Tag: Co-expression

CLIC v1.0 – Clustering by Inferred Co-expression

CLIC v1.0

:: DESCRIPTION

CLIC is a computational tool for helping users identify new members of a pathway of interest, as well as the RNA expression datasets in which that pathway is relevant.

::DEVELOPER

Jun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOS

:: DOWNLOAD

CLIC

:: MORE INFORMATION

Citation

Li Y, Jourdain AA, Calvo SE, Liu JS, Mootha VK.
CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets.
PLoS Comput Biol. 2017 Jul 18;13(7):e1005653. doi: 10.1371/journal.pcbi.1005653. PMID: 28719601; PMCID: PMC5546725.

AMOUNTAIN 1.18.0 – Active modules for multilayer weighted Gene co-expression networks

AMOUNTAIN 1.18.0

:: DESCRIPTION

AMOUNTAIN is a novel algorithm to identify active modules from multilayer weighted gene co-expression networks based on a convex optimization approach.

::DEVELOPER

Shan He Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R package / BioConductor

:: DOWNLOAD

AMOUNTAIN

:: MORE INFORMATION

Citation

Li D, Pan Z, Hu G, Anderson G, He S.
Active module identification from multilayer weighted gene co-expression networks: a continuous optimization approach.
IEEE/ACM Trans Comput Biol Bioinform. 2020 Jan 30;PP. doi: 10.1109/TCBB.2020.2970400. Epub ahead of print. PMID: 32011261.

decode 1.2 – Differential Co-Expression and Differential Expression Analysis

decode 1.2

:: DESCRIPTION

DECODE is a novel analytical approach to integrate DC and DE analyses of gene expression data.

::DEVELOPER

Thomas Lui <tlui27 at yahoo.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX
  • R

:: DOWNLOAD

 DECODE

:: MORE INFORMATION

Citation

DECODE: an integrated differential co-expression and differential expression analysis of gene expression data.
Lui TW, Tsui NB, Chan LW, Wong CS, Siu PM, Yung BY.
BMC Bioinformatics. 2015 May 31;16:182. doi: 10.1186/s12859-015-0582-4.

DCGL 2.1.2 – R package for unveiling differential Regulation from Differential Co-expression

DCGL 2.1.2

:: DESCRIPTION

DCGL is an R package for differential co-expression analysis (DCEA) and differential regulation analysis (DRA).

::DEVELOPER

System Biology Group, Shanghai Center for Bioinformation Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 DCGL

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 20;8(11):e79729. doi: 10.1371/journal.pone.0079729. eCollection 2013.
DCGL v2.0: an R package for unveiling differential regulation from differential co-expression.
Yang J1, Yu H, Liu BH, Zhao Z, Liu L, Ma LX, Li YX, Li YY.

COEXPEDIA – Exploring Biomedical Hypotheses via co-expressions Associated with Medical Subject Headings (MeSH)

COEXPEDIA

:: DESCRIPTION

Coexpedia is a database of context-associated co-expression networks inferred from individual series of microarray samples for human and mouse of GEO.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2017 Jan 4;45(D1):D389-D396. doi: 10.1093/nar/gkw868. Epub 2016 Sep 26.
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH).
Yang S, Kim CY, Hwang S, Kim E, Kim H, Shim H, Lee I.