Tag: Genes

Lever 2.0 – Maps Metazoan DNA Regulatory Motifs to sets of Genes

Lever 2.0

:: DESCRIPTION

Lever systematically maps DNA regulatory motifs or motif combinations to the sets of genes that they likely regulate. Lever accomplishes this by assessing whether the motifs are enriched within cis regulatory modules (CRMs), predicted by our PhylCRM algorithm, in the noncoding sequences surrounding genes in a collection of gene sets.

::DEVELOPER

The Bulyk Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Lever

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1446-54. doi: 10.1093/bioinformatics/bts155. Epub 2012 Apr 5.
LOESS correction for length variation in gene set-based genomic sequence analysis.
Aboukhalil A, Bulyk ML.

Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2.
Systematic identification of mammalian regulatory motifs’ target genes and functions.
Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.

SnIPRE – Identifying Genes under Natural Selection

SnIPRE

:: DESCRIPTION

SnIPRE (Selection Inference using a Poisson Random Effects model) is a new methodology for identifying genes under natural selection.

:: DEVELOPER

the Bustamante Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R pacakge

:: DOWNLOAD

   SnIPRE

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2012;8(12):e1002806. doi: 10.1371/journal.pcbi.1002806. Epub 2012 Dec 6.
SnIPRE: selection inference using a Poisson random effects model.
Eilertson KE1, Booth JG, Bustamante CD.

GeneNomenclatureUtils – Tools for Annotating Genes and Comparing Gene Lists with Community Resources

GeneNomenclatureUtils

:: 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

  • Linux

:: DOWNLOAD

 GeneNomenclatureUtils

:: MORE INFORMATION

Harmonizome 1.5 – Integrated Knowledge About Genes & Proteins

Harmonizome 1.5

:: DESCRIPTION

Harmonizome is a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from over 70 major online resources.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

Harmonizome 

:: MORE INFORMATION

Citation

Database (Oxford). 2016 Jul 3;2016. pii: baw100. doi: 10.1093/database/baw100. Print 2016.
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.
Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma’ayan A.

Mashup – Compact Integration of Multi-Network Topology for Functional Analysis of Genes

Mashup

:: DESCRIPTION

Mashup is a framework for compact integration of multi-network topology for functional analysis of genes.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab

:: DOWNLOAD

Mashup

:: MORE INFORMATION

Citation:

Compact Integration of Multi-Network Topology for Functional Analysis of Genes
Hyunghoon Cho, Bonnie Berger, Jian Peng
Cell Systems 3 (6), 2016

Wigwams – Identifies Genes Working Across Multiple Biological Situations

Wigwams

:: DESCRIPTION

Wigwams is a simple and efficient method to identify gene modules showing evidence for co-regulation in multiple time series of gene expression data.

::DEVELOPER

Dr Sascha Ott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • MatLab

:: DOWNLOAD

 Wigwams

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):962-70. doi: 10.1093/bioinformatics/btt728. Epub 2013 Dec 18.
Wigwams: identifying gene modules co-regulated across multiple biological conditions.
Polanski K1, Rhodes J, Hill C, Zhang P, Jenkins DJ, Kiddle SJ, Jironkin A, Beynon J, Buchanan-Wollaston V, Ott S, Denby KJ.

EMPANADA – Evidence-based Assignment of Genes to Pathways in Metagenomic data

EMPANADA

:: DESCRIPTION

EMPANADA is a tool for evidence-based, non-uniform, and sample-specific assignment of gene families to pathways in metagenomic data.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

EMPANADA

:: MORE INFORMATION

 

Catapult – Associating new Genes with Traits, Phenotypes, and Diseases

Catapult

:: DESCRIPTION

Catapult (Combining dATa Across species using Positive-Unlabeled Learning Techniques), is a supervised machine learning method that uses a biased support vector machine where the features are derived from walks in a heterogeneous gene-trait network.

::DEVELOPER

the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Catapult

:: MORE INFORMATION

Citation:

Prediction and validation of gene-disease associations using methods inspired by social network analyses.
Singh-Blom UM, Natarajan N, Tewari A, Woods JO, Dhillon IS, Marcotte EM.
PLoS One. 2013 May 1;8(5):e58977. doi: 10.1371/journal.pone.0058977.

EdgeExpressDB 0.954 – Integrated database of Promoters, Genes, microRNAs, Expression Dynamics and Regulatory Interactions.

EdgeExpressDB 0.954

:: DESCRIPTION

EdgeExpressDB (eeDB) is a federated data abstraction system designed for integrating, interpreting, and visualizing very large biology datasets.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

::  REQUIREMENTS

  • Linux
  • Perl DBI/DBD, MySQL, SQLite.

:: DOWNLOAD

 EdgeExpressDB

:: MORE INFORMATION

Citation

Genome Biol. 2009;10(4):R39. doi: 10.1186/gb-2009-10-4-r39. Epub 2009 Apr 19.
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
Severin J1, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR.

STRING 11.0 – Search Tool for the Retrieval of Interacting Genes/Proteins

STRING 11.0

:: DESCRIPTION

STRING (search tool for recurring instances of neighbouring genes) is a database and web resource dedicated to protein-protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C.
Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003

Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29.
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini A1, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ.

STRING 8–a global view on proteins and their functional interactions in 630 organisms.
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C.
Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. Epub 2008 Oct 21.

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C.
Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. Epub 2010 Nov 2.