Complete exercises 1, 2 and 3 of the Pathway and Network Analysis homework. Complete instructions can be found here. Follow the steps and submit your work as a Word.doc attachment.
Please note: the DAVID software has been updated and behaves differently than the slides indicate. For the assignment, please use DAVID found at https://david.ncifcrf.gov/ (Links to an external site.).
You will also need the following files to complete the assignment:
Ex. 1: 100 Genes for Enrichr.txt
Ex. 2: 20 Genes for STRING.txt
Finally, optional – on your own: Try your hand at completing exercises 4 and 5 of the Pathway and Network Analysis.
Stomach cancer or gastric cancer is cancer developing from the lining of the stomach. The most common cause is infection by the bacteria Helicobacter pylori, which accounts for more than 60% of cases. Certain types of H. pylori have greater risks than others. Further, other common causes include eating pickled vegetables and smoking.
The integrated assignment day 1 showed how transcriptomics and also pathway analysis is used for trying to understand how a cancerous tissue has evolved from normal tissue. Another common strategy it to sequence the DNA of cancerous tissue to find out the mutations. MutSig is a mutation signal processing tool created by Broad Institute. It estimates the significance of the gene mutation rate based on abundances of the mutations, clustering of the mutations in hotspots and also conservation of the mutated positions.
The gene list for this assignment is the output from MutSig run based on Stomach Adenocarcinoma somatic mutations found in ~300 samples. It is publicly available through TCGA portal.