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Browse Help


focusgroups

Focus by Organ/System

By using the anatomical focus groups, listed on the right-hand side on the GUDMAP gene expression homepage, users can browse within a broad subset of the anatomy.

Simply click on the focus group you want to use and this should be displayed at the top of the homepage:

All results returned from a browse will be restricted to this subset.

homepage_focus


Making Next Gen data accessible through the GUDMAP website is a work in progress. The help described here indicates how users will be able to browse this data when it has become available. Some or all aspects of it may not be visible or fully functional yet (May 2014).

Browsing next gen data


Browsing Next Gen data by series

Clicking on Browse > Next Gen > Next Gen Series from the GUDMAP gene expression page gives a list of all Next Gen series that are available. Clicking on the name of a series (e.g. ) will access the series page where a full description is given, along with a list of the individual samples (entries) available. Individual samples can then be accessed by clicking on the GUDMAP sample ID (e.g. ).

Clicking on a GEO ID (e.g. ) links out to the series entry on the GEO (Gene Expression Omnibus) website.


Browsing Next Gen data by sample

Clicking on Browse > Next Gen > Sample from the GUDMAP gene expression page gives a list of all the Next Gen samples (entries) available. Samples are accessed by clicking on the relevant ID number in the 'GUDMAP Entry Details' column (e.g. )




Browsing microarray data


Browsing microarray data by series

Clicking on Browse > Array > Series from the GUDMAP gene expression page gives a list of all microarray series that are available. Clicking on the name of a series (e.g. Gene expression in whole ovary at gd 11, 12, 14, 16, 18 and pnd2) will access the series page where a full description is given, along with a list of the individual samples (entries) available. Individual samples can then be accessed by clicking on the GUDMAP sample ID (e.g. GUDMAP:2217).

Clicking on a GEO ID (e.g. GSM120839) links out to the series entry on the GEO (Gene Expression Omnibus) website. The Platform column gives the GEO platform ID, clicking on it links out to the platform entry on the GEO website.


Browsing microarray data by sample

Clicking on Browse > Array > Sample from the GUDMAP gene expression page gives a list of all the microarray samples (entries) available. Samples are accessed by clicking on the relevant ID number in the 'GUDMAP Entry Details' column (e.g. GUDMAP:2217)


Browsing microarray data by platform

Clicking on Browse > Array > Platform from the GUDMAP gene expression page gives a list of all the different microarray platforms used, alongside the number of microarray series conducted on each platform. Clicking on the ID in the GEO ID column will ink out to the platform entry on the GEO website.



Browsing by Theiler stage


Browsing by Theiler stage

Clicking on Browse > Theiler stage from the GUDMAP gene expression page gives a list of all the GUDMAP entries by Theiler stage (TS), from TS17 to TS28. The corresponding age range to each Theiler stage is indicated in the alternate staging column. The user can then choose In situ data or microarray data of the Theiler stage of interest.


Browsing by gene


Browsing by gene

The GUDMAP database can be browsed by gene names in alphabetic order. For each gene, ISH data are listed for present, not detected or uncertain in situ expressions. The numbers of ISH for each category is indicated. Clicking on this number links to the corresponding GUDMAP entries.



Browsing ISH & IHC data



Browsing In-Situ Hydridisation (ISH) and Immunohistochemistry (IHC) Data

There are three options for browsing the In-Situ data in the GUDMAP database :

 


Browsing transgenics


Browsing Transgenics

Browse the GUDMAP database for the mouse strains that have been generated to genetically mark and manipulate particular cell types.