ArticleBMC bioinformatics2008
SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 37 citations in OpenAlex.
- Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine.Network and systems medicine · 2020Review
- Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges.Frontiers in genetics · 2016Review
- Recurring DNA copy number gain at chromosome 9p13 plays a role in the activation of multiple candidate oncogenes in progressing oral premalignant lesions.Cancer medicine · 2014Article
- Genovar: a detection and visualization tool for genomic variants.BMC bioinformatics · 2012Article
- Lessons from a decade of integrating cancer copy number alterations with gene expression profiles.Briefings in bioinformatics · 2012Article
- Article
- Dysfunctions associated with methylation, microRNA expression and gene expression in lung cancer.PloS one · 2012Article
- TRAF6 is an amplified oncogene bridging the RAS and NF-κB pathways in human lung cancer.The Journal of clinical investigation · 2011Article
- FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.Journal of clinical bioinformatics · 2011Article
- Tumor profiling: development of prognostic and predictive factors to guide brain tumor treatment.Current oncology reports · 2011Review
- MicroRNA gene dosage alterations and drug response in lung cancer.Journal of biomedicine & biotechnology · 2011Article
- The use of global profiling in biomarker development for gliomas.Brain pathology (Zurich, Switzerland) · 2011Review
- Deciphering squamous cell carcinoma using multidimensional genomic approaches.Journal of skin cancer · 2011Article
- Expectations, validity, and reality in gene expression profiling.Journal of clinical epidemiology · 2010Review
- 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
- CHESS (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome.BMC bioinformatics · 2009Article
- Integrated analysis of DNA copy number and gene expression microarray data using gene sets.BMC bioinformatics · 2009Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundHigh throughput microarray technologies have afforded the investigation of genomes, epigenomes, and transcriptomes at unprecedented resolution. However, software packages to handle, analyze, and visualize data from these multiple 'omics disciplines have not been adequately developed.
resultsHere, we present SIGMA2, a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. Multi-dimensional datasets can be simultaneously visualized and analyzed with respect to each dimension, allowing combinatorial integration of the different assays belonging to the different 'omics.
conclusionThe identification of genes altered at multiple levels such as copy number, loss of heterozygosity (LOH), DNA methylation and the detection of consequential changes in gene expression can be concertedly performed, establishing SIGMA2 as a novel tool to facilitate the high throughput systems biology analysis of cancer.
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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.