NGSEA – Network-augmented Gene Set Enrichment analysis tool

NGSEA

:: DESCRIPTION

NGSEA (network-based GSEA) measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Cells. 2019 Aug 31;42(8):579-588. doi: 10.14348/molcells.2019.0065.
NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets.
Han H, Lee S, Lee I

eSNPO – SNP Annotation Database and Enrichment analysis platform

eSNPO

:: DESCRIPTION

eSNPO (eQTL based SNP Ontology) is a SNP annotation database and enrichment analysis platform. GWAS is an examination of many common genetic variants in different individuals to see if any variant is associated with a trait. GWASs typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major diseases. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in expression levels of mRNAs. Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Sci Rep. 2016 Jul 29;6:30595. doi: 10.1038/srep30595.
eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform.
Li J, Wang L, Jiang T, Wang J, Li X, Liu X, Wang C, Teng Z, Zhang R, Lv H, Guo M.

PAEA – Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool

PAEA

:: DESCRIPTION

PAEA (Principal Angle Enrichment Analysis) is a new multivariate approach to gene-set enrichment which uses the geometrical concept of the principal angle to quantify gene-set enrichment.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2015 Nov;2015:256-262.
Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.
Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR1, Ma’ayan A.

GEN3VA – Gene Expression and Enrichment Vector Analyzer

GEN3VA

:: DESCRIPTION

GEN3VA is a web-based system that enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Nov 15;17(1):461.
GEN3VA: aggregation and analysis of gene expression signatures from related studies.
Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma’ayan A

Enrichr – HTML5 Gene List Enrichment Analysis Tool

Enrichr

:: DESCRIPTION

Enrichr is an integrative web-based and mobile gene-list enrichment analysis tool that includes over 30 gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library Data Driven Documents (D3).

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Apr 15;14:128. doi: 10.1186/1471-2105-14-128.
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma’ayan A.
0″ marginheight=”0″ scrolling=”no”>

MBRole 2.0 – Enrichment Analysis of Metabolomic data

MBRole

:: DESCRIPTION

MBRole (Metabolites Biological Role) is a server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms.

::DEVELOPER

[Computational Systems Biology Group @CNB-CSIC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MBROLE 2.0-functional enrichment of chemical compounds.
López-Ibáñez J, Pazos F, Chagoyen M.
Nucleic Acids Res. 2016 Apr 15. pii: gkw253.

Chagoyen, M. and Pazos, F. (2011)
MBRole: enrichment analysis of metabolomic data
Bioinformatics 27: 730-731

hiddenDomains 2.2 – A modern HMM to Identify ChIP-seq Enrichment

hiddenDomains 2.2

:: DESCRIPTION

hiddenDomains uses a Hidden Markov Model to identify enriched domains in ChIP-seq data. It accepts BAM files for input and can perform an analysis with or without control data. The output is a BED file, ready for the UCSC genome browser, that contains the domains and is color coded according to their posterior probabilities.

::DEVELOPER

hiddenDomains team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Perl
  • R

:: DOWNLOAD

 hiddenDomains

:: MORE INFORMATION

Citation

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains.
Starmer J, Magnuson T.
BMC Bioinformatics. 2016 Mar 24;17(1):144. doi: 10.1186/s12859-016-0991-z.

EmpiricalGO – Measure Enrichment using an Empirical Sampling Approach

EmpiricalGO

:: DESCRIPTION

EmpiricalGO is a Python script that generates the empirical distribution of the number of microRNA target genes in GO terms and returns p-values for term enrichment.

::DEVELOPER

SGJlab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOs / Windows
  • Python

:: DOWNLOAD

 EmpiricalGO

:: MORE INFORMATION

Citation:

Bias in microRNA functional enrichment analysis.
Bleazard T, Lamb J, Griffiths-Jones S.
Bioinformatics. 2015 Jan 20. pii: btv023.

GREGOR 1.3.1 – Evaluating Enrichment of Any set of Genetic Variants with any set of Regulatory Features

GREGOR 1.3.1

:: DESCRIPTION

GREGOR (Genomic Regulatory Elements and Gwas Overlap algoRithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.

::DEVELOPER

GREGOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 GREGOR

:: MORE INFORMATION

Citation

GREGOR: Evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach.
Schmidt EM, Zhang J, Zhou W, Chen J, Mohlke KL, Chen YE, Willer CJ.
Bioinformatics. 2015 Apr 16. pii: btv201.

BELT 1.0.2 – Bin-based Enrichment Level Threshold Peak-calling program for ChIP-seq data

BELT 1.0.2

:: DESCRIPTION

BELT (Bin-based Enrichment Level Threshold) is a ChIP-seq peak calling tool. This is the engine used in our published web application W-ChIPeaks, meant to be used as a command-line application. Although it does not include all of the features of W-ChIPeaks (such as archive support and target FDR) as some of these are implemented by the Web-based framework, it is nonetheless a full-fledged standalone peakcalling utility.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows

:: DOWNLOAD

 BELT

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):428-30. doi: 10.1093/bioinformatics/btq669. Epub 2010 Dec 7.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Lan X1, Bonneville R, Apostolos J, Wu W, Jin VX.