:: DESCRIPTION
MEDEA identifies lineage-specifying transcription factors (TFs) from chromatin accessibility assays.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mariani L, Weinand K, Gisselbrecht SS, Bulyk ML.
MEDEA: analysis of transcription factor binding motifs in accessible chromatin.
Genome Res. 2020 May;30(5):736-748. doi: 10.1101/gr.260877.120. Epub 2020 May 18. PMID: 32424069; PMCID: PMC7263192.
:: DESCRIPTION
Broad-Enrich tests sets of broad genomic regions (e.g., from ChIP-seq data for histone modifications or copy number variations) for enriched biological pathways, Gene Ontology terms, or other gene sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Broad-Enrich: functional interpretation of large sets of broad genomic regions.
Cavalcante RG, Lee C, Welch RP, Patil S, Weymouth T, Scott LJ, Sartor MA.
Bioinformatics. 2014 Sep 1;30(17):i393-i400. doi: 10.1093/bioinformatics/btu444.
:: DESCRIPTION
ChIP-Enrich tests ChIP-seq peak data for enrichment of biological pathways, Gene Ontology terms, and other types of gene sets
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ChIP-Enrich: gene set enrichment testing for ChIP-seq data.
Welch RP, Lee C, Imbriano PM, Patil S, Weymouth TE, Smith RA, Scott LJ, Sartor MA.
Nucleic Acids Res. 2014 May 30. pii: gku463.
:: DESCRIPTION
CAGEd-oPOSSUM is a web-based tool used to detect the over-representation of transcription factor binding sites (TFBS) in regions containing transcription start sites (TSS) derived from Cap Analysis of Gene Expression (CAGE) peaks. It applies the methods of over-representation analysis from our oPOSSUM tool to CAGE derived TSSs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Arenillas DJ, Forrest AR, Kawaji H, Lassmann T; FANTOM Consortium, Wasserman WW, Mathelier A.
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.
Bioinformatics. 2016 Sep 15;32(18):2858-60. doi: 10.1093/bioinformatics/btw337. Epub 2016 Jun 9. PMID: 27334471; PMCID: PMC5018375.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
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:: DESCRIPTION
SeAMotE allows fast and accurate large-scale de novo motif discovery in nucleic acid sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2014 Oct 23;15:925. doi: 10.1186/1471-2164-15-925.
SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences.
Agostini F, Cirillo D, Ponti RD, Tartaglia GG1.
:: DESCRIPTION
MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genome Biol. 2014;15(10):474.
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.
Harmanci A1, Rozowsky J, Gerstein M.
:: DESCRIPTION
EnrichNet is a network-based enrichment analysis method to identify functional associations between user-defined gene or protein sets and cellular pathways. The datasets are mapped onto a protein interaction network (or other user-defined molecular network) and their pairwise associations are assessed by computing a graph-based statistic, i.e. distances between the network nodes are mapped against a background model. In contrast to the classical overlap-based enrichment analysis, associations can also be identified for non-overlapping gene/protein sets and the user can investigate them in detail by visualizing corresponding sub-graphs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2012 Sep 15;28(18):i451-i457. doi: 10.1093/bioinformatics/bts389.
EnrichNet: network-based gene set enrichment analysis.
Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A.
