Frequently Asked Questions
How do I .....?
Contents of the database
General Background and Theory (biological and technical)
Q. What is the HUDSEN database?
A. The HUDSEN human gene expression spatial database is a collaboration between the Institute of Human Genetics in Newcastle, UK, and the MRC Human Genetics Unit in Edinburgh, UK, and was developed as part of the Electronic Atlas of the Developing Human Brain (EADHB) project (funded by the NIH Human Brain Project). The database is based on the Edinburgh Mouse Atlas gene expression database (EMAGE), and is designed to be an openly available resource to the research community holding gene expression patterns during early human development.
The HUDSEN Database is built on a framework containing two parts. The first is a set of standard 3D virtual models at different stages of development from CS12 to CS23, in which various anatomical regions have been defined. Experimental data is captured and converted to digital format and then mapped to the appropriate 3D model. The second is a set of anatomical terms at various stages of development (known as an ontology). This ontology is used to define sites of gene expression using a set of standard descriptions and to link the expression data to an 'anatomical tree'. The anatomy ontology currently being used is based on the Edinburgh Human Developmental Anatomy Database which encompasses all developing structures from CS1 to CS20 but is not detailed for developing brain structures. The ontology is being extended and refined (by Prof Luis Puelles, University of Murcia,Spain) and will be incorporated into the HUDSEN database as it is developed.
Q. How do I perform a search of the HUDSEN database?
A. There are currently two main ways to search HUDSEN - using a gene/protein name or a named anatomical structure as the query term. The entire contents of the database can be browsed using the data browser. We have made some short demo movies showing how to search.
Q. How do I save the results from a search?
Q. How do I submit data to the HUDSEN database?
A. Results from in situ hybridisation or immunocytochemistry can be emailed to this address. More information about the data submission process can be found here.
Q. What types of expression data are found in HUDSEN?
A. HUDSEN contains in situ gene/protein expression data, assayed using in situ hybridisation (ISH) or immunohistochemistry (IHC). The HUDSEN database contains data from stages CS12 (approx 26 dpc) to CS23 (approx 56 dpc).
Q. Who enters the data into HUDSEN?
A. Data is entered into HUDSEN by full-time HUDSEN curators who make entries based on information supplied by the data submitter. HUDSEN curators assess such entries for consistency and accuracy before adding to the public database.
Q. What constitutes one HUDSEN entry?
A. One HUDSEN entry = one specimen stained for the expression of one gene/protein at one point in embryonic development. Associated with each entry are details of the detection reagent, the specimen, sites of expression (denoted by both text annotation and spatial annotation), the names and details of the data submitter/source, related publications and relevant links to the same gene in external databases.
Q. How is expression data annotated in HUDSEN?
A. Expression data is annotated using two methods to denote sites of expression in the embryo: spatial annotation and text annotation. Additionally, many aspects of the detection reagent and specimen are also annotated during this process (assignment of IDs, nucleotide sequences for probes etc). Further information on the curation process.
Q. What is a Carnegie Stage and how does it relate to dpc values?
A. A Carnegie Stage is a stage of human embryo development based on the external and/or internal morphological development of the embryo, that is not directly dependent on either age or size. The human embryonic period proper is divided into 23 Carnegie stages. Criteria beyond morphological features include age in days, number of somites present, and embryonic length. Named after the Carnegie Institution, Washington DC, where collecting and classifying of human embryos began in the early 1900s.
Comparisons of Human and Mouse Development
|Carnegie Stage||Post-ovulatory Days||Size (mm) Greatest Length||Theiler Stage||Days post conception||Size (mm) Crown-rump|
|11||24||2.5 - 4.5||14||9 - 9.5||2.1|
|12||26||3 - 5||15||9.5 - 10.25||2.5|
|13||28||4 - 6||16||10.25 - 10.5||3.6|
|14||32||5 - 7||17||10.5||4.1|
|15||33||7 - 9||18||11||4.6|
|16||37||8 - 11||19||11.5||6 - 7|
|17||41||11 - 14||20||12||7|
|18||44||13 - 17||21||12.5 - 13||8.2|
|19||47.5||16 - 18||21||12.5 - 13||8.2|
|20||50.5||18 - 22||22||13.5 - 14||9.1|
|21||52||22 - 24||22||13.5 - 14||9.1|
|22||54||23 - 28||22||13.5 - 14||9.1|
|23||56.5||27 - 31||22||13.5 - 14||9.1|
|26||17.5 - 18||17.8|
(nb figures are approximations, as are the equivalences)
*Adapted from Kaufman MH (1992) The Atlas of Mouse Development. Academic Press, London.
More information about Carnegie staging is available from the http://embryology.med.unsw.edu.au/wwwhuman/Stages/Allst.htm
Q. How does the LOSSST algorithm work?
A. Briefly, by comparing shape similarities between all the spatial annotation patterns in the database to your query region, calculating a value of spatial similarity, and then ranking the results. Detailed explanation.