CORN Help

This Web page offers a matching tool for discovering potential treatment and transcriptional regulatory mechanisms, and displays information of condition-based (natural compound/small molecule/drug treatments and gene perturbations) transcriptional regulatory sub-networks (TRSNs) that constructed from ChIP-X data and transcriptomic changes data after specific conditional treatment in cells. Users are able to identify the closest complimentary TRSNs with a set of input Differentially Expressed Genes (DEGs) or search and browse TRSNs by inputting the condition, target gene, or transcription factor.

Tool

Conditional Match

Conditional Match

Two steps are required to carry out an online conditional match:

Select TRSN collection

1. Select TRSN collection

You can choose "ALL TRSNs" or TRSN collection of interest (categorized by condition or disease) as a matching reference. For example, if you want to explore potential natural compounds, choose "Categorized by conditions" → "TRSNs of natural compounds". Similarly, if you Choose "Categorized by diseases" → "TRSNs of breast cancer cell lines", matching will only be conducted within TRSNs from breast cancer cell line.

2. Input differentially expressed profile

We provide sample data related to Applications or you can input differentially expressed profile of interest (a list of differentially expressed genes (DEGs) and corresponding level of alterations in terms of log2 fold change). For example, the gene expression alterations between normal and cancer tissue.

3. Processing

Click "Match" and the task will run for a few minutes. The page will update automatically when completed. Do not close this page or you may save the result link provided.

Processing

4. Results

The matching result will show 10 possible potential networks which have been matched. Here the "score" is used to reflect the contribution of different TRSNs fitting into the inputted transcriptomic changes. The larger the magnitude of the resulted score would represent a closer resemblance between the TRSN and the differential expression profile.

A negative score would represent the regulatory direction of the inputted (DEGs) that were in tune with the regulatory direction of the reference TRSN. If researchers possess a set of DEGs induced by an unknown cause, exploring matching TRSNs with negative scores would be useful.

As for positive scores, they represent the inputted DEGs were in the counter regulatory direction to the matched TRSN. Searching condition-oriented TRSNs with positive scores would be helpful for researchers who are seeking conditions/drugs with the therapeutic potential for counteracting the expression changes induced by a pathological state.

Example: CORN RESULT (1. "Categorized by diseases" → "TRSNs of breast cancer cell lines" 2. "Use sample data" → "Breast cancer clinical samples vs normal samples (TCGA-BRCA)")

Results

5. Detailed page of TRSN

Click the Network ID (e.g., CN314), and then a detailed page describing the TRSN would be shown. Information below includes:

Information about the corresponding condition will be specified, such as the type of condition/chemical used (compound/ligand/shRNA/overexpression/CRISPR, etc.), the chemical/small molecule name, the chemical structure, molecular formula, molecular weight, simplified molecular-input line-entry system (smiles), clinical phase.

6. Matching Tool Source Code Download

If you wish to conduct regulatory sub-network to transcriptomic alteration matching in a local server, please follow the commands using the data and scripts downloaded from https://qinlab.sysu.edu.cn/corn/home/download_page

Search or Browse

Search by Condition

Users can search TRSNs by selecting "condition name", "condition dose", "Condition Time", "Cell Line". The options are multi-select and allow blank (i.e., all-select).

Search by Target Gene

Users can search TRSNs that include certain target genes. "Target gene" is mandatory.

Search by Transcription Factor

Users can search TRSNs that regulated by certain transcription factor.

Browse

Users can browse the data based on the following filters: "Condition categories", "Tissue location", "Cell line".