- Links for Classroom Practice -

Lecture 12 (3/13) Gene Ontology and Analysis of HTS data

A. Gene Ontology

  • Search for a biological process of interest to you in Gene Ontology . Example - programed cell death

  • Enrichment analysis .
    1. Log in via OOD, download the "deseq2_results.csv" file to your laptop.
    2. Open the file in excel, first sort small-large on the padj column, copy the list with padj,0.001 to a new sheet.name the new sheet to "Padj<0.001"
    3. Sort large-small on the LogFoldChange column. copy those with positive value to another sheet, these are the genes significantly (padj<0.001) increased in old stage whole gut.
    4. copy the gene id, past to g:profiler , select Drosophila genome and run the analysis.
    Try the list if yours did not work.

    • B. Displaying genomic dataset with UCSC browser

  • UCSC Genome Browser is a popular server for viewing genomic data -- pay attention to select the right genome release. Sign up with the service will allow you to save the analysis sessions and share the results with others. Example
  • An example of a saved session , which will persist and you can send the link to collaborators
  • An alternative to UCSC Browser is the IGB genome browser, which you can download and install on your own computer

    • C. Machine learning and bioinformatics

  • A review on AI and Science.
  • AI and Medicine a recent review .
  • Application of AI in oncology reviews 1 and 2 .

    • Links for past lectures.