Tag: Expression

ErmineJ 3.2 – Analysis of Gene sets in Expression Microarray data

ErmineJ 3.2

:: DESCRIPTION

ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are “doing something interesting” in the data. The software is designed to be used by biologists with little or no informatics background.

::DEVELOPER

Pavlidis lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • java

:: DOWNLOAD

 ErmineJ

:: MORE INFORMATION

Citation

Lee H.K., Braynen W., Keshav K. and Pavlidis P. (2005)
ErmineJ: Tool for functional analysis of gene expression data sets.
BMC Bioinformatics 6:269.

Context-MMIA – miRNA-mRNA Target Prediction system combining Expression data and Literature data.

Context-MMIA

:: DESCRIPTION

Context-MMIA is miRNA-mRNA target prediction system combining expression data and literature data.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Oh M, Rhee S, Moon JH, Chae H, Lee S, Kang J, Kim S.
Literature-based condition-specific miRNA-mRNA target prediction.
PLoS One. 2017 Mar 31;12(3):e0174999. doi: 10.1371/journal.pone.0174999. PMID: 28362846; PMCID: PMC5376335.

mimiRNA – microRNA Expression Profiler

mimiRNA

:: DESCRIPTION

mimiRNA is an online resource that integrates expression data from 1483 samples and permits visualization of the expression of 635 human miRNAs across 188 different tissues or cell types.

::DEVELOPER

Centenary Institute – Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Ritchie W, Flamant S, Rasko JE.
mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets.
Bioinformatics. 2010 Jan 15;26(2):223-7. doi: 10.1093/bioinformatics/btp649. Epub 2009 Nov 17. PMID: 19933167.

miRNAmRNA 1.0 – miRNA mRNA Expression Integration

miRNAmRNA 1.0

:: DESCRIPTION

miRNAmRNA: Integrated analysis of microRNA and mRNA

::DEVELOPER

Maarten van Iterson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 miRNAmRNA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Aug;41(15):e146. doi: 10.1093/nar/gkt525. Epub 2013 Jun 14.
Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions.
van Iterson M1, Bervoets S, de Meijer EJ, Buermans HP, ‘t Hoen PA, Menezes RX, Boer JM.

miRseqViewer 1.0 – Visualization of Sequence, Structure and Expression for Analysis of microRNA Sequencing data

miRseqViewer 1.0

:: DESCRIPTION

miRseqViewer is a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multi-panel windows.

::DEVELOPER

miRseqViewer team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Java

:: DOWNLOAD

 miRseqViewer

:: MORE INFORMATION

Citation

miRseqViewer: Multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data.
Jang I, Chang H, Jun Y, Park S, Yang JO, Lee B, Kim W, Kim VN, Lee S.
Bioinformatics. 2014 Oct 15. pii: btu676.

rSeqDiff 0.1 – Detecting differential Isoform Expression from RNA-seq data

rSeqDiff 0.1

:: DESCRIPTION

rSeqDiff is an R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions.

::DEVELOPER

Hui Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 rSeqDiff

:: MORE INFORMATION

Citation:

PLoS One. 2013 Nov 18;8(11):e79448. doi: 10.1371/journal.pone.0079448. eCollection 2013.
rSeqDiff: detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test.
Shi Y1, Jiang H.

rSeqNP 1.0 – Detecting Differential Expression and Splicing from RNA-Seq data

rSeqNP 1.0

:: DESCRIPTION

rSeqNP is an R package using a non-parametric approach to test for differential expression (DE) and differential splicing (DS) of genes from RNA-seq data.

::DEVELOPER

Hui Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 rSeqNP

:: MORE INFORMATION

Citation:

rSeqNP: A non-parametric approach for detecting differential expression and splicing from RNA-Seq data.
Shi Y, Chinnaiyan AM, Jiang H.
Bioinformatics. 2015 Feb 24. pii: btv119.

IDEM – Identifying Direction from Expression and Methylation

IDEM

:: DESCRIPTION

IDEM is a method for identifying the causal direction of edges by combining DNA methylation and mRNA transcription data.

::DEVELOPER

David M Simcha dsimcha@gmail.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 IDEM

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Nov 1;7:118. doi: 10.1186/1752-0509-7-118.
Identification of direction in gene networks from expression and methylation.
Simcha DM1, Younes L, Aryee MJ, Geman D.

UNDO 1.34.0 – Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

UNDO 1.34.0

:: DESCRIPTION

UNDO (UNsupervised DecOnvolution) is an R package that can be used to automatically detect cell-specific marker genes located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample, and deconvolute mixed expressions into cell-specific expression profiles.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • Bioconductor

:: DOWNLOAD

 UNDO

:: MORE INFORMATION

Citation

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.
Wang N, Gong T, Clarke R, Chen L, Shih IM, Zhang Z, Levine DA, Xuan J, Wang Y.
Bioinformatics. 2015 Jan 1;31(1):137-9. doi: 10.1093/bioinformatics/btu607.

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