Resources
Publicly available resources generated by the center.
SERV: Sequence-based Estimation of Repeat Variability
An algorithm to predict the variability of tandem repeats.
Indel arrays for genotyping of Arabidopsis populationsAvailable genotyping approaches for Arabidopsis mapping populations such as PCR and whole genome-microarrays are either very labor intensive or prohibitively expensive. To meet this challenge, we have developed a novel genotyping array which combines the advantages of high-throughput genotyping with the precision of PCR. Our genotyping array assesses 240 unique markers in a single hybridization experiment at a cost of ~ $50 per line. The array elements represent insertion/deletion (indel) polymorphisms between the accessions Col and Ler. Indel polymorphisms are recognized with great precision, eliminating the need for array replicates and complex statistical analysis. We demonstrated the utility of the array for accurate mapping of recessive mutations, RIL populations, and mixed genetic backgrounds from accessions other than Col and Ler. A manuscript describing this method and its applications is in press in The Plant Journal. In addition to detailed method descriptions, printed arrays are available at cost to academic researchers at www.cgr.harvard.edu/Queitschlab/index.html .
Given the increasing ease of generating partial genomic sequences of non-model species, this approach is readily transferable to a wide range of organisms, including crop species. In fact, in collaboration with R. Waterston at the Department of Genome Sciences, University of Washington, Seattle, we have begun to build a similar tool for genotyping of natural isolates of the nematode C. briggsae.
Cancer Module Map data mining website
Web access to our comprehensive modular analysis of transcriptional responses in human cancer, including the full cancer expression compendium, detailed clinical annotations, and all the significant modules. Various searching, browsing and visualization capabilities are provided.
Segal, E., Friedman, N., Koller, D. & Regev, A. A module map showing conditional activity of expression modules in cancer. Nature Genetics 36, 1090-1098 (2004). [PDF]
GeneXPress
A
comprehensive tool for visualization, integration and analysis
of genomic data, from a modular perspective. We have recently
introduced a new tool, Genomica (http://genomica.weizmann.ac.il,
now under separate funding) a redesign of GeneXPress to
accommodate additional modular analysis. To facilitate Genomica's
use by any genomics researcher, we developed an extensive
online tutorial and basic analysis packages for several
organisms. Further resources for analysis were developed
as an online repository (GeneSets, below).
Segal, E., Kaushal, A., Yelensky, R., Pham, T., Regev, A.,
Koller, D. & Friedman, N. GeneXPress: a visualization
and statistical analysis tool for gene expression and sequence
data. Proc. 12th Intl Conf. on Intelligent Systems for
Molecular Biology (2004). [PDF]
Fungal Orthogroups Repository
We provide the orthogroup assignments for all predicted protein-coding genes across 13 Ascomycete fungal genomes.
Ilan Wapinski, Avi Pfeffer, Nir Friedman and Regev, A. A Natural history and evolutionary principles of gene duplication in fungi. Nature 449, 54-61 (2007).
Mutation mapping method
Software for using microarray data on DNA hybridization to detect single feature polymorphisms (SFP) and use them to map genetic traits in crosses between different strain backgrounds.
