WGCNA on TCGA case-control

I want to conduct Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-Seq data from TCGA-PRAD. I am comparing it with control data from GTEx. Can I perform the WGCNA only on "primary tumor" samples? or should I include the control also?

tcga-prad wgcna tcga

• 604 views • link

written 2.7 years ago by Maliha •

0 answers

No answers yet.

More posts like this

Can PC1 (eigengenes) from different gene sets be compared in WGCNA/hdWGCNA?
written 4 months ago by Shriyansh •

Hi all, My colleague and I are working with bulk RNA-seq (and some single-cell data using hdWGCNA) and constructing co-expression modules. For each module, I …
Why does WGCNA use weighted correlation instead of Pearson correlation?
written 2.2 years ago by remagen •

I am a beginner in bioinformatics, currently learning about Weighted Gene Co-expression Network Analysis (WGCNA). I understand that WGCNA is a powerful method for constructing …
How to download RNAseq data of only male KIRC patients?
written 2.4 years ago by bioinfo_enthusiast •

Hello everyone. I am want to perform WGCNA analysis of only male Kidney Clear Cell Carcinoma (KIRC) patients. I am trying to download trancriptome data …
Problems encountered during the survival analysis with TCGA data
written 2.9 years ago by applepie •

Hello Everyone, recently I have been conducting the survival analysis of liver cancer patients expressing CD47, using the TCGA data. The project in this case …
TCGA: How to detect normal and tumor samples in PRAD dataset?
written 5.5 years ago by carolgalah •

I did the downloaded DNA methylation - Illumina Human Methylation 450 dataset (GDC TCGA Prostate Cancer (PRAD)) using https://gdc.xenahubs.net. I want to methylation analysis correlation …
How can I use WGCNA for constructing a co-expression network using TCGA project?
written 5.6 years ago by akhoundi.fatemeh68 •

Hi. I downloaded the level 3 mRNA expression data TCGA-CESC project as expression estimates per gene from the GDC data portal with the TCGAbiolinks package. …
Find top genes that correlate with my gene of interest using WGCNA
written 6.1 years ago by StartR •

HI I want to know how to use WGCNA package to find gene expression networks related to your gene of interest. For example, If I …
Negative scale free topology index WGCNA
written 6.2 years ago by gabriella.wangyi1986 •

Hi, I'm try to do weighted gene co-expression network with WGCNA. I have 13 mouse samples, one condition, I know it's not ideal to perform …
WGCNA analysis in normal and tumor case
written 7.9 years ago by shivangi.agarwal800

Hi I want to perform WGCNA analysis, i am having RNA seq data (gene expression) in normal and tumor cases. I want to compare between …
How to construct Co-expression network between Coding and lncRNAs?
written 8.0 years ago by Biologist

Hi, I have RNA-seq data. I performed differential analysis between Tumor and Normal samples for coding and lncRNAs separately. I have 1300 differentially expressed coding …