Web Services

MicroArray Gene expression Network Evaluation Toolkit (MAGNET)

Category: Systems Biology/Interactomics
URL: http://magnet.case.edu
PI: Gurkan Bebek
Reference: Linderman, G.C., Chance, M.R., Bebek, G. MAGNET: MicroArray Gene expression and Network Evaluation Toolkit, Nucleic Acids Research, 2012 (in press).

This online toolbox can be used to analyze gene expression and proteomic datasets, and generate weighted protein-protein interaction networks or gene coexpression networks based on these datasets. The mRNA gene expression data can be provided from NCBI's Gene Expression Omnibus.

Bimodality of Coexpression (BiC)

Category: Systems Biology/Interactomics
Website: http://bimodality.case.edu
PI: Gurkan Bebek
Reference: Linderman GC, Patel VN, Chance MR, Bebek G. (2011) BiC: a web server for calculating bimodality of coexpression between gene and protein networks. Bioinformatics.

This online tool calculates bimodality of coexpression between genelists for a given mRNA expression profile. The mRNA gene expression data can be provided from NCBI's Gene Expression Omnibus.

Subnetwork Analysis and Scoring SYstem (SASSy)

Category: Systems Biology/Interactomics
Website: https://bioengine.case.edu/sassy
PI: Mark Chance

SASSy performs exhaustive scoring by mutual information of any protein-protein interaction subnetwork using gene expression data (microarrray) with a suitable number of control and test samples. Result sets include: rank-ordered table of high-scoring modules; two statistical significance tests; heatmap expression of high-scoring subnetwork targets.

VAVIEN

Category: Systems Biology/Interactomics
Website: http://www.diseasegenes.org
PI:Mehmet Koyutürk
Reference: Erten, S., Bebek, G., Koyuturk, M. VAVIEN: An algorithm for prioritizing candidate disease genes based on network topology, Journal of Computational Biology, 2011 Nov; 18(11):1561-74. Epub 2011 Oct 28. (PMID: 22035267)

Prioritize disease genes based on topological similarity: VAVIEN is a tool for prioritizing candidate genes for human diseases. It uses the topological similarity of the gene products in a Protein-Protein Interaction Network to known disease genes.

Degree-Aware Disease Gene Prioritization (DaDa)

Category: Systems Biology/Interactomics
Website: http://compbio.case.edu/dada
PI: Mehmet Koyutürk
Reference: Erten, S., Bebek, G., Ewing, R.M., Koyuturk, M. DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. BioData Min. 2011 Jun 24; 4:19. (PMID: 21699738)

DADA is a MATLAB Toolbox used for prioritizing candidate diseases genes with respect to a disease of interest, based on the proximity of candidate genes with disease associated genes using Protein-Protein Interaction Networks.Network proximity calculations are based on Random Walk with Restarts simulations. DADA provides several statistical adjustment models to remove the bias with respect to degree of target genes in existing algorithms based on Random Walk with Restarts simulation.

MassMatrix

Category: Proteomics
Website: http://massmatrix.case.edu
PI: Hua Xu

MassMatrix is a newly developed database search software package for tandem mass spectrometric data. It uses a mass accuracy sensitive probabilistic scoring model to rank peptide and protein matches.