Class 2
Lab session 1
I. Browsing the NCBI and Entrez
Task1:
1. Open the site http://www.ncbi.nlm.nih.gov/.
[Google search: type NCBI and you will get the site, no need to memorize the url]
2. Left site bar give you the list of resource.
3. In All Database choice search area type Kibra and press the search button.
4. Under Literature topics click PubMed
5. Choose any item from the upper part and see the changes by choosing the options.
6. Click the first journals available.
7. Authors name is hyperlinked, if you click any authors name authors all available
publication will be listed and viewed to you.
8. Clicking in Advanced just beneath the upper button will give you a advance search you
can use AND, OR, and NOT button construct a logic for your approach (the default is AND).
II. GENE NAME EVOLUTION
Task 2: Search by gene name:
1. Search pubmed with the gene name Kibra . You will find 96 items.(_____)
2. Search pubmed with the official gene symbol WWC1. Items 70. (________)
Which one is better to search?
3. Search as Kibra OR WWC1, Item no. 104. Suggest to use both the name.
Reason: There are thousands of laboratories around the world and many laboratories make
the same discoveries and publish their names for the same gene, some times same laboratory
might have different names as the research progress.
Task 3: Finding gene synonyms:
1. URL: www.ihop-net.org
2. Type Kibra in first search button and search
3. Clicking the left icon of Homo sapiens we get the information of the WWC1.
4. Find the synonyms of Kibra gene.
5. Below these links are actual sentence taken from publication.
6. MeSH terms and other gene names in these sentences are hyperlinked.
III. OMIM
Task 4: Searching OMIM
1. NCBI home page you can choose dropdown buttons and choose OMIM.
2. Search with WWC1
3. Click 610533
IV. RETRIEVING NUCLEOTIDE SEQUENCES
Task 5: Searching nucleotide sequences
1. Open the NCBI home page
2. Drop down button choose NUCLEOTIDE
Class 2
Lab session 1
3. In search type KIBRA AND SAPIENS (163)
V. GENE ONTOLOGY
Task 6: Exploring gene ontology
1. URL: www. geneontology.org
2. Type Kibra in Search Go data (Upper Left of the screen)
3. Click in Gene and Gene products.
4. Click WWC1
5. And explore the site and filtering unit.
VI. THE GENE DATABASE
Task 7: Searching gene database in NCBI
1. Open the NCBI home page and dropdown choose Gene
2. Click WWC1
2. Get the idea of the reports from the book text.
VII. UniGene
1. Open NCBI and from the Resource all find the UniGene
2. Click UniGene
3. Click in UniGene Statistics
4. Find the homo sapiens UniGene Number.
5. Click in the UniGene (Uper left --> Home page of UniGene come back)
6. Type Kibra in search button
7. Select the homo sapiens one with WWC1
8. Click in EST show all sequences
9. Find DA228505.1 and click it
10. Click dbEST 18318. unigene EST information AND click in DA228505.1 sequence information
VIII. UniGene Library Browser
1. From the UniGene base click UniGene
2. Click library browser
3. Find the brain list