Niu-lab & ChosenMed

HotSpot3D provides you with a high-performance runtime environment, you only need to upload files to analysize mutations in protein 3D structures. Two functions included:

• Upload files (upload maf files or paste less than 1000 lines of data)
• Complex visualization result
  

• HotSpot3D software supports MAF format files, including 11 names of gene names, chromosomes, start and end positions of mutations, variant types, reference alleles, tumor sample barcodes, transcriptome names, and amino acid changes.
• See the detailed Format Description

Yes, the current version of HotSpot3D requires that you must include the 11 columns of data in the input file.

• The first nine columns of data formats must be strict with the naming requirements for HOTSPOT3D column names.
• The names of the last two columns are non-standard and can be modified as appropriate. But we recommend adhering to the naming rules.

You can click here to see how our pre-prepared demo file works.

Demo data is the pattern file we have prepared for you, in order to show you the effect of HotSpot3D. This file is small and your own file runs will produce a larger result set.

• If you see following message on the page, your file has been uploaded successfully.
  
• We use a high performance computing cluster to process your calculation files, but you still need to wait patiently. You can refresh the page to keep checking the status of the job until you see the icon below:
  COMPLETED
  

• WAITING FOR PROCESSING
  Your job is waiting to be processed, please press F5 to refresh
• INVALID ResultId
  The submitted job has been more than 24 hours and the resultID is invalid.
• EXECUTE ERROR
  Execution error, please contact us (see contact information).
• COMPLETED
  Task has been completed.
• PROCESSING
  Your job is running, please press F5 to refresh.
• ResultId ERROR
  The resultID you entered is incorrect.
• NET ERROR
  Please check your network.

After running, HotSpot3D will present a three-dimensional structure of the protein. You can display specific clustering results on the PDB structure.

You can select the protein structure by clicking on the drop down list.(Try)

After selection, the visualization interface will automatically load the newly selected protein structure.

We used protein structure data from RSCB PDB.

The picture shows the visualization window we provide (Try):



We use the 3D structure plugin provided by 3Dmol, which provides powerful visualization capabilities.
You can place your mouse on the structure to rotate the angle and zoom in and out.

• Style: The overall structural style of the protein structure, including cartoon, line, stick, sphere, cross.
• Color: The color of each chain of the protein structure, the default is the spectrum.
• BackgroundColor: visible window background color.
• Surface-opticity, Suface-color: transparency and color of the entire protein sueface, surface-opticity=0 means no surface.

Click on the Label of the cluster you are going to project, then you can see this cluster on the protein structure.(Try)

The PDB structure you choose may not correspond to the cluster. This clustering result is based on other protein structures.

• When multiple clusters appear in the results, different clusters are displayed with different colors.
• ou can click on "Label" to add a label to each cluster to distinguish(Try):
  
  

The re-visualization function can be implemented by uploading summary and pairwise files, both of which come from the results of running with HOTSPOT3D software.

You have two ways to get these two files:

1. Click the download button on the results display page as shown:


2. HotSpot3D will provide you with the summary and pairwise files as attachments after the end of the run, which requires you to fill in your email before uploading the file to run the software.(RUNNING).As shown below:
   
   

HotSpot3D will save the results of your submitted assignments for 24 hours

24 hours after the submission of the job, you can use this feature whenever you are connected to the Internet.

We applied Hotspot3D to TCGA to >4,400 TCGA tumors across 19 cancer types including BLCA, BRCA, CESC and so on. We directly provide results and visualization of clustering data on mutations here . For detailed results and analysis, please refer to the paper:

Protein-structure-guided discovery of functional mutations across 19 cancer types; Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L;Nature Genetics volume 48, pages 827?837 (2016)

• Query which are proximity pairwise mutations between two genes.
  
  
  


• Query which are proximity pairwise mutations in one gene.
  
  
  


• Query which mutations of this gene are close to.Allows users to set the protein type, max P-value and distance.
  
  
  


• Perform the above searches based on the type of cancer.
  
  
  

• Mutation1 and mutation2 represent proximity mutation pairs.
  
• White columns: information about protein structures of mutation pair, including protein structure id and distance between two mutations (sdis).
  
• Green and Orange columns: information about gene names, amino acid changes (aac), mutation types, and chain of mutation.

Click on a row in the query results, the page will automatically load and link to visual panel.

• Basic information of the protein structure based on the visualization results (as shown below), including cancer type, protein ID, three-dimensional distance and one-dimensional distance
  
  
  
• Proximity pairs include mutation1 and mutation2, as well as visualizations. You can set the protein structure properties according to your needs, including style, color, label, etc.
  
  
  
• Green columns indicate the mutations that are close to mutation1. The following figure shows mutation information close to the mutation on HISTIH3G, including gene name, amino acid change (AAC), mutation type, chain and distance, etc.
  
  
  
  
• Orange column is mutations close to mutation2

• For proximity pairwises, the cluster and label are automatically loaded into the protein structure when the radio button is clicked. Otherwise canceled.
  
  
  
• For mutations in the green and orange columns, click on the first radio button to add clsuter and the second to add label
  
  
  

Protein-structure-guided discovery of functional mutations across 19 cancer types; Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L;Nature Genetics volume 48, pages 827?837 (2016)

HotSpot3D is provided as freeware, but only for non-commercial use, if you wish to use HotSpot3D for commercial purposes, please contact us.