inst/tutorials/GeneAnnotation.md

In juanbot/CoExpNets: Co-expression network management based on WGCNA + k-means

Introduction

Let us suppose we have a set of genes to annotate and we want to use the CoExp Web tool to do that. We are interested in seeing

• whether there are natural groups of genes wihtin the whole group

• what are these genes doing in relevant conditions for the phenotype we are studying

• what is the predominant cell type, if any, associated to those genes in such phenotype and condition

We will use as an example, the list of monogenic forms of Parkinson from the Genomics England panel App (only the green genes)

ATP13A2 ATP1A3 C19orf12 CSF1R DCTN1 DNAJC6 FBXO7 FTL GBA GCH1 GRN LRRK2 LYST MAPT OPA3 PANK2 PARK7 PINK1 PLA2G6 PRKN PRKRA RAB39B SLC30A10 SLC39A14 SLC6A3 SNCA SPG11 SPR SYNJ1 TH TUBB4A VPS13A VPS35 WDR45

First thing we have to do is to choose which are the conditions in which we want to study the genes. So in order to see what is available

juanbot/CoExpNets documentation built on May 15, 2021, 12:20 p.m.