Gene expression profiles of mouse facial development

Published: 01-08-2017| Version 1 | DOI: 10.17632/5y2hgyz5ng.1
Contributors:
Trevor Williams,
Sonia M Leach,
Weiguo Feng

Description

These data are related to the research articles entitled "Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences" by Feng et al, 2009 and “Systems Biology of facial development: contributions of ectoderm and mesenchyme” by Hooper et al. (submitted). Contained here is a new HTML library wherein individual gene expression profiles are presented as an indexed and clickable list of the genes, each linked to a graphical image of that gene's expression profile in the ectoderm, mesenchyme, or intact prominence, and augmented by functional annotations relevant for craniofacial biology. The data represent a valuable visual alternative to the raw data available elsewhere for analysis purposes (The raw data (.cel files) and normalized expression data are available at GEO (www.ncbi.nlm.nih.gov/geo) under accession numbers GSE7759 [1] and GSE62214 [3] and at FaceBase (www.facebase.org) under accession FB00000803). The data presented here as HTML pages will enable investigators to obtain a rapid assessment of the relative expression level of any gene on the array with respect to time, tissue, prominence and expression trajectory. The data are contained in a tar.gz archive, TrevorHTMLs.tar.gz, designed to be uncompressed in a single location, where hyperlinks use relative file path names to navigate the set of files. 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.

Steps to reproduce

Uncompress the tar.gz file. It should contain 111,785 Files, 6 Folders, totaling around 10.6GB. Viewing the top-level index.html file will allow navigation through the whole data set.