Literature DB >> 15593402

CGH-Plotter: MATLAB toolbox for CGH-data analysis.

Reija Autio1, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi.   

Abstract

CGH-Plotter is a MATLAB toolbox with a graphical user interface for the analysis of comparative genomic hybridization (CGH) microarray data. CGH-Plotter provides a tool for rapid visualization of CGH-data according to the locations of the genes along the genome. In addition, the CGH-Plotter identifies regions of amplifications and deletions, using k-means clustering and dynamic programming. The application offers a convenient way to analyze CGH-data and can also be applied for the analysis of cDNA microarray expression data. CGH-Plotter toolbox is platform independent and requires MATLAB 6.1 or higher to operate.

Mesh：

Year:  2003        PMID： 15593402     DOI： 10.1093/bioinformatics/btg230

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  26 in total

1.  Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data.

Authors:  Weil R Lai; Mark D Johnson; Raju Kucherlapati; Peter J Park
Journal:  Bioinformatics       Date:  2005-08-04       Impact factor: 6.937

2.  CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.

Authors:  Weil Lai; Vidhu Choudhary; Peter J Park
Journal:  Bioinformatics       Date:  2008-02-22       Impact factor: 6.937

3.  An improved method for detecting and delineating genomic regions with altered gene expression in cancer.

Authors:  Björn Nilsson; Mikael Johansson; Anders Heyden; Sven Nelander; Thoas Fioretos
Journal:  Genome Biol       Date:  2008-01-21       Impact factor: 13.583

4.  Discovering tumor suppressor genes through genome-wide copy number analysis.

Authors:  S Michael Rothenberg; Jeff Settleman
Journal:  Curr Genomics       Date:  2010-08       Impact factor: 2.236

5.  A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

Authors:  Jie Chen; Yu-Ping Wang
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2009 Oct-Dec       Impact factor: 3.710

6.  Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP).

Authors:  Jamileh Hashemi; Claire Worrall; Daiana Vasilcanu; Mårten Fryknäs; Luqman Sulaiman; Mohsen Karimi; Wen-Hui Weng; Weng-Onn Lui; Christina Rudduck; Magnus Axelson; Helena Jernberg-Wiklund; Leonard Girnita; Olle Larsson; Catharina Larsson
Journal:  PLoS One       Date:  2011-03-14       Impact factor: 3.240

7.  On the adaptive partition approach to the detection of multiple change-points.

Authors:  Yinglei Lai
Journal:  PLoS One       Date:  2011-05-24       Impact factor: 3.240

8.  Genetic profiling differentiates second primary tumors from metastases in adult metachronous soft tissue sarcoma.

Authors:  Josefin Fernebro; Ana Carneiro; Anders Rydholm; Henryk A Domanski; Anna Karlsson; Ake Borg; Mef Nilbert
Journal:  Sarcoma       Date:  2009-02-02

9.  Potential predictive markers of chemotherapy resistance in stage III ovarian serous carcinomas.

Authors:  Lovisa Osterberg; Kristina Levan; Karolina Partheen; Ulla Delle; Björn Olsson; Karin Sundfeldt; György Horvath
Journal:  BMC Cancer       Date:  2009-10-18       Impact factor: 4.430

10.  Tumor genome wide DNA alterations assessed by array CGH in patients with poor and excellent survival following operation for colorectal cancer.

Authors:  Kristina K Lagerstedt; Johan Staaf; Göran Jönsson; Elisabeth Hansson; Christina Lönnroth; Ulf Kressner; Lars Lindström; Svante Nordgren; Ake Borg; Kent Lundholm
Journal:  Cancer Inform       Date:  2007-10-12
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