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Page 12 of 17 for News & Events | FaceBase

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News & Events

New Gene Expression Profiles (06 September 2017)

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.”

Take the New FaceBase User Survey! (30 August 2017)

In order to help us get a better understanding of the usefulness of this website and the craniofacial data we publish, we are asking our users to fill out a brief survey.

Almost of all of the questions are multiple choice although there are options to fill in more detail if you would like. It is also optional to include your name and we do not retain your email address (unless you agree to be contacted for further questions at the end of the survey).

This should only take a few minutes and would be invaluable information that will go towards improving this website and our contribution to the craniofacial research community.

Just follow the link below. Thank you so much for your participation!

https://uscviterbi.qualtrics.com/jfe/form/SV_9ZZHnzGBHvfyTyZ

Note, the survey will be available until Wednesday, September 16th.

New Datasets - Mouse RNA-Seq and Spry1 microCT images and landmarking protocols (09 August 2017)

FaceBase has just added a new dataset of RNA-Seq for Mouse from the RNA Dynamics of the Developing Mouse Face project: Temporal analysis of ectoderm and mesenchyme expression in the developing mouse facial prominences

We also added microCT images and landmarking protocols regarding Spry1 from the Inbred Background Genetic Effects on Craniofacial Dysmorphology project: Sprouty Background Effect. Here is the full description of this data:

Inbred genetic background significantly influences the expression of phenotypes associated with known genetic perturbations and can underlie variation in disease severity between individuals with the same mutation. However, the effect of epistatic interactions on the development of complex traits, such as craniofacial morphology, is poorly understood. We use the morphometric landmarks associated with a previous FaceBase analysis (Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate) to 1) quantify the effect of three Sprouty null mutations on craniofacial shape and 2) to quantify how the associated dysmorphology is modulated by three inbred backgrounds. While it is commonly known that a given mutation may have different phenotypic effects across mouse backgrounds, our quantitative results represent an important first step towards elucidating genetic interactions underlying variation in robustness to known genetic perturbations in mice. Taking background effects into account will be necessary to identify genetic and developmental interactions that modulate the severity of craniofacial dysmorphology, because variation in the penetrance or severity of a disease mutation among humans is almost certainly based on similar interactions. In addition, identical micro-CT image and landmarking protocols make this a valuable comparative dataset to the Collaborative Cross mouse dataset of adult mouse morphology already found on FaceBase (see them listed on the Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate project page).

Presentations from the 2017 FaceBase Annual Meeting in Boston (12 May 2017)

Our thanks go out to Dr. Richard Maas, Victoria Perroni and all of the people at Harvard Medical School for being wonderful hosts for our recent Annual Meeting. Our first day was again open to the public and attended onsite as well as via webcast. We thank you all for joining us.

For those who weren’t able to make it, we’ve posted presentations and videos from May 1st that have been approved for public viewing.

  • Updated FaceBase Agenda with the speaker names for each presentation (thanks for the suggestion, remote attendee Robert Cornell!)

  • Slides from that day are available on our Presentations page here.

  • View videos of the presentations on our YouTube playlist.

The next Annual Meeting will be in Los Angeles on May 15th and 16th. To keep informed, please consider signing our mailing list here.

Updated 'curated' datasets (13 March 2017)

Updated data models

The FaceBase Hub has made a major upgrade of the underlying database schema for the Data Browser. What this means to users is that moving forward, our new data will provide far more details to help you discover data in new ways. Note that as a result, the URL schema of data records has changed and older bookmarks to datasets will no longer work.

Updated processing

The new data model requires more extensive curation of the data. To accelerate access of data to the community, we will provide access to minimally curated data sets as soon as we can after they’re submitted.

Then, after a round of careful curation, we will update the datasets on the website and change their status to ‘Curated’.

Newly curated datasets

Our first set of finely curated datasets are the ones we released last month.