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

PCC highlight information

Panel information Click to see more information

No family information

No family information

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Among 27,445 Araport 11 loci, 5,845 loci don't have any significant protein domain informaion with Pfam database information.
In this case, CAFRI just shows expression of the quried locus and indicate it as gray panel.

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Full family information

Full family information

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CAFRI show phylogenetic tree consisted of all protein domain sharing genes as full tree.
In this case, CAFRI 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.

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Pruned family information

Pruned family information

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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 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.

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Document

CAFRI-Arabidopsis: An Intuitive Web-Based Functional Redundancy Inspector in Arabidopsis. doi: 10.1007/s12374-024-09421-z

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