diwis / bufet Goto Github PK
View Code? Open in Web Editor NEWBoosting the Unbiased Functional Enrichment Analysis
License: GNU General Public License v3.0
Boosting the Unbiased Functional Enrichment Analysis
License: GNU General Public License v3.0
Hi there,
I was using BUFET to enrich my DE miRNAs, but found there were no involved genes or miRNAs in the results. Could you help me with that?
Best,
We were trying to understand how do you calculate the Observed.Target.Gene.Overlap.Proportio by doing the operations by hand.
Let me provide a concrete term example:
This is our results:
GO.term.ID GO.term.size Observed.Target.Gene.Overlap.Proportio Mean.Random.Simulated.MicroRNA.Target.Overlap.Proportion
hsa03010~Ribosome 27 0.00276243 0.00445511
One.sided.empirical.p.value Benjamini.Hochberg.0.05.FDR
0.345034 -
This is involved-genes.txt
>hsa03010
MIR1
MIR2 GEN1,GEN2
MIR3
MIR4
MIR5
MIR6
MIR7
MIR8
MIR9
MIR10
What we are expecting is
Observed.Target.Gene.Overlap.Proportio = 2 / 27
Being 2 (GEN1,GEN2) the number of target genes and 27 the number of genes annotated in hsa03010.
But 2/27 (0.07407407) is not the reported Observed.Target.Gene.Overlap.Proportio (0.00276243).
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.