ArticleBMC genomics2006
SIGMA: a system for integrative genomic microarray analysis of cancer genomes.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- A Multi-way Multi-task Learning Approach for Multinomial Logistic Regression*. An Application in Joint Prediction of Appointment Miss-opportunities across Multiple Clinics.Methods of information in medicine · 2017Article
- Loss of the Notch effector RBPJ promotes tumorigenesis.The Journal of experimental medicine · 2015Article
- The COP9 signalosome subunit 6 (CSN6): a potential oncogene.Cell division · 2013Article
- Roles of COP9 signalosome in cancer.Cell cycle (Georgetown, Tex.) · 2011Review
- FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.Journal of clinical bioinformatics · 2011Article
- Subunit 6 of the COP9 signalosome promotes tumorigenesis in mice through stabilization of MDM2 and is upregulated in human cancers.The Journal of clinical investigation · 2011Article
- Deciphering squamous cell carcinoma using multidimensional genomic approaches.Journal of skin cancer · 2011Article
- An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer.BMC systems biology · 2010Article
- Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer.Cancer metastasis reviews · 2010Review
- Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE.PloS one · 2010Article
- Article
- Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.PloS one · 2009Article
- KEAP1 E3 ligase-mediated downregulation of NF-kappaB signaling by targeting IKKbeta.Molecular cell · 2009Article
- SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.BMC bioinformatics · 2008Article
- DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers.Oncogene · 2008Article
- SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels.BMC genomics · 2008Article
- Public databases and software for the pathway analysis of cancer genomes.Cancer informatics · 2007Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundThe prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes.
resultsWe have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types.
conclusionIn this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA) of cancer genomes, can be accessed at http://sigma.bccrc.ca.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.