CHRONOS 1.0 – microRNA-mediated sub-pathway Enrichment Analysis

CHRONOS 1.0

:: DESCRIPTION

CHRONOS (time-vaRying enriCHment integrOmics Subpathway aNalysis tOol) is an R package by integrating time-series mRNA/microRNA expression data with KEGG pathway maps and microRNA-target interactions.

::DEVELOPER

the Biosignal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 CHRONOS

:: MORE INFORMATION

Citation

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis.
Vrahatis AG, Dimitrakopoulou K, Balomenos P, Tsakalidis AK, Bezerianos A.
Bioinformatics. 2015 Nov 14. pii: btv673

miR2Gene 201107 – Gene Pattern discovery by Enrichment Analysis of their microRNA Regulators

miR2Gene 201107

:: DESCRIPTION

miR2Gene for gene pattern discovery by enrichment analysis of their microRNA regulators is a web-accessible program, which is used to mine potential patterns for one single gene, multiple genes, and KEGG pathway genes based on miRNA set enrichment analysis of the miRNAs regulating given genes.

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2011 Dec 14;5 Suppl 2:S9. doi: 10.1186/1752-0509-5-S2-S9. Epub 2011 Dec 14.
miR2Gene: pattern discovery of single gene, multiple genes, and pathways by enrichment analysis of their microRNA regulators.
Qiu C1, Wang J, Cui Q.

SeqGSEA 1.9.0 – Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

SeqGSEA 1.9.0

:: DESCRIPTION

SeqGSEA generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing.

::DEVELOPER

Xi Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R package
  • BioConductor

:: DOWNLOAD

 SeqGSEA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 6. [Epub ahead of print]
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.
Wang X1, Cairns MJ.

BMC Bioinformatics. 2013;14 Suppl 5:S16. doi: 10.1186/1471-2105-14-S5-S16. Epub 2013 Apr 10.
Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing.
Wang X, Cairns MJ.

GSEA 2.2.0 – Gene Set Enrichment Analysis

GSEA 2.2.0

:: DESCRIPTION

GSEA (Gene Set Enrichment Analysis) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

::DEVELOPER

GSEA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 GSEA

:: MORE INFORMATION

Citation:

Subramanian, Tamayo, et al. (2005,)
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
PNAS 102, 15545-15550

npGSEA 1.4.0 – Permutation Approximation methods for Gene Set Enrichment Analysis

npGSEA 1.4.0

:: DESCRIPTION

npGSEA  (non-permutation GSEA) calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

::DEVELOPER

Jessica Larson <larson.jess at gmail.com> and Art Owen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 npGSEA

:: MORE INFORMATION

Citation

Moment based gene set tests.
Larson JL, Owen AB.
BMC Bioinformatics. 2015 Apr 28;16(1):132.

PEIMAN – Enrichment Analysis in Post Translational Modification (PTM) types

PEIMAN 1.0

:: DESCRIPTION

PEIMAN (Post translational modification, Enrichment, Integration and Matching ANalysis ) is a standalone software for enrichment analysis in post translational modification (PTM) types. The software also provides the comparison between two different lists of proteins, focusing on PTM types. Investigating the PTM frequency in each list is also available.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 PEIMAN

:: MORE INFORMATION

Citation

PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis.
Nickchi P, Jafari M, Kalantari S.
Database (Oxford). 2015 Apr 23;2015. pii: bav037. doi: 10.1093/database/bav037.

POEAS – Plant Ontology Enrichment Analysis Server

POEAS

:: DESCRIPTION

POEAS is a plant ontology enrichment analysis server. The server uses a simple list of genes as an input and perform enrichment analysis and provide results in two levels: a table with enrichment results and a visulaization utilitity to generate ontological graphs that can be used in publications.

::DEVELOPER

POEAS Team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinform Biol Insights. 2014 Dec 21;8:209-14. doi: 10.4137/BBI.S19057. eCollection 2014.
POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.
Shameer K, Naika MB, Mathew OK, Sowdhamini R

longIGSEA 1.0 – Gene Set Enrichment Analysis for Longitudinal Microarray Experiments

longIGSEA 1.0

:: DESCRIPTION

The R package longiGSEA uses a novel nonparametric statistical method to identify the significant enriched gene sets during a longitudinal microarray study.

::DEVELOPER

Kurt Zhang, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • R package

:: DOWNLOAD

 longiGSEA

:: MORE INFORMATION

Citation

BMC Genomics. 2011 Dec 23;12 Suppl 5:S10. doi: 10.1186/1471-2164-12-S5-S10. Epub 2011 Dec 23.
A hidden Markov model-based algorithm for identifying tumour subtype using array CGH data.
Zhang K1, Yang Y, Devanarayan V, Xie L, Deng Y, Donald S.

MEAGA 1.2 – Minimum distance-based Enrichment Analysis for Genetic Association

MEAGA 1.2

:: DESCRIPTION

MEAGA performs functional/pathway enrichment test while integrating network information from biological interactome (e.g. protein-protein interaction network) using graphical algorithm techniques.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MEAGA

:: MORE INFORMATION

Citation

Graphical algorithm for integration of genetic and biological data: Proof of principle using psoriasis as a model.
Tsoi LC, Elder JT, Abecasis GR.
Bioinformatics. 2014 Dec 4. pii: btu799.

TAFFEL 1.01 – Independent Enrichment Analysis of Gene Sets

TAFFEL 1.01

:: DESCRIPTION

TAFFEL implements a novel method called Independent Enrichment Analysis (IEA) and eases the task by clustering genes to subgroups using Gene Ontology categories and transcription regulators.TAFFEL can be used to analyze gene lists in order to find separate gene subgroups that are coregulated by the same transcription factors or carry out the same biological function, and perform comparison of correlation between co-regulation and co-function with these gene subsets.

::DEVELOPER

TAFFEL team

:: SCREENSHOTS

TAFFEL

:: REQUIREMENTS

  • Winodws/Linux/MacOsX
  • Java

:: DOWNLOAD

 TAFFEL

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 May 19;12:171. doi: 10.1186/1471-2105-12-171.
TAFFEL: Independent Enrichment Analysis of gene sets.
Kurki MI1, Paananen J, Storvik M, Ylä-Herttuala S, Jääskeläinen JE, von Und Zu Fraunberg M, Wong G, Pehkonen P.