Gene expression profiles of mouse facial development

Published: 1 Aug 2017 | Version 1 | DOI: 10.17632/5y2hgyz5ng.1
Contributor(s):

Description of this data

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.

Experiment data files

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.

This data is associated with the following publication:

Gene expression pro file data for mouse facial development

Published in: Data in Brief

Latest version

  • Version 1

    2017-08-01

    Published: 2017-08-01

    DOI: 10.17632/5y2hgyz5ng.1

    Cite this dataset

    Williams, Trevor; Leach, Sonia M; Feng, Weiguo (2017), “Gene expression profiles of mouse facial development”, Mendeley Data, v1 http://dx.doi.org/10.17632/5y2hgyz5ng.1

Categories

Gene Expression, Time Series, Mouse Model, Craniofacial Biology

Mendeley Library

Organise your research assets using Mendeley Library. Add to Mendeley Library

Licence

CC BY 4.0 Learn more

The files associated with this dataset are licensed under a Creative Commons Attribution 4.0 International licence.

What does this mean?

This dataset is licensed under a Creative Commons Attribution 4.0 International licence. What does this mean? You can share, copy and modify this dataset so long as you give appropriate credit, provide a link to the CC BY license, and indicate if changes were made, but you may not do so in a way that suggests the rights holder has endorsed you or your use of the dataset. Note that further permission may be required for any content within the dataset that is identified as belonging to a third party.

Report