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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
- A. Subramanian, P. Tamayo, +8 authors J. Mesirov
- Medicine, Biology
- Proceedings of the National Academy of Sciences…
- 30 September 2005
It is demonstrated how the GSEA method yields insights into several cancer-related data sets, including leukemia and lung cancer, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer. Expand
MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations.
A computer package, called MAPMAKER, designed specifically for the construction of linkage maps in a number of organisms, including the human and several plants, and it is outlined the mapping strategies that have been used. Expand
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.
A generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case and suggests a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge. Expand
Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results
Specific standards designed to maintain rigor while also promoting communication are proposed for the interpretation of linkage results in genetic studies under way for many complex traits. Expand
Integrative Genomics Viewer
- James T. Robinson, H. Thorvaldsdóttir, +4 authors J. Mesirov
- Biology, Computer Science
- Nature Biotechnology
- 1 January 2011
The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. Expand
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
In situ Hi-C is used to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types, identifying ∼10,000 loops that frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Expand
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
An analytical strategy is introduced, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes, which identifies a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle. Expand
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes. Expand
Initial sequencing and analysis of the human genome.
The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence. Expand
The Structure of Haplotype Blocks in the Human Genome
It is shown that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. Expand