A curated online resource for SOX10 and pigment cell molecular genetic pathways

Abstract

We describe the creation of a specialized web-accessible database named the Pigment Cell Gene Resource, which contains information on the genetic pathways that regulate pigment cell development and function. This manually curated database is comprised of two sections, an annotated literature section and an interactive transcriptional network diagram. Initially, this database focuses on the transcription factor SOX10, which has essential roles in pigment cell development and function, but the database has been designed with the capacity to expand in the future, allowing inclusion of many more pigmentation genes. Database URL: http://research.nhgri.nih.gov/pigment_cell/

Figure 1.

A representative page from the annotated literature section for SOX10 of the Pigment Cell Gene Resource. The navigation sidebar at left includes the 17 literature summary subcategories; each of these categories is located on a separate page. Links to PubMed abstracts for each summarized article are in blue, and bold text indicates the main points of the summary. The navigation sidebar also contains links to access the Pigment Cell Gene Network, to submit data directly and to download data.

Figure 2.

A representative image from the interactive, BioTapestry-generated Pigment Cell Gene Network. The portion of the network containing neural crest and melanoblasts with associated dermatome are shown. Red numbers represent interactive notes, which in the online network become visible by mouse-over. Regions included in the complete diagram are categorized by developmental stage/cell type, as follows: neural crest, melanoblasts and associated dermatome, follicular melanocyte stem cells, follicular/dermal melanocytes and associated keratinocytes and RPE.

Figure 3.

Published SOX10 coding region mutations and polymorphisms. For clarity, the mutations are color-coded based upon clinical phenotype/disorder. Human SOX10 developmental mutations are shown above the protein, and melanoma mutations and polymorphisms are shown below the protein. The orthologous changes to published mouse and zebrafish coding mutations are also shown. SOX10 nucleotide/amino acid numbering correlates with NP_008872. Mutation nomenclature is per Human Genome Variation Society guidelines (http://www.hgvs.org/mutnomen/).