Answers.Body: <p>I familiar with the inflammatory bowel disease  which is quite complicated: 
  It affects multiple sites and depending on when it appears it is different. So you can look at the GEO for microarrays and RNA-seq data of this disease and I'm sure you'll find datasets from the same patients from several tissues or time. </p>
  
  <p>In this disease there is a <a href="https://ibdmdb.org/" rel="nofollow noreferrer">multi'omics project</a> that fits your needs. You can find (and download) data of high dimensionality: there are samples for the same time, tissue (but different locations), gene, over a period of time and for several omics (not only expression data).<br>
  The only problem is that there are some mistakes on the metadata. </p>
  
  <p>However, I don't think they are usually described as 3rd order tensors and I doubt you'll find enough data to train a machine learning method. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-22T14:13:46.360Z
Answers.LastActivityDate: 2018-06-22T14:13:46.360Z
Answers.UserDisplayName: llrs
Body: <p>I need good sources of gene expression data in the form of 3rd order tensors. Typically the commonly available datasets are in the form of a matrix, for instance, $sample \times gene$ or $gene \times time$. I need good sources for 3-dimensional data, for example $gene \times sample \times tissue$ or $gene \times sample \times time$ ... etc.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-22T07:33:17.683Z
Comments.Text: Analysis packages rarely use that format for analysis, so find a nice time course dataset (there won't be many matching your needs) and reshape the matrix for it into the correct dimensions. As a aside, it's rarely useful to refer to a 3D matrix or 3 factor experiment as a "3rd order tensor" outside of machine learning.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-22T07:58:59.623Z
Comments.Text: I am working on tensor decomposition. I am interested in testing an idea on gene expression 3-d dataset. The papers who have worked on such gene expression dataset haven't made their data public. So...
Comments.UserDisplayName: Satwik
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-22T14:10:08.700Z
Comments.Text: @Satwik, you can ask them for the data and do a collaboration (if they and you wish).
Comments.UserDisplayName: llrs
Tags: <rna-seq><public-databases><microarray>
Title: What are some good sources of 3rd order gene expression data
ThreadText: # What are some good sources of 3rd order gene expression data
  
  (Asked by: username_0 on 2018-06-22)
  
  I need good sources of gene expression data in the form of 3rd order tensors. Typically the commonly available datasets are in the form of a matrix, for instance, $sample \times gene$ or $gene \times time$. I need good sources for 3-dimensional data, for example $gene \times sample \times tissue$ or $gene \times sample \times time$ ... etc.
  
  **Tags:** rna-seq, public-databases, microarray
  
  > **Comments:**
  > **username_1**: Analysis packages rarely use that format for analysis, so find a nice time course dataset (there won't be many matching your needs) and reshape the matrix for it into the correct dimensions. As a aside, it's rarely useful to refer to a 3D matrix or 3 factor experiment as a "3rd order tensor" outside of machine learning.  
  > **username_0**: I am working on tensor decomposition. I am interested in testing an idea on gene expression 3-d dataset. The papers who have worked on such gene expression dataset haven't made their data public. So...  
  > **username_2**: @username_0, you can ask them for the data and do a collaboration (if they and you wish).  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2018-06-22. Score: 1
  
  I familiar with the inflammatory bowel disease which is quite complicated:
  It affects multiple sites and depending on when it appears it is different. So you can look at the GEO for microarrays and RNA-seq data of this disease and I'm sure you'll find datasets from the same patients from several tissues or time.
  
  In this disease there is a [multi'omics project](https://ibdmdb.org/) that fits your needs. You can find (and download) data of high dimensionality: there are samples for the same time, tissue (but different locations), gene, over a period of time and for several omics (not only expression data).  
  The only problem is that there are some mistakes on the metadata.
  
  However, I don't think they are usually described as 3rd order tensors and I doubt you'll find enough data to train a machine learning method.
  
  
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