The visualization dataset was sourced from work done at the Yi Lab. The data visualized used yeast 2 hybrid screens to discover the impact of mutations in genes on the associated protein by looking at its interaction profile.
The full dataset visualizes all reported interactions, and is therefore somewhat crowded due to the highly connected nature of the mutatome network. The abbreviated visualization helps with this, by only including known disease causing genes to help with the clutter. Visualization specific legends are on the visualization page, accessible above.
Integration of many more similar datasets is currently underway, please keep checking back from time to time.
Examination of individual gene summaries is key to understanding the impact of any given gene within a network. Enter a gene name below and select (if any) matches from our dataset. Hit the search button to view a generated summary.
Details
The generated report includes a summary table and an interaction visualization.
The primary gene is in the top left, PRPF3 in this case, with all of its interactors in the top row to the right. The column below the primary gene lists the Wild-Type Interaction, and all mutations available in the dataset. A green square means the interaction is not perturbed due to the given mutation, and a yellow square indicates perturbation.
The interaction visualization summarizes the same information, but with spatial information. The primary gene is visualized, and mutations are spatially indicated on it as labeled. Perturbed interactions are red dashed lines.
A unified computational toolkit integrating multiple established mutational analyses all in one place is essential to quickly and comprehensively compute possibilities for a given gene. Includes computed analyses for genes from work done at the Yi Lab, alongside other datasets. Integration of more datasets is underway, please keep checking back.
Note: The mutation database will download a summary CSV file to your computer for the gene you indicate in the search bar.
The summary CSV file/tables include integrated information from other databases, and multiple computational analyses. The name of the file corresponds to the query gene symbol(s). Explanations for each column follow.
Details (Mutations)
Interaction Type
This column details the pathology of the interaction, summarized from HGMD for each mutation of interest.
Disease
This column details any known diseases caused by a given mutation, summarized from multiple public databases.
Inheritance
The mode of inheritance was retrieved from Online Mendelian Inheritance in Man (OMIM), and UniProt. Finally, the fraction of each inheritance mode in different classes of disease mutations is calculated and a (one-sided) Chi-Squared test is performed to ensure the statistical significance of the annotation. Non Disease interactions or those that fail this test are marked N/A.
EntrezID_AlleleID
The Entrez ID for the gene of interest and the specific allele ID for a given mutation.
Mutation-RefSeq:NT
The Reference Sequence ID for any given mutation, and the specific nucleotide point mutation with its position in the sequence.
Solvent Accessibility
First, the solvent accessible surface area (SASA) was calculated using DSSP. Then, the scores are normalized and categorized into three categories - Buried (Normalized SASA < 10%), Medium (10% ≤ Normalized SASA < 42.5%) , and Exposed (Normalized SASA ≥ 42.5%).
IUPred Disorder
This is the likelihood that a given mutation is spatially located in an intrinsically disordered region of the protein product from a mutated gene, calculated using IUPred.
PolyPhen2 Score [Designation]
This is the PolyPhen2 Score, indicating the impact of any given mutation on functionality. The designations for each score were assigned accounting for the FPR thresholds obtained by using HumVar (all disease-causing mutations from UniProtKB and non-disease variants) trained PolyPhen2 models. FPR ≤ 10% are designated damaging, >10% but ≤20% are designated possibly damaging and the rest (>20%) are designated benign.
Details (Gene Fusion)
Head & Tail Gene
Genes that form the head and tail of the fusion
Head & Tail Breakpoints
Gene Fusion breakpoints
Head & Tail Chromosome
Chromosome on which Gene is known to be located, useful when using the breakpoint position for a visual alignment/annotation.
Head & Tail Strand Types
Strand type from which this particular fusion gene was identified.
Thank you for visiting our website! Our chief goal with this portal is to create a unified suite of visualization and computational tools regarding mutations & gene fusions.
This website is under active development, please don't hesitate to contact us with any questions, comments or concerns! Please direct any input about bugs, glitches or functionality to the Webmaster.
Most data is sourced from work done at the Yi Lab. Please contact Dr. Stephen Yi for more details.
Tools
IUPred
Dosztányi, Zsuzsanna. “Prediction of Protein Disorder Based on IUPred.” Protein Science, vol.
27, no. 1, Nov. 2017, pp. 331–40, https://doi.org/10.1002/pro.3334
Joosten, R. P., et al. “A Series of PDB Related Databases for Everyday Needs.” Nucleic Acids
Research, vol. 39, no. Database, Nov. 2010, pp. D411–19,
https://doi.org/10.1093/nar/gkq1105
Kabsch, Wolfgang, and Christian Sander. “Dictionary of Protein Secondary Structure: Pattern
Recognition of Hydrogen-Bonded and Geometrical Features.” Biopolymers, vol. 22, no.
12, Dec. 1983, pp. 2577–637, https://doi.org/10.1002/bip.360221211
PolyPhen-2
Adzhubei, Ivan A., et al. “A Method and Server for Predicting Damaging Missense Mutations.”
Nature Methods, vol. 7, no. 4, Apr. 2010, pp. 248–49, https://doi.org/10.1038/nmeth0410-248
Project Lead Stephen Yi, PhDDirector of Bioinformatics Faculty Member and Principal Investigator
Livestrong Cancer Institutes Dell Medical School and Oden Institute for Computational Engineering & SciencesThe University of Texas at Austin
Webmaster Aditya ShrawatThe University of Texas at Austin
Did you come here from one of the visualizations? If so you likely clicked on a tertiary node with only one interaction or on a node that corresponds to a gene not yet summarized. Try clicking on the more central nodes, they usually have associated summary info. Integration of datasets is underway, please check back from time to time for added entries. Click here to return to the visualize page.
Alternatively, if you came here from the examine/compute page you likely entered an invalid gene name. Please select one of the suggestions from the drop-down in the bar to ensure the proper gene name is sent to our database. Click here to return to the examine page, or here to return to the compute page.
If you came to this page from any other source, please contact the webmaster with details.
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