Answers.Body: <p>The genes related to the environment can be identified using a linear model where each organoid is compared to the correspondent original tumor. This is assuming that the environment for all the organoids is the same and that the differences between tumors is just from different patient but are from the same organ/region.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-15T15:50:11.347Z
Answers.LastActivityDate: 2019-03-15T15:50:11.347Z
Answers.UserDisplayName: llrs
Body: <p>I have RNA-seq .bam files for 3 patients, tumour and its <strong>matched derived model</strong>, namely <strong>organoid</strong>, but I don't have any matched normal sample. </p>
  
  <p>Differentially expressed genes between a tumour and its model mainly come from the presence and lack of <strong>microenvironment</strong> in cancers and organoids respectively and response to stimuli (artificial environment in organoid culture vs cancer.</p>
  
  <p>How I can get the differentially expressed genes specific to microenvironment?</p>
  
  <p>Any intuition please?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-15T13:10:32.623Z
Comments.Text: Sauret package for unsupervised learning is a start, lots of discussion on this board about it
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-15T15:50:09.500Z
Comments.Text: I can't find a package named Sauret, if you refer to Seurat it is for scRNA-seq which this question is not tagged with it so I think it won't work well in this case.
Comments.UserDisplayName: llrs
Tags: <rna-seq><deseq2><cancer>
Title: Finding genes especific to microenvironment
ThreadText: # Finding genes especific to microenvironment
  
  (Asked by: username_0 on 2019-03-14)
  
  I have RNA-seq .bam files for 3 patients, tumour and its **matched derived model**, namely **organoid**, but I don't have any matched normal sample.
  
  Differentially expressed genes between a tumour and its model mainly come from the presence and lack of **microenvironment** in cancers and organoids respectively and response to stimuli (artificial environment in organoid culture vs cancer.
  
  How I can get the differentially expressed genes specific to microenvironment?
  
  Any intuition please?
  
  **Tags:** rna-seq, deseq2, cancer
  
  > **Comments:**
  > **username_1**: Sauret package for unsupervised learning is a start, lots of discussion on this board about it  
  > **username_2**: I can't find a package named Sauret, if you refer to Seurat it is for scRNA-seq which this question is not tagged with it so I think it won't work well in this case.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2019-03-15. Score: 1
  
  The genes related to the environment can be identified using a linear model where each organoid is compared to the correspondent original tumor. This is assuming that the environment for all the organoids is the same and that the differences between tumors is just from different patient but are from the same organ/region.
  
  
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