What is SinCMat?

The SinCMat web interface essentially includes 3 sections: the webtool, which enables users to apply SinCMat algorithm to their specific target cell, the database which allows the users to browse all maturation TF evidences collected from the literature, and finally, an atlas section that provides maturation TFs for a series of mouse and human celltypes.

Webtool

The webtool panel provides a very intuitive interface to predict maturation TF from their own single-cell RNA-seq dataset.

How to use the webtool?

1. Go to the Webtool panel
2. Select the species of your single-cell RNA seq data: Mouse or Human
3. Submit the input file which should be the scRNA-seq data of your target celltype. This webtool accepts the input file in tab-delimited text file (.txt). The gene expression matrix must have gene symbols as rownames and cell identifiers/barcodes as colnames. User can check the example of the input file in the Webtool panel.
4. Optionally, submit your email address. You will then be notified by email when the output files are ready for download.

Output files

Final_predictions_User.tsv

This file contains the pairs of ITF/STF predicted by SinCMat. Next to each pair is indicated the related maturation score and provides the number of functional co-target genes.

Cobinding_result_User.csv

This file contains the entire set of results for all possible combinations ITF/STF. For each combination are indicated the Jaccard index score, the number of common target genes, the sum of Pearson correlation scores and the maturation score.

Database

The database section allows user to browse literature evidences of maturation TFs collected, classified by systems. The search area enables users to search in the database based on the TFs, celltypes, species and types of experiment (of note, “up-regulated” TFs correspond to overexpressed and/or activated TFs). To retrieve the original article of a given evidence, users can click on the URL link or search with the Pubmed ID.

To achieve the batch download of the whole database, users can go to the Download section.

Atlas

The atlas section allows users to browse predicted maturation TFs for a series of celltypes in mouse (Mouse Cell Atlas) and human (Tabula Sapiens).

On the left part of the panel, users can select a celltype of interest. The results are displayed as a table on the right part of the panel. The 2 first columns represent the 5 predicted pairs of ITF/STF. The 2 next columns indicate the users if the TFs predicted were already experimentally validated (see Database section).

To achieve the batch download of the predictions for the MCA or TS, users can go to the Download section.

Terms and conditions

For more information, please refer to our Terms and Conditions at the following link: Terms and conditions