phylogenetic heatmap

In the era of genome editing, one of urgently required technology in plant biology is finding out proper target which doesn't have functional redundancy. CAFRI-Rice is a simple web-based tool that help user to find proper target in genome editing with CRISPR system. It visualizes functional redundancy of quried gene as phylogenetic heatmap and pearson correlation coefficient score. Possible redundant genes are highlighted with yellow, orange, and orange-red background.

Color scale log2 expression value (Anatomy and Anatomy_expand DB)

Color scale log2 foldchange value (Abiotic, Biotic, Hormone, and Nutrient DB )

PCC highlight information

Panel information Click to see more information

No family information

No family information

×

Among 55,801 MSU7 genes, 21,140 genes don't have any significant protein domain informaion with Pfam database information.
In this case, CAFRI-Rice just show expression of the quried gene and indicate it as gray panel.

Close

Full family information

Full family information

×

CAFRI-Rice show phylogenetic tree consisted of all protein domain sharing genes as full tree.
In this case, CAFRI-Rice just show phylogenetic heatmap of the quried gene and indicate it as yellow panel.
In addition, PCC values of each genes calculated with quried gene have served at the right side of the heatmap.

Close

Pruned family information

Pruned family information

×

After generating full phylogenetic tree with all genes sharing same protein domain, CAFRI-Rice simplifies the tree with quried gene and its sister nodes.
In this case, CAFRI-Rice just show simplified phylogenetic heatmap of the quried gene and indicate it as blue panel.
Right side of the heatmap, PCC value with similar genes with quried gene have served.
Researchers can make decision about gRNA design according to its expression pattern and PCC value.

Close