PATHiVar – Assessing Functional Impact of Mutations over Human Signalling Network

PATHiVar

:: DESCRIPTION

PATHiVar is a web-based tool that integrates genomic variation data with gene expression tissue information.

::DEVELOPER

Computational Genomics Department ,Principe Felipe Research Center, Valencia, Spain

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Assessing the impact of mutations found in next generation sequencing data over human signaling pathways.
Hernansaiz-Ballesteros RD, Salavert F, Sebastián-León P, Alemán A, Medina I, Dopazo J.
Nucleic Acids Res. 2015 Apr 16. pii: gkv349.

xseq 0.2.1 – Assessing Functional Impact on Gene Expression of Mutations in Cancer

xseq 0.2.1

:: DESCRIPTION

Cancer driver mutations control outcomes indirectly through intermediate phenotypes, e.g., gene expression and protein expression. xseq is a probabilistic model which aims to encode the impact of somatic mutations on gene expression profiles.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

xseq

:: MORE INFORMATION

Citation

Nat Commun. 2015 Oct 5;6:8554. doi: 10.1038/ncomms9554.
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
Ding J et al.

MutationAssessor r3 – Functional Impact of Protein Mutations

MutationAssessor r3

:: DESCRIPTION

MutationAssessor server predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs.

::DEVELOPER

MutationAssessor team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Reva B, Antipin Y, Sander C.
Nucl. Acids Res. (2011) 39 (17): e118. doi: 10.1093/nar/gkr407
“Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics“

EFIN – Evaluation of Functional Impact of Nonsynonymous SNPs

EFIN

:: DESCRIPTION

EFIN is a free tool which predict whether amino acids substitution would related to disease evaluated by random forests based on protein conservation.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jun 10;15:455. doi: 10.1186/1471-2164-15-455.
EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome.
Zeng S, Yang J, Chung BH, Lau YL, Yang W