FIGURE SUMMARY
Title

Harmonizing model organism data in the Alliance of Genome Resources

Authors
Alliance of Genome Resources Consortium
Source
Full text @ Genetics

The Alliance Portal provides a harmonized view of research organism information. Left, current MOD pages; Right, current Alliance release 4.0 gene pages.

Example of Alliance JBrowse. The top is the standard control bar. Next are curated variants, often with known phenotypic consequences. The gene structure models (introns and exons) for each gene are shown, with the high throughput variants shown in the next track. The reference sequence in all reading frames is followed by a conservation track from University of California, Santa Cruz. Two alleles are highlighted in this figure: the blue box shows the e1417 allele to be in a conserved intron region, while the gold box shows the n378 allele to be in a coding exon.

Conceptual map of gene-centered information. Perturbations of gene activity include alleles, variants, RNAi, knockdown, and transgenic overexpression.

The expression widget. This example is for the Drosophila gene per. The links to primary sources are customized and the number varies among species depending on data.

Montage of types of variant information and displays. The variant page has a summary, snapshot of Genomic Location, and then tables of Phenotypes, Molecular Consequences, and Disease Associations.

Automatically generated gene summaries from structured data. Example of a gene summary for C. elegans gene tra-1 showing different data categories highlighted in different colors.

Views of pathways. GO-CAM model with simplified view for pmk-1.

AllianceMine. Screen shots of AllianceMine output. Using a template query of disease ontology (DO) to all genes with the term “autism” a) returns 1088 genes b). Mousing over petena pops up a brief description of that gene c).

Acknowledgments
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