Tag: Expression

CONEXIC – COpy Number and EXpression In Cancer

CONEXIC

:: DESCRIPTION

CONEXIC is an algorithm that integrates matched copy number (amplifications and deletions) and gene expression data from tumor samples to identify driving mutations and the processes they influence.

::DEVELOPER

Dana Pe’er Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 CONEXIC

:: MORE INFORMATION

Citation

Cell. 2010 Dec 10;143(6):1005-17. doi: 10.1016/j.cell.2010.11.013. Epub 2010 Dec 2.
An integrated approach to uncover drivers of cancer.
Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe’er D.

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.

SEEK – Search-Based Exploration of Expression Compendium

SEEK

:: DESCRIPTION

SEEK is a computational gene co-expression search engine. SEEK provides biologists with a way to navigate the massive human expression compendium that now contains thousands of expression datasets. SEEK returns a robust ranking of co-expressed genes in the biological area of interest defined by the user’s query genes. In the meantime, it also prioritizes thousands of expression datasets according to the user’s query of interest. The unique strengths of SEEK include its support for multi-gene query and cross-platform analysis, as well as its rich visualization features.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SEEK

:: MORE INFORMATION

Citation

Zhu Q, Wong AK, Krishnan A, Aure MR, Tadych A, Zhang R, Corney DC, Greene CS, Bongo LA, Kristensen VN, Charikar M, Li K, Troyanskaya OG.
Targeted exploration and analysis of large cross-platform human transcriptomic compendia.
Nat Methods. 2015 Mar;12(3):211-4, 3 p following 214. doi: 10.1038/nmeth.3249. Epub 2015 Jan 12. PMID: 25581801; PMCID: PMC4768301.

BM-DE 2 – Bayesian Method of Calling Differential Expression

BM-DE 2

:: DESCRIPTION

BMDE is a Bayesian hierarchical model for the inference on the differential gene expression based on RNA-Seq data

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 BM-DE

 :: MORE INFORMATION

Citation

Cancer Inform. 2011;10:205-15. doi: 10.4137/CIN.S7473. Epub 2011 Aug 1.
On differential gene expression using RNA-Seq data.
Lee J1, Ji Y, Liang S, Cai G, Müller P.

CREEDS – Crowd Extracted Expression of Differential Signatures

CREEDS

:: DESCRIPTION

CREEDS is a portal for visualizing and querying the collections of the gene expression signatures.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nat Commun. 2016 Sep 26;7:12846. doi: 10.1038/ncomms12846.
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.
Wang Z etc.

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.

LOX 1.8beta – Inferring Level of Expression from Diverse Methods of Census Sequencing

LOX 1.8beta

:: DESCRIPTION

LOX (Level Of eXpression) is a program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++Compiler

:: DOWNLOAD

 LOX

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 1;26(15):1918-9. Epub 2010 Jun 10.
LOX: inferring Level Of eXpression from diverse methods of census sequencing.
Zhang Z, López-Giráldez F, Townsend JP.

MADE 20110209 – Metabolic Adjustment by Differential Expression

MADE 20110209

:: DESCRIPTION

MADE uses the statistical significance of changes in gene or protein expression to create a functional metabolic model that most accurately recapitulates the expression dynamics.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 MADE

:: MORE INFORMATION

Citation:

Jensen, P.A. and J.A. Papin. 2011.
Functional integration of a metabolic network model and expression data without arbitrary thresholding.
Bioinformatics, 27(4):541-547.

TIGER 1.2.0-beta – Toolbox for Integrating Genome-scale metabolism, Expression, and Regulation

TIGER 1.2.0-beta

:: DESCRIPTION

TIGER is a software platform for building and analyzing genome-scale models of metabolism. TIGER provides methods for combining gene-protein-reaction associations, transcriptional regulation, and other biological constraints into a single mixed-integer linear programming (MILP) framework.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab
:: DOWNLOAD

 TIGER

:: MORE INFORMATION

Citation

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
Jensen PA, Lutz KA, Papin JA.
BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147.

CIBERSORTx / CIBERSORT – Determining Cell Type Abundance and Expression from Bulk Tissues

CIBERSORTx / CIBERSORT

:: DESCRIPTION

CIBERSORTx is an analytical tool to impute gene expression profiles and provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data.

CIBERSORT is an analytical tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Determining cell type abundance and expression from bulk tissues with digital cytometry
Newman AM, et al.
Nat Biotechnol, 37 (7), 773-782 Jul 2019

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