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 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

- Pearson correlation coefficient

~ 0.5

0.5 ~ 0.7

0.7 ~ 0.85

0.85 ~

- Family information Click to see more informaiton

No family information

Full family information

Pruned family information

Among 44,303 B73v5 loci, 17,921 loci don't have any significant protein domain informaion with Pfam database information.
In this case, CAFRI just shows expression of the quried locus.

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

After generating full phylogenetic tree with all genes sharing same protein domain, CAFRI simplifies the tree with quried gene and its sister nodes.
In this case, CAFRI show simplified phylogenetic heatmap of the quried gene.
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.