MeTRN Help and Documentation


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The cassava whole-genome transcriptional regulatory network (MeTRN) was built using three approaches: (1) template-based, (2) reverse engineering-based, and (3) cis-regulatory element-based methods. This database contains 4,812,519 transcriptional interactions between 33,006 protein-coding genes (covered 99.9% of all genes in the cassava genome) and 2,116 transcription factor genes. This database provide user to search on transcription regulators of interested target genes, target genes of transcription regulators, and MeTRN sub-network of interest pathways.


How to search for transcription regulators of target genes?

How to search for target genes of transcription factor?

How to search for transcription regulators related to a pathway of interest?

We divided the search results into two sessions: (i) gene information and (ii) TRN interaction information in table and network view.

Gene information:

This session show input gene information, including,

Responsive image

TRN Interaction information:

This session shows statistics of predicted MeTRN interaction of your input genes, including

For TRN regulated in pathway the table is shown

Description of terminology

Target Gene ID
A gene ID of your interested based on Phytozome database (cassava genome version 6.1)
TF Gene ID
A transcription factor gene that predicted as regulator of your interested gene (based on cassava genome version 6.1).
Inferred information using templated-based method from AtRegNet (2017).
Predicted based on reverse-engineering method of cassava under developmental stages (Li et al., 2010 and Yang et al., 2011) and Arabidopsis diurnal circle (Smith et al., 2004; Blasing et al., 2005; and Li et al. 2009).
Predicted based on cis-regulatory element analysis on xxx bp upstream of target gene via PlantPAN version 2 and PlanRegMap.
Found in tissue
Potential of gene expressed based on gene expression data of both genes, which expressed more than 25 percentiles at particular condition (Wilson et al., 2017). There are 11 tissues including leaf, shoot apical meristem (SAM), midvein, petiole, stem, lateral bud, storage root (SR), fibrous root (FR), root apical meristem (RAM), friable embryogenic callus (FEC), and organized embryogenic structures (OES).
Consistency score
Consistence Score (\(CS\)) represents consistence of predicted interactions based on evidence of 3 prediction methods, calculated from \[CS = {\sum_{i=1}^{3} M_i \over 3 } \]
\(M_i \) represents binary representation 1 if can predict by method \(i \). \(i \) represents 3 prediction approaches, template-based (\(M_1 \)), reverse engineering-based (\(M_2 \)), and cis-regulatory element-based (\(M_3 \)) methods that possible in interaction prediction.


Sriwichai N, Saithong T, Kalapanulak S (2022) MeTRN 1.0: An integrative database for reconstructing transcriptional regulatory network in cassava (Manihot esculenta crantz). Proceedings of The 13th International Conference on Application of Information Technology in Agriculture Asian-Pacific region (APFITA2022), 24-26 November 2022, Hanoi, Vietnam. [Proceeding]