In silico Transcriptome (iTranscriptome)

Geo-sequencing: 3D Transcriptome of mouse embryo at gastrulation

Please Uploading your transcriptome file  

How to process?
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  • - The format of data in the file must be the same to the following matrix:
  • - We strongly reconmend the genes in the uploaded file contains all zip-code genes. The zip-code gene list can be found here.
  • - The page will only display the correaltion results of the first sample in the uploaded file. Users can download all correlation results from the hyperlinks below the table.
  • - User can download our CornPlotter script to draw the corn plot of correaltion for all samples in the uploaded file.
  • - Below shows the correlaton distribution between reference embryo (E1) and other two embryos (E2/E3), top 10% RCC value are highlighted by res dashed lines.


 
 
 
 
 
 
 
 
 
 
 
 
The correlations between all samples in reference embryo and based on zip-code genes:

To download all correlation data in text, please click here.

To visualize correlation data in corn plots by yourself, please download the CornPlotter, which is coded in Matlab.

Key features

  • - High resolution
  • - 2D & 3D visualization

 

  • - More sensitive
  • - Searchable web service

Accessing iTranscriptome

Pattern search by gene
Querying and displaying the expression pattern of a query gene in either a corn plot or a 3D embryo model
Gene search by gene
Searching for genes that share similar expression patterns of a query gene.
Gene search by pattern
Searching for genes using a query pattern (There are 20 predefined patterns).
Zipcode Mapping
Identifying potential regions in the reference embryo from which a sample is derived based on sample’s transcriptome data.