ◽  
Jaegyoon Ahn ◽  
Youngmi Yoon ◽  
Sanghyun Park

2010 ◽  
Vol 3 (1) ◽  
Author(s):  
Jorma J de Ronde ◽  
Christiaan Klijn ◽  
Arno Velds ◽  
Henne Holstege ◽  
Marcel JT Reinders ◽  
...  
Keyword(s):  

Genomics ◽  
2009 ◽  
Vol 94 (5) ◽  
pp. 317-323 ◽  
Author(s):  
Ki-Yeol Kim ◽  
Gui Youn Lee ◽  
Jin Kim ◽  
Hei-Cheul Jeung ◽  
Hyun Cheol Chung ◽  
...  
Keyword(s):  

2006 ◽  
Vol 2 ◽  
pp. 117693510600200 ◽  
Author(s):  
Ganesh Shankar ◽  
Michael R. Rossi ◽  
Devin E. Mcquaid ◽  
Jeffrey M. Conroy ◽  
Daniel G. Gaile ◽  
...  

Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark.org/aCGHview/ .


2008 ◽  
Vol 24 (16) ◽  
pp. i139-i145 ◽  
Author(s):  
E. Ben-Yaacov ◽  
Y. C. Eldar
Keyword(s):  

2014 ◽  
Vol 26 (12) ◽  
pp. 2855-2895 ◽  
Author(s):  
Saverio Salzo ◽  
Salvatore Masecchia ◽  
Alessandro Verri ◽  
Annalisa Barla

We present an algorithm for dictionary learning that is based on the alternating proximal algorithm studied by Attouch, Bolte, Redont, and Soubeyran ( 2010 ), coupled with a reliable and efficient dual algorithm for computation of the related proximity operators. This algorithm is suitable for a general dictionary learning model composed of a Bregman-type data fit term that accounts for the goodness of the representation and several convex penalization terms on the coefficients and atoms, explaining the prior knowledge at hand. As Attouch et al. recently proved, an alternating proximal scheme ensures better convergence properties than the simpler alternating minimization. We take care of the issue of inexactness in the computation of the involved proximity operators, giving a sound stopping criterion for the dual inner algorithm, which keeps under control the related errors, unavoidable for such a complex penalty terms, providing ultimately an overall effective procedure. Thanks to the generality of the proposed framework, we give an application in the context of genome-wide data understanding, revising the model proposed by Nowak, Hastie, Pollack, and Tibshirani ( 2011 ). The aim is to extract latent features (atoms) and perform segmentation on array-based comparative genomic hybridization (aCGH) data. We improve several important aspects that increase the quality and interpretability of the results. We show the effectiveness of the proposed model with two experiments on synthetic data, which highlight the enhancements over the original model.


2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e16544-e16544
Author(s):  
D. P. Gaile ◽  
L. Shepherd ◽  
S. Liu ◽  
K. Darcy ◽  
M. Brady ◽  
...  

e16544 Background: An R software library was created with the goal of creating customizable, platform independent, and portable visualization tools for the annotation, dissemination and interrogation of high dimensioned genomic data. Methods: A set of R functions were created to extend the functionality of the sendplot R library. The functions were applied to BAC aCGH data generated for several GOG studies. Results: The iGenomicViewer function calls created and populated a directory structure which was then ported to a password protected server for interrogation by research team members. The linked html and image output allows users to examine genome wide plots of aberration frequencies and p-values and then drill down to visualizations of regions of interest. Users can interrogate a panel of plots which includes: 1) a heat map of the aCGH data for with tool-tip display of sample and assay specific data (e.g., assay values, sample IDs, and hyperlinks to UCSC browser and sample specific images); 2) a set of interactive annotation tracks which display location of cancer, disease and DNA repair genes; and 3) a plot which displays -log10 p-values and/or aberration frequencies for the BAC assays depicted in the heatmap. For the smallest regions of interest, the panel of plots contains a tiled heatmap which depicts the overlap and gaps in BAC coverage and their alignment with the gene locations represented in the adjacent annotation track. Conclusions: The iGenomicViewer library provides open source software for creation of customizable visualization tools for collaborative research projects involving high dimensioned genomic data. No significant financial relationships to disclose.


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