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Collections

 

 

Help with Collections

Collections allow the user to:

  1. Save and store  both ISH or microarray data as a collection (unique user data set) following a QUERY or BROWSE search function within the GUDMAP Expression Database
  2. Determine gene expression patterns that may either be unique between 2 data sets ie. differences or shared between 2 or more data sets ie. similarities.
  3. Download search results as text files to the user’s computer and share collection data sets/analyses with other users within GUDMAP
  4. To make a collection on the clipboard the user does not require a login. 
  5. To use the advanced collections functions the user requires a login and password which can be obtained by contacting the Editorial Office at gudmap-editors@hgu.mrc.ac.uk

1)  Making a Collection

The collection features are displayed at the bottom of each page following a QUERY or BROWSE search.

Collection Features


The add functions enables the user to place the data to the temporary collections clipboard data as;

  1. Entries set ie. data viewable by GUDMAP ID or
  2. Genes set ie. data viewable as gene strips.

GUDMAP entries or gene strips can be selected using the tick box function.  Select All / Deselect All options are also available.  The user can Add or Replace GUDMAP entries/gene strips to the temporary clipboard. 
‘View my Entries/Genes (or other selections)’ allows the user to view the temporary clipboard prior to saving it as a collection in GUDMAP (Store my Entires/Genes in database) or further editing of the clipboard. ie.  remove selected Entries/Genes etc.


Display of an Entries Data Set on Clipboard

 


Display of a Genes Data Set on Clipboard

 

Collection Options available from the ‘View my Entries/Genes (or other selections)’ option


The user can Download or Share their temporary clipboard collection.
‘View stored collections’ allows the user to view their collection lists and access the collection analysis functions.

 

2)  Collection Analysis

The user can access their collections, other public collections and the collection analysis functions from the ‘Collections’ page or from the ‘View stored collections’ function. By selecting from the ‘List of collections’ drop down menu the user is able to view their list of collections made from using GUDMAP entries, gene lists, images or probes.

 

‘Get Union’ combines the GUDMAP entry or gene data from several selected collections in to one new collection. 
‘Get Intersection’ identifies those entries or genes that may be common to several selected collections.
A comparison of two collections allows the user to identity those entries or genes that are unique to each collection and those entries or genes that are common to both selected collections.
Previously downloaded collections can be uploaded from the user’s computer for further analysis.