The goal of the exercise is to show you how to query the UniGene and TIGR Gene Index databases.

UniGene

Go to the UniGene web page.

Go to the Bos taurus (cow) gene index.
  • How many clusters have been build for cow?
  • How many sequences have been used to build the clusters?
  • Why mRNAs sequences are present in the clusters?
Go to the UniGene Library Browser.

Select the "Library for" pull-down menu to Bos taurus and the "minimum sequences" text box to 50.
  • Which is the total number of libraries from the mammary gland tissue?
  • How many libraries from the mammary gland tissue are not shown because they have fewer than 50 sequences?
  • Which is the ID of the library having the great number of sequences?
Have a look to the library Lib.18991.
  • How many cluster do you get?
  • How many sequences contains the 'Lib.18991'?
Have a look in details to cluster Bt.61865 (don't hesitate to click around, there is a lot of information around!)
  • On which chromosome this cluster lies?
  • How many mRNAs are integrated in the cluster? How many ESTs?
You can also browse the different EST libraries by typing a keyword in the Bos taurus Gene Index home page. You can find here the general rules for properly serching UniGene clusters.
  • Try the keyword "casein alpha" and search in the restriction field [TEXT].
    Query string: "Bos taurus"[ORGN] AND "casein alpha"[TEXT]
    How many clusters do you get?
  • How many mRNAs are integrated in the first cluster? How many ESTs?
Digital Differential Display (DDD) allow you to do in silico differential gene expression analysis. See the Digital Differential Display Guide to know more about DDD.
  • Follow the DDD link from the Bos taurus Gene Index home page.
  • Choose library 20419 FLM [mammary gland] and then press the CONTINUE button to create PULL A
  • Choose library19023 BMUA [mastitic mammary] and then press the CONTINUE button to create PULL B
  • Look at the differentially expressed genes between these libraries.


TIGR Gene Indeces

Enter the TIGR Gene Indeces web page.
  • Enter the Cattle Gene Index
  • How many TC sequences are present in the last database release?How many singleton ESTs
  • Why Bos taurus ET are present?
  • Follow the Identifiers or Keywords link to search the gene index by keyword.
    Use the keyword "casein alpha".
  • Look in more details the report for TC354595
  • How many ESTs are assembled to generate the TC?
  • How many are 5' ESTs?
  • Follow the Libraries link to search the gene index by library.
    Use the keyword "mastitic mammary".
  • How many libraries do you retrieve? Please indicate the number of unique transcripts (TCs + singletons) per library
Look at the Functional Classification based on the Gene Ontology Assignments. All TIGR Gene Indeces are classified using the Gene Ontology vocabulary.