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 populations

Available 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).

GeneSets

A publicly available online repository of gene sets and modules for ten model organisms , providing access to two types of gene set. Annotation-based gene sets are automatically derived and regularly updated from public functional, pathway and genomics resources, and computationally derived gene sets are automatically generated from genomic data. An easy-to-use interface provides access to files in a simple format that facilitates input into any subsequent analysis algorithm, and a collection of links to tools and sites that allow gene-set-level analysis is included in the repository. Finally, an online form is available to allow users to request the addition of gene sets from additional resources or datasets.

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. This site is under development and should be available by 20 June 2006.

Two-component clone sets and deletion strains for Caulobacter crescentus

The following clone sets and deletion collections are available on request by email:

1) Deletion mutant collection for the 106 C. crescentus two-component signal transduction genes.

2) Sequence-verified Gateway pENTR clones for each C. crescentus response regulator gene.

3) Sequence-verified Gateway pENTR clones for each E. coli response regulator gene.

Skerker, J., Prasol, M., Perchuk, B., Biondi, E. & Laub, M. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biol. 3, e334 (2005). [PDF]

Microarray data on nucleosome positioning and modification and on the effects of histone modifications on gene expression

Dion_et_al_H4_mutagenesis_gene_expression.xls

Gene expression data for yeast strains expressing mutation forms of histone H4 that modify the charge of the histone tail by systematically mutating lysine to arginine residues.

Dion, M., Altschuler, S., Wu, L. & Rando, O. J. Genomic characterization reveals a simple histone H4 acetylation code. PNAS 102, 5501-5506 (2005). [PDF]

Yuan_2005_nucleosome_positions.xls

Nucleosome positions for 0.5 Mb of the yeast genome.

Yuan, G. C., Liu, Y.-J., Dion, M. F., Slack, M. D., Wu, L. F., Altschuler, S. J. & Rando, O. J. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309, 626-630 (2005). [PubMed]

Liu_et_al_Dataset_S1.xls

Histone modification data for ~2,300 nucleosomes identified in the previous dataset.

Liu, C., Kaplan, T., Kim, M., Buratowski, S., Schreiber, S. L., Friedman, N. & Rando, O. J. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 3, e328 (2005). [PDF]

Cichlid ESTs, gene index, and genomics database

1) Astatotilapia burtoni ESTs:

Genbank accession numbers CN468542 - CN472211
Genbank accession numbers DY625779 - DY632420

2) TIGR Gene Index for Astatotilapia burtoni (in collaboration with John Quackenbush's group):

A gene index for A. burtoni (release 1.0)

Release 2.0 is scheduled for early June, 2006.

3) Cichlid EST and microarray database (beta version):

Cichlid genomics site
A comprehensive database resource that connects all sequenced clones to data, including pertinent information on physical location, array coordinates, BLAST results, and functional annotation.