GenomePlot

Manual

FuzFinder : Gene Fusion Events Detection Tool

1. Introduction

FuzFinder uses PCDB to identify plausible gene fusion events among a set of submitted genomes. The criteria for finding a putative gene fusion event are based on a mutual best hit as follows;

Fig 1. Nucleic Acids Research, 2004, Vol. 32, Database issue D273~D276

Each of the two reference genes must match the same ORF in the target genome with the higher Z-scores than a given value.
When split between the two hits, the two halves of the target ORF must match back to the original two reference genes with the higher Z-score than a given value
The reference genes must not be homologous to each other.

GeneFuz needs more improvement at this stage. Currently the overlap between two putative gene fusion components on a target gene is not considered, but 10% of the size of the smaller of the two target genes seems to be a reasonable overlap cutoff

2. How to Use

Fig 2. Service Request Form

FuzFinder starts with a simple service request form. A user need to submit cut-off value (Z-score), a query genome, and reference genome(s). A query genome can be chosen from full-down menu and multiple reference genomes can also be selected by checking checkboxes. Default Z-score is 500 and default reference genome is Echerichia coli K-12.

When all fields are selected, click the SUBMIT button.

Fig 3. Gene Fusion Search Result

This result page shows a list of detected gene fusion events. The first column is fusion protein, the second and third are fused proteins. Each proteins (gi numbers) are linked to NCBI's EntRez Protein Information site (Fig 4).

Fig 4. NCBI's Protein Information

The following colums indicate Z-score, E-value, SW-score, Percent Identity, SW overlap, (Start,End) location for the first fused protein, and (Start,End) location for the second fused protein.

Fig 5. Graphical Representation of Gene Fusion Event

Graphical Respresentation is also provides from the search researt page (Fig 2). When you click "Click to generate graphical representation" link, a new page is generate to show a list of fusion proteins. Then just click one of them. Orange stands for fusion protein and other colors represent fused proteins. Each number means the location of matched area (domain).

Then, just try to click a colored block.

Fig 6. NCBI's CDD Reference

Each protein is linked to NCBI's CDD database. This database provides well-known domain information of a given protein. You may test FuzFinder's capability by comparing CDD database with FuzFinder's search researts.

Kwangmin Choi @ School of Informatics, Indiana University, Bloomington, IN, USA
Last Updated on 8/1/2004