New Gene Expression Profiles

The RNA Dynamics of the Developing Mouse Face project has published the following paper this past summer that details gene expression in the mouse facial prominences on the basis of time, prominence and tissue layer utilizing microarray platform for these analyses. They are now expanding these studies to look at isoform differences in these samples using RNAseq data that are available for download at FaceBase. The microarray data are described in this paper:

Hooper, J. E., W. Feng, H. Li, S. M. Leach, T. Phang, C. Siska, K. L. Jones, R. A. Spritz, L. E. Hunter, T. Williams. (2017). Systems biology of facial development: contributions of ectoderm and mesenchyme. Dev. Biol. 426, 97-114. PMID: 28363736.

They are now expanding these studies to look at isoform differences using RNAseq data. They have made the processed data available as a download of HTML pages to make it easier to explore the data on a gene-by-gene basis. The relevant paper is:

Leach, S.M., W. Feng, T. Williams. (2017). Gene expression profile data for mouse facial development. Data in Brief 13, 242-247.

And the following is a link to the data itself:

https://data.mendeley.com/datasets/5y2hgyz5ng/1 (7.9 GB)

Basically, following download, an investigator can search for an individual gene and see its expression profile in the developing facial prominences as a graphical representation for time, tissue and prominence.

Here is the description from the website:

“Within this folder are three items: two folders and an index.html. Opening the top-level index.html file in a web browser will provide information concerning the two data sets. The index provides an overview, using color-coded boxes for each named gene, to illustrate the gene expression profile found within each of the data sets. Hyperlinks are also available to access details for each gene in the Whole Prominence or Ectoderm/Mesenchyme data sets.

The two subfolders, WholeProminence and EctoMesen, contain expression profiles and database annotations for every named gene available as .html pages, indexed by gene name for the two studies. Again, within each data subfolder there is a specific index for the whole prominence or ectoderm/mesenchyme dataset . There is also a folder “HTMLS” that connects directly to the list of genes and a folder “JPEGS” which has a list of images used to populate the html pages. Within the whole prominence or ectoderm/mesenchyme datasets, a gene-specific webpage visualizes the expression and detection values for each gene as heatmaps and line graphs (raw and log2 scale). Each gene-specific webpage also lists annotations from the Mammalian Phenotype, Kyoto Encyclopedia of Genes and Genomes (KEGG), InterPro and Gene Ontology (GO) databases. Terms relevant to craniofacial biology are highlighted in red.”