:: DESCRIPTION
CORNA is a package for R that analyses microarray data and miRNA target prediction data to find statistically over-represented miRNA-target relationships.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Mar 15;25(6):832-3. doi: 10.1093/bioinformatics/btp059. Epub 2009 Jan 29.
CORNA: testing gene lists for regulation by microRNAs.
Wu X1, Watson M.
:: DESCRIPTION
GLAD4U is a new, free web-based gene retrieval and prioritization tool. GLAD4U takes advantage of existing resources of the NCBI to ensure computational efficiency.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
BMC Genomics. 2012;13 Suppl 8:S20. doi: 10.1186/1471-2164-13-S8-S20. Epub 2012 Dec 17.
GLAD4U: deriving and prioritizing gene lists from PubMed literature.
Jourquin J1, Duncan D, Shi Z, Zhang B.
:: DESCRIPTION
GeneValorization is a web-based Java application tool which aims at making the most of the text-mining effort done downstream to all high throughput technology assays.GeneValorization gives a very clear and handful overview of the bibliography corresponding to one particular gene list.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Apr 15;27(8):1187-9. doi: 10.1093/bioinformatics/btr073. Epub 2011 Feb 23.
Gene List significance at-a-glance with GeneValorization.
Brancotte B1, Biton A, Bernard-Pierrot I, Radvanyi F, Reyal F, Cohen-Boulakia S.
:: DESCRIPTION
WeiSum is an R package which calculates the statistics for the comparison of two ranked gene lists related to two diseases and estimates the number of potentially overlapping genes between the diseases.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Quan Chen, Xianghong Jasmine Zhou, Fengzhu Sun (2015)
Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists.
In Press. Journal of Computational Biology.
:: DESCRIPTION
NetVenn is a network-based web platform for the comparison and analysis of gene lists by combining Venn diagram and gene set enrichment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
NetVenn: an integrated network analysis web platform for gene lists.
Wang Y, Thilmony R, Gu YQ.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W161-6. doi: 10.1093/nar/gku331.
:: DESCRIPTION
GeneNomenclatureUtils is a command-line utilities for using MGI, Entrez, HGNC, PubMed, and OMIM files.
::DEVELOPER
Genes to Cognition (G2C)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
EHR-Phenolyzer is a python pipeline to automatically translate raw clinical notes into meaningfully ranked candidate causal genes. It might greatly shorten the time for disease causal genes identification and discovery.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Son JH, Xie G, Yuan C, Ena L, Li Z, Goldstein A, Huang L, Wang L, Shen F, Liu H, Mehl K, Groopman EE, Marasa M, Kiryluk K, Gharavi AG, Chung WK, Hripcsak G, Friedman C, Weng C, Wang K.
Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes.
Am J Hum Genet. 2018 Jul 5;103(1):58-73. doi: 10.1016/j.ajhg.2018.05.010. Epub 2018 Jun 28. PMID: 29961570; PMCID: PMC6035281.
:: DESCRIPTION
ChEA (ChIP-X Enrichment Analysis) database contains manually extracted datasets of transcription-factor/target-gene interactions from over 100 experiments such as ChIP-chip, ChIP-seq, ChIP-PET applied to mammalian cells. We use the database to analyze mRNA expression data where we perform gene-list enrichment analysis as the prior biological knowledge gene-list library. The system is delivered as web-based interactive software. With this software users can input lists of mammalian genes for which the program computes over-representation of transcription factor targets from the ChEA database.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma’ayan A.
Nucleic Acids Res. 2019 Jul 2;47(W1):W212-W224. doi: 10.1093/nar/gkz446.
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.
Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma’ayan A.
Bioinformatics. 2010 Oct 1;26(19):2438-44.
:: 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
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.
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:: DESCRIPTION
GeneVenn is a web application creating Venn diagrams from two or three gene lists. Each gene in the group list has link to the related information in NCBI’s Entrez Nucleotide database.
::DEVELOPER
the Experimental Bioinformatics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
GeneVenn – A web application for comparing gene lists using Venn diagrams.
Pirooznia M, Nagarajan V, Deng Y.
Bioinformation. 2007 Apr 10;1(10):420-2.