In silico Transcriptome (iTranscriptome)

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

Querying the interested expression pattern

Select one pre-defined patterns
pattern1 pattern2 pattern3 pattern4 pattern5

pattern6 pattern7 pattern8 pattern9 pattern10
OR, input an interested pattern index in the below box (~30 seconds): ( Example Clear)
The format of the input:
  • - The format of input values must be 11x4 matrix.
  • - The values in each row must be separated by only one white space.
  • - The columes from left to right represent A, L, R, P.
  • - The rows from up to down represent 11-1 layers
  • - The minimum is recommented as 0, and the maximun as 42.
  • - Below shows the illustration for input.

Please input the cutoff for correlation analysis:

Top 10 gene with the highest corrlation to :

To download all the related data, please click here.

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.