CREEDS – Crowd Extracted Expression of Differential Signatures

CREEDS

:: DESCRIPTION

CREEDS is a portal for visualizing and querying the collections of the gene expression signatures.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nat Commun. 2016 Sep 26;7:12846. doi: 10.1038/ncomms12846.
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.
Wang Z etc.

ARCHS4 – All RNA-seq and CHIP-seq Signature Search Space

ARCHS4

:: DESCRIPTION

ARCHS4 is a web resource that makes the majority of published RNA-seq data from human and mouse available at the gene and transcript levels.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nat Commun. 2018 Apr 10;9(1):1366. doi: 10.1038/s41467-018-03751-6.
Massive mining of publicly available RNA-seq data from human and mouse.
Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma’ayan A.

Genefu 3.9 – Computation of Gene Expression-Based Signatures in Breast Cancer

Genefu 3.9

:: DESCRIPTION

Genefu contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 Genefu

:: MORE INFORMATION

Citation:

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.
Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B.
Bioinformatics. 2015 Nov 24. pii: btv693.

GeneExpressionSignature 1.16.0 – Gene Expression Signature based Similarity Metric

GeneExpressionSignature 1.16.0

:: DESCRIPTION

GeneExpressionSignature gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

::DEVELOPER

Yang Cao <yiluheihei at gmail.com>, Fei Li <pittacus at gmail.com>,Lu Han <hanl8910 at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 GeneExpressionSignature

:: MORE INFORMATION

Citation

OMICS. 2013 Feb;17(2):116-8. doi: 10.1089/omi.2012.0087.
GeneExpressionSignature: an R package for discovering functional connections using gene expression signatures.
Li F1, Cao Y, Han L, Cui X, Xie D, Wang S, Bo X.

QuasiMotiFinder v4 – Protein Annotation Using a Search for Signature Like Patterns

QuasiMotiFinder v4

:: DESCRIPTION

QuasiMotiFinder is a server for the identification of signatures and signature-like patterns in protein sequences

::DEVELOPER

The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W255-61.
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns.
Gutman R, Berezin C, Wollman R, Rosenberg Y, Ben-Tal N.

SASE-hunter – Signatures of Accelerated Somatic Evolution Hunter

SASE-hunter

:: DESCRIPTION

SASE-hunter is a software to identify regions of interest with a higher than expected number of mutations than the near-by regions.

::DEVELOPER

SjD Laboratory, Cancer Genome Informatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 SASE-hunter

:: MORE INFORMATION

Citation

Smith KS, Yadav VK, Pedersen BS, Shaknovich RS, Geraci MW, Pollard KS, De S.
Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.
Nucleic Acids Res. 2015 Jun 23;43(11):5307-17. doi: 10.1093/nar/gkv419.

SIGNATURE 20111025 – Gene Expression Signature Analysis

SIGNATURE 20111025

:: DESCRIPTION

SIGNATURE is a platform for gene expression signature analysis.

::DEVELOPER

the Microarray Core Facility at microarray@duke.edu.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX
  • Java

:: DOWNLOAD

 SIGNATURE

:: MORE INFORMATION

Citation

Chang JT, Gatza ML, Lucas JE, Barry W, Vaughn P, and Nevins JR (2011).
SIGNATURE: A Workbench for Gene Expression Signature Analysis.”
BMC Bioinformatics 12:443.

3PEAT – Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

3PEAT

:: DESCRIPTION

3PEAT (Plant PEAT Peaks) predicts the probability of a TSS at any given nucleotide in the Arabidopsis genome solely from the DNA sequence surrounding that nucleotide.

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 3PEAT

:: MORE INFORMATION

Citation

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. (2014).
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Plant Cell, 26:2746-60.

StemChecker – Discover and Explore Stemness Signatures in Gene Set

StemChecker

:: DESCRIPTION

StemChecker is a web-server that enables researchers to rapidly check whether a given list of genes can be associated with stemness.

::DEVELOPER

Systems Biology and Bioinformatics Laboratory @ University of Algarve

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.
Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RS, Machado S, Pacheco-Leyva I, Duarte I, Futschik ME.
Nucleic Acids Res. 2015 May 24. pii: gkv529

SCUDO – Signature-based Clustering of Expression Profiles

SCUDO

:: DESCRIPTION

SCUDO (Signature-based ClUstering for DiagnOstic purposes) is a tool for clustering gene expression profiles for diagnostic purposes using a new type of rank-based signatures

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SCUDO: a tool for signature-based clustering of expression profiles.
Lauria M, Moyseos P, Priami C.
Nucleic Acids Res. 2015 May 9. pii: gkv449.