Body: <p>I need to analyze expression of ~ 400 genes with a certain function in the embryonic stem cells. All these genes are combined into one database with RefSeq IDs. What is a recommended workflow to quantify differential expression of these genes in RNA-Seq data of cells and visualize it?</p>
  <p>All genes for analysis concern Human E3 Ubiquitin Ligases originally located here, <a href="https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases" rel="nofollow noreferrer">hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases</a> and the updated database is here:
  <a href="https://esbl.nhlbi.nih.gov/Databases/KSBP2/Targets/Lists/E3-ligases/" rel="nofollow noreferrer">https://esbl.nhlbi.nih.gov/Databases/KSBP2/Targets/Lists/E3-ligases/</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-04T09:08:25.183Z
Comments.Text: By database do you mean a table? Your question is a bit broad.. have you tried anything so far?
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-04T09:15:16.127Z
Comments.Text: I really apologize for it being so broad because I am a very new to bioinformatics and a little bit lost. I mean all genes I need to analyze are in a database https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases/
Comments.UserDisplayName: Ina Izumi
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-04T10:21:34.073Z
Comments.Text: Hey no problem. Ok if you have 400+ genes, and expression values, you need to have them onto a count table, where rows are genes, and columns are your samples. If you can do some basic R, then try to run DESeq (https://www.nature.com/articles/nprot.2013.099) or edgeR (https://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day3/rnaSeq_DE.pdf)
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-05T07:50:13.350Z
Comments.Text: You might have a look at papers such as this one: https://www.embopress.org/doi/10.15252/msb.20188746
Comments.UserDisplayName: bli
Tags: <rna-seq><sequence-analysis><transcriptome>
Title: How to analyze expression of certain group of genes in certain types of cell?
ThreadText: # How to analyze expression of certain group of genes in certain types of cell?
  
  (Asked by: username_0 on 2019-11-04)
  
  I need to analyze expression of ~ 400 genes with a certain function in the embryonic stem cells. All these genes are combined into one database with RefSeq IDs. What is a recommended workflow to quantify differential expression of these genes in RNA-Seq data of cells and visualize it?
  
  All genes for analysis concern Human E3 Ubiquitin Ligases originally located here, [hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases](https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases) and the updated database is here:
  <https://esbl.nhlbi.nih.gov/Databases/KSBP2/Targets/Lists/E3-ligases/>
  
  **Tags:** rna-seq, sequence-analysis, transcriptome
  
  > **Comments:**
  > **username_1**: By database do you mean a table? Your question is a bit broad.. have you tried anything so far?  
  > **username_0**: I really apologize for it being so broad because I am a very new to bioinformatics and a little bit lost. I mean all genes I need to analyze are in a database https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases/  
  > **username_1**: Hey no problem. Ok if you have 400+ genes, and expression values, you need to have them onto a count table, where rows are genes, and columns are your samples. If you can do some basic R, then try to run DESeq (https://www.nature.com/articles/nprot.2013.099) or edgeR (https://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day3/rnaSeq_DE.pdf)  
  > **username_2**: You might have a look at papers such as this one: https://www.embopress.org/doi/10.15252/msb.20188746  
  
  ---
  
  ## 0 answers
  
  