Genome

Other software

Ingenuity

Login: There are web started version https://analysis.ingenuity.com/pa and Java applet version https://analysis.ingenuity.com/pa/login/choice.jsp.

Features:

• easily search the scientific literature/integrate diverse biological information.
• build dynamic pathway models
• quickly analyze experimental data/Functional discovery: assign function to genes
• share research and collaborate. On the other hand, IPA is web based, so it takes time for running analyses.

Start Here

Expression data -> New core analysis -> Functions/Diseases -> Network analysis
                                        Canonical pathways        |
                                              |                   |
Simple or advanced search --------------------+                   |
                                              |                   |
                                              v                   |
                                        My pathways, Lists <------+
                                              ^
                                              |
Creating a custom pathway --------------------+

Resource:

• http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures09/Pathway%20Analysis.pdf
• http://libguides.mit.edu/content.php?pid=14149&sid=843471
• http://people.mbi.ohio-state.edu/baguda/PathwayAnalysis/
• IPA 5.5 manual http://people.mbi.ohio-state.edu/baguda/PathwayAnalysis/ipa_help_manual_5.5_v1.pdf
• Help and supports
• Tutorials which includes
  • Search for genes
  • Analysis results
  • Upload and analyze example data
  • Upload and analyze your own expression data
  • Visualize connections among genes
  • Learn more special features
  • Human isoform view
  • Transcription factor analysis
  • Downstream effects analysis