magi.brown.edu

MAGI

MAGI is a tool for annotating, exploring, and analyzing gene sets that may be associated with cancer. View aberrations in and interactions among gene sets. Upload your mutation data. View in combination with TCGA Pan-Cancer data. Collaboratively annotate aberrations and interactions while exploring your data. View the aberrations in a tumor sample, prioritized by their annotations. If you use MAGI in your work, please cite Leiserson, et al. Search by sample ID. Select datasets from the dropdown. The subn...

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MAGI is a tool for annotating, exploring, and analyzing gene sets that may be associated with cancer. View aberrations in and interactions among gene sets. Upload your mutation data. View in combination with TCGA Pan-Cancer data. Collaboratively annotate aberrations and interactions while exploring your data. View the aberrations in a tumor sample, prioritized by their annotations. If you use MAGI in your work, please cite Leiserson, et al. Search by sample ID. Select datasets from the dropdown. The subn...

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MAGI | magi.brown.edu Reviews

https://magi.brown.edu

MAGI is a tool for annotating, exploring, and analyzing gene sets that may be associated with cancer. View aberrations in and interactions among gene sets. Upload your mutation data. View in combination with TCGA Pan-Cancer data. Collaboratively annotate aberrations and interactions while exploring your data. View the aberrations in a tumor sample, prioritized by their annotations. If you use MAGI in your work, please cite Leiserson, et al. Search by sample ID. Select datasets from the dropdown. The subn...

INTERNAL PAGES

magi.brown.edu

1

MAGI

http://magi.brown.edu/datasets

Datasets Click a dataset's name to view a summary of its mutations. Firebrowse (January 28, 2016). A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago. A few seconds ago.

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MAGI

http://magi.brown.edu/upload

You must be logged in to do that. Please login via Google by clicking the button below. Updated: January 11th, 2016.

3

MAGI

http://magi.brown.edu/acknowledgements

MAGI was created by the Raphael research group. MAGI is supported by Brown University, the National Science Foundation and National Institutes of Health. MAGI uses public mutation data from The Cancer Genome Atlas's Pan-Cancer and stomach cancer projects [1-2],. Interaction networks [3-6],. Protein domain databases [7-10]. MAGI also uses annotations from the Database of Curated Mutations. Wildstein, J. et al. 2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113 1120. Letunic, I...

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MAGI

http://magi.brown.edu/support

We are eager to hear your success stories or challenges using MAGI. Please feel free to post to our Google Group. Or contact Max Leiserson. Generating files for upload. We understand that it can be a challenge to generate data in the proper format for upload to MAGI. We provide a script that will convert data in TCGA MAF format. Into the SNV TSV format used by MAGI. And a script that will convert data in GISTIC2 format. And we'll be happy to post it here for anyone to use. Updated: January 11th, 2016.

5

MAGI

http://magi.brown.edu/cancers

List of cancer types. MAGI includes 44 cancer types and abbreviations from TCGA and ICGC. MAGI requires each dataset to be assigned to a particular cancer type, so if you don't see the cancer type for your dataset here, you can. Using the form on the right. Add a new cancer type. Hex; initialize randomly. Brain Lower Grade Glioma. Cervical squamous cell carcinoma and endocervical adenocarcinoma. Early Onset Prostate Cancer. Head and Neck squamous cell carcinoma. Kidney renal clear cell carcinoma.

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annotations.cs.brown.edu

Protein-protein interactions for STAG2

http://annotations.cs.brown.edu/annotations/interactions/STAG2

Protein-protein interactions for STAG2. Annotate (You must be logged in.). No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on. No reference to vote on.

annotations.cs.brown.edu

MAGI :: Login

http://annotations.cs.brown.edu/annotations/interactions/add

Updated: June 21st, 2016.

annotations.cs.brown.edu

Annotations for PDGFRA

http://annotations.cs.brown.edu/annotations/PDGFRA

Create a new mutation and reference for this gene. Updated: June 21st, 2016.

annotations.cs.brown.edu

MAGI :: Login

http://annotations.cs.brown.edu/account

Updated: June 21st, 2016.

annotations.cs.brown.edu

MAGI :: Login

http://annotations.cs.brown.edu/annotations/create/mutation

Updated: June 21st, 2016.

compbio.cs.brown.edu

Raphael Lab // CoMEt

http://compbio.cs.brown.edu/projects/comet

CoMEt improves upon the Dendrix. Algorithms to identify collections of exclusive alterations in cancer without prior information. CoMEt uses a novel statistical score for exclusivity collections of alterations and an MCMC algorithm to compute the marginal probability of observing pairs of alterations in the same exclusive set. CoMEt is released as a software package on GitHub. The exact test used by CoMEt is also available as the cometExactTest R package. Proceedings of the 19th Annual International Conf...

compbio.cs.brown.edu

Raphael Lab // PREGO

http://compbio.cs.brown.edu/projects/prego

PREGO: Paired-End Reconstruction of Genome Organization. PREGO is an algorithm that reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired-end sequencing data. Current Release: PREGO Version 1.2 (5/29/2013). The algorithm is described in the following paper:. L Oesper, A. Ritz, S.J. Aerni, R. Drebin, and B.J. Raphael. (2012) Reconstructing cancer genomes from paired-end sequencing data. 13(Suppl 6):S10. Publisher Link.

compbio.cs.brown.edu

Raphael Lab // Gremlin

http://compbio.cs.brown.edu/projects/gremlin

Gremlin is an interactive visualization model for the comparative analysis of structural variation in human and cancer genomes. The model is described in the paper referenced below. Description of the visualization views: GremlinOverview.pdf. Description of the visualization interaction: GremlinInteraction.pdf. Gremlin download coming soon! TM O’Brien, A. Ritz, B.J. Raphael, and D.H. Laidlaw. (2010) Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements.

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MAGI is a tool for annotating, exploring, and analyzing gene sets that may be associated with cancer. View aberrations in and interactions among gene sets. Upload your mutation data. View in combination with TCGA Pan-Cancer data. Collaboratively annotate aberrations and interactions while exploring your data. View the aberrations in a tumor sample, prioritized by their annotations. If you use MAGI in your work, please cite Leiserson, et al. Search by sample ID. Select datasets from the dropdown. The subn...

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