QuickStartGuide
This page demonstrates an example use of ChiBE. For detailed description of ChiBE features please refer to the User Guide.
Open ChiBE and go "Query --> Pathway Commons (Level 3) --> Paths From To ...". Search for paths from AR to TP53 with length limit 3.
You will get the following path.
Load profiling data of TCGA prostate cancer study from cBioPortal by going "Data --> Fetch from cBio Portal ...".
Node colors are updated with the alteration frequencies.
Alteration frequencies are also displayed in the tooltip text. TP53 is altered in 11% of the loaded cases. The details of the alteration data can be reached through the right-click menu of the nodes.
Below window displays the types of the loaded alterations and alteration ratios for each type.
TP53 is lost in 4 cases and mutated in 5 cases.
Let's check if any protein here is differentially expressed between primary prostate samples and metastatic samples. Such an experiment exists in GEO database with ID GSE3325.
Go to "Data --> Fetch From GEO ...".
By default, ChiBE uses the comparison of the first two experiments in the loaded dataset. To compare primary tumors with metastatic, go to "Data --> Data Selection ...", and select to compare related samples.
First group is the primary tumors and the second is the metastatic ones in the dataset. Node colors are updated accordingly.
So we see that metastatic tumors have higher expression of AR, MAPK11, GNG2, GNAI2, and lower expression for TP53 and GNAI1, in that particular dataset.