In silico Transcriptome (iTranscriptome)

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

Querying the interested gene

Please input the interested gene symbol:

General information of this gene:
Gene symbol:
Gene ID:
Ensembl ID:
Gene Type:

Corn plot and FPKM of this gene:
* Values in corn plot are log10(FPKM+1) transformed
* Values in table are original FPKM.

3D profile of this gene:
Section 1 Section 2 Section 3
Section 4 Section 5 Section 6
Section 7 Section 8 Section 9
Section 10 Section 11 Coordinate

To download all 3D mapping file, please click here

How to use?

How to use the downloaded files for 3D visualization?
  • - Download the .zip file from the download link
  • - Unzip the downloaded file
  • - Download the visualization software from the VAA3D
  • - Load the unzipped figures into the software (VAA3D)
  • (For more information about how to use the VAA3D, please refer to VAA3D)

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.