TimeTP 1.0 – Influence Maximization in Time bounded network Identifies Transcription Factors Regulating Perturbed Pathways

TimeTP 1.0

:: DESCRIPTION

TimeTP is a novel time-series analysis method for determining transcription factors (TFs) regulating pathway perturbation, which narrows the focus to perturbed sub-pathways and utilizes the gene regulatory network and protein-protein interaction network to locate TFs triggering the perturbation.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

TimeTP

:: MORE INFORMATION

Citation

Jo K, Jung I, Moon JH, Kim S.
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways.
Bioinformatics. 2016 Jun 15;32(12):i128-i136. doi: 10.1093/bioinformatics/btw275. PMID: 27307609; PMCID: PMC4908359.

OncodriveCIS 1.1.0 – Assesses the Influence of Copy Number Alterations (CNA) in the Gene Expression

OncodriveCIS 1.1.0

:: DESCRIPTION

OncodriveCIS is a method to identify genes that accumulate copy number alterations important for tumour development. This is done by computing the functional impact of CNAs by measuring their effect on the expression of the genes affected.

::DEVELOPER

The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Python

:: DOWNLOAD

OncodriveCIS

:: MORE INFORMATION

Citation

Tamborero D, Lopez-Bigas N and Gonzalez-Perez A.
Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression.
PLoS ONE 8(2): e55489. doi:10.1371/journal.pone.0055489

PhosSNP 1.0 – Influence of Protein Phosphorylation by nsSNP

PhosSNP 1.0

:: DESCRIPTION

PhosSNP is a database of Phosphorylation-related SNP. we defined a phosphorylation-related SNP (phosSNP) as a non-synonymous SNP (nsSNP) that affects the protein phosphorylation status.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

WIndows / Linux / MacOsX
Java

:: DOWNLOAD

PhosSNP

:: MORE INFORMATION

Citation

PhosSNP for Systematic Analysis of Genetic Polymorphisms That Influence Protein Phosphorylation
Jian Ren, Chunhui Jiang, Xinjiao Gao, Zexian Liu, Zineng Yuan, Changjiang Jin, Longping Wen, Zhaolei Zhang, Yu Xue and Xuebiao Yao.
Mol Cell Proteomics. 2010;9(4):623-634

NIAS-Server 1.0 – Neighbors Influence of Amino acids and Secondary Structures in Proteins

NIAS-Server 1.0

:: DESCRIPTION

NIAS is a server to help the analysis of the conformational preferences of amino acid residues in proteins.

::DEVELOPER

SBCB – Structural Bioinformatics and Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Borguesan, B.; Inostroza-Ponta, M.; Dorn, M.
NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.
Journal of Computational Biology. March 2017, 24(3): 255-265.