In silico Transcriptome (iTranscriptome)

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

Usages for iTranscriptome
 
1. Pattern search by gene

For this part, users only need to input the query gene symbol (case-insensitive). After submit the query, this page will return the four parts of results: General information for this gene, Corn plot for this gene, 3D plot file and Original gene expression values.
General information displays the Gene symbol, Gene ID, Ensembl ID and Description for the query gene.
Corn plot displays the expresson pattern for query gene, one dot represent each sample. The gene expression level is represented by color gradients.
3D plot file can be downloaded from below hyperlink for 3D visualization. The user also need to download the VAA3D to perform visualization. By clicking "How to use?" can know the main steps for 3D visualization. The detailed processes are as follows:
   Open VAA3D--File--Import--Import general image series to an image stack...--(Unzip the downloaded 3D plot file and import all images)--(Click) OK (don't need to modify any value)--Visualize--3D viewer for the entire image--(Click) Alpha--(Setting) Z-thick (as x15.0)--View and rotate the 3D modal from any angles.
Original gene expression values display the FPKM (fragment per kilobase per million) for this query gene, which are calculated by Cufflinks. The values are hided by default. User can view them by clicking the Expand/Hide hyperlink beside.
 
2. Gene search by gene

This section is designed for users to search for genes whose expressions are highly correlated with a query gene(evaluated by Pearson correlation coefficient). The users need to input query gene symbol (case-insensitive) and the cutoff value of PCC. After submiting the query, this page will dispay top 10 genes with the highest correlation to query gene. To know the detailed information about these 10 genes, users only need to click the gene symbol, then a new page with detailed information of this gene will open. All satisfacttory genes can be downloaded from the hyperlink below.
 
3. Gene search by pattern

This section is designed for users to seach genes whose expreesions are similar to a certain predefined pattern. There are a total of 20 typical predefined expression patterns. This page only display 10 predefined patterns, and the other 10 patterns are hided by default. To dispaly all predefined patterns, users only need to click the More/Less>>. To perform the match, the users first need to select one pattern and then input the cutoff value for correlation (evaluated by Spearman rank correlation coefficient, RCC). After submiting the query, this page will dispay top 10 genes with the highest correlation to selected pattern. To know the detailed information about thses 10 gene, users only need to click the gene symbol, then a new page with detailed information of this gene will open. All satisfacttory genes can be downloaded from the hyperlink below.
 
4. Zipcode mapping

This section is designed for users to identify the potential regions in the reference embryo (E1) from which a query sample is derived based on the sample’s gene expression pattern. RCC are calculated between all samples in E1 and query sample based on identified zip-code genes. Users can click How to do? in Zipcode Finder page for more information. Transcriptome file with the size <1.0MB is acceptable. When the genes in the uploaded file don't contain all zip-codes genes, only overlapped genes will be used to calculate the RCC, and then a warning information will be displayed in the output page. The Zipcode Finder can process more than one samples contained in transcriptome file, but only the result of the first sample can be shown in the output page, and we recommed users to limite the numer of samples in the uploaded file (one sample is strongely recommeded). In the output page, a hyperlink is provided to download the RCC results for all samples in uploaded file. We also provide CornPlotter downloading hyperlink in the output page, which can draw the corn plots for downloaded RCC results of all query samples.