canEvolve – Integrative Cancer Genomics analysis of Expression, Copy Number, miRNAs and Network

canEvolve

:: DESCRIPTION

canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets.

::DEVELOPER

CanEvolve Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

canEvolve: a web portal for integrative oncogenomics.
Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C, Shah PK.
PLoS One. 2013;8(2):e56228. doi: 10.1371/journal.pone.0056228.

miRDeep2 2.0.0.7 / miRDeep* 3.6 – Discovering Known and Novel miRNAs from Deep Sequencing Data

miRDeep2 2.0.0.7 / miRDeep* 3.6

:: DESCRIPTION

miRDeep is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples. Last, a new module for preprocessing of raw Illumina sequencing data produces files for downstream analysis with the miRDeep2 or quantifier module.

miRDeep* is an integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. MiRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and SAM/BAM format.

::DEVELOPER

Systems Biology of Gene Regulatory Elements / Systems Biology of Gene Regulatory Elements

:: SCREENSHOTS

miRDeep

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl / java

:: DOWNLOAD

 miRDeep , miRDeep*

:: MORE INFORMATION

Citation

An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013)
miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data.
Nucleic Acids Res, 41, 727-737.

Friedländer MR., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., Rajewsky, N.
Discovering microRNAs from deep sequencing data using miRDeep‘,
Nature Biotechnology, 26, 407-415 (2008)

DREAM – Detecting RNA Editing Association with MiRNAs

DREAM

:: DESCRIPTION

DREAM is a webserver for the identification of mature microRNA editing events using deep sequencing data

::DEVELOPER

DREAM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data.
Alon S, Erew M, Eisenberg E.
Bioinformatics. 2015 Apr 2. pii: btv187.

miR_Path – Inferring Cancer-related miRNAs based on Gene Expression data

miR_Path

:: DESCRIPTION

miR_Path is a software for inferring cancer-related miRNAs based on gene expression data. It is a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles which can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches.

::DEVELOPER

ZhaoGroup at the Tongji University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • R

:: DOWNLOAD

 miR_Path

:: MORE INFORMATION

Citation

Identifying cancer-related microRNAs based on gene expression data.
Zhao XM, Liu KQ, Zhu G, He F, Duval B, Richer JM, Huang DS, Jiang CJ, Hao JK, Chen L.
Bioinformatics. 2014 Dec 12. pii: btu811

omiRas – Differential Expression Analysis of miRNAs

omiRas

:: DESCRIPTION

omiRas is a web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions

::DEVELOPER

GenXPro GmbH

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 15;29(20):2651-2. doi: 10.1093/bioinformatics/btt457. Epub 2013 Aug 13.
omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.
Müller S1, Rycak L, Winter P, Kahl G, Koch I, Rotter B.