StCoExpNet : Solanum tuberosum Co-expression Network

Welcome to StCoExpNet
a platform dedicated to the visualization and analysis of co-expression and co-function networks in potatoes.

Potato (Solanum tuberosum L.) is one of the most important crops with a worldwide production of 370 million metric tons. The remarkable rise in potato transcriptome studies over the years generated an enormous amount of RNA-seq data, encompassing various tissues, environmental conditions and genotypes.

In this study, we have collected data from 2636 publicly available potato RNA-Seq samples, processed the raw sequencing reads and mapped them to the potato reference genome (dAg), assembled transcripts, quantified expression, constructed a rank-based co-expression matrix and identified co-expression clusters in a systematic fashion.

The dataset compiled here constitutes a new community resource, which can be used to investigate the expression and co-expression of potato genes of interest or downloaded. This comprehensive transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research. Click here for the workflow used in this study.

Quickly search the database for a gene or a function of interest:

Features available at StCoExpNet database

Quickly retrieve genes

Use our Search function to quickly find genes of interest.

Expression profiles and expression specificity

See in which tissues and conditions a gene of interest is expressed or find genes specifically expressed in a certain tissue/condition.

Co-expression networks

Browse co-expression networks based on thousands of publicly available RNA-Seq samples! Find clusters of co-expressed genes enriched for certain functions.

Co-expression clusters

Browse co-expression networks based on thousands of publicly available RNA-Seq samples! Find cluster of co-expressed genes enriched for certain functions.

Analyse custom gene sets

Create heatmap and expression profiles for user defined sets of genes. Build a custom co-expression network for a set of selected genes.

Cite Us:

Venkata Suresh Bonthala and Benjamin Stich. (2024) StCoExpNet: A global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes (Submitted).