ProMISe 1.24.0 – Infer miRNA-mRNA interactions using paired expression data from a single sample

ProMISe 1.24.0

:: DESCRIPTION

ProMISe is a novel approach to infer Probabilistic MiRNA-mRNA Interaction Signature from a single pair of miRNA-mRNA expression profile. Our model considers mRNA and miRNA competition as a probabilistic function of the expressed seeds (matches).

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ProMISe

:: MORE INFORMATION

Citation

Li, Y., Liang, C., Wong, KC, Jin, K., and Zhang, Z. (Feb, 2014)
Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach. Nucleic Acids Research
Nucl. Acids Res. (2014) doi: 10.1093/nar/gku182

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.

NLDMseq – Expression Calculation at both Gene and Isoform levels from RNA-seq data given a Reference Transcriptom

NLDMseq

:: DESCRIPTION

NLDMseq is a bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.

::DEVELOPER

Xuejun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 NLDMseq

:: MORE INFORMATION

Citation

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
Liu X, Shi X, Chen C, Zhang L.
BMC Bioinformatics. 2015 Oct 16;16(1):332. doi: 10.1186/s12859-015-0750-6.

miRlastic 1.0 – Integrative Analysis of miRNA and mRNA Expression data

miRlastic 1.0

:: DESCRIPTION

miRlastic is a novel method  which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network.

::DEVELOPER

Computational Cell Maps Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

 miRlastic

:: MORE INFORMATION

Citation

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma.
Sass S, Pitea A, Unger K, Hess J, Mueller NS, Theis FJ.
Int J Mol Sci. 2015 Dec 18;16(12):30204-22. doi: 10.3390/ijms161226230.

miR-isomiRExp – Analysis of Expression of miRNA at the miRNA/isomiR levels

miR-isomiRExp

:: DESCRIPTION

miR-isomiRExp is an approach to analyze expression pattern of miRNA at the miRNA/isomiR levels, provide insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveal functional characteristics of miRNA/isomiR.

::DEVELOPER

miR-isomiRExp team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 miR-isomiRExp

:: MORE INFORMATION

Citation

miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels.
Guo L, Yu J, Liang T, Zou Q.
Sci Rep. 2016 Mar 24;6:23700. doi: 10.1038/srep23700.

SNPExpress 1.00 – Interrogation of the localized effects of common SNPs on Exon and Transcript level Expression

SNPExpress 1.00

:: DESCRIPTION

SNPExpress is a database interface that we developed to permit interrogation of the effects of common SNPs on exon and transcript level expression. This database enables researchers to input a SNP, gene, or a genomic region to investigate regions of interest for localized effects of SNPs on exon and gene level expression changes.

::DEVELOPER

SNPExpress team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 SNPExpress

:: MORE INFORMATION

Citation

PLoS Biol. 2008 Dec 23;6(12):e1.
Tissue-specific genetic control of splicing: implications for the study of complex traits.
Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, Gabriel WN, Welsh-Bohmer KA, Hulette CM, Denny TN, Goldstein DB.

Periscope 20150806 – A Predictor for Soluble Protein Expression in the Periplasm of Escherichia coli

Periscope 20150806

:: DESCRIPTION

Constructed based on the rising popularity of periplasmic expression, Periscope is a sequence-based predictor with a two-stage architecture that estimates the expression level and yield of soluble protein in the periplasm of E. coli.

::DEVELOPER

Periscope team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 Periscope

:: MORE INFORMATION

Citation

Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli.
Chang CC, Li C, Webb GI, Tey B, Song J, Ramanan RN.
Sci Rep. 2016 Mar 2;6:21844. doi: 10.1038/srep21844.

PERT 1.0 – Expression Deconvolution under Varied Environmental Conditions

PERT 1.0

:: DESCRIPTION

The PERT algorithm is designed for expression deconvolution of samples of mixed cell types, where the expression profiles of most of the individual cell types are available and we simply want to estimate the proportion of each mixed sample that is attributable to each individual cell type.

::DEVELOPER

QUON-TITATIVE BIOLOGY LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /
  • Octave

:: DOWNLOAD

 PERT 

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2012;8(12):e1002838. doi: 10.1371/journal.pcbi.1002838. Epub 2012 Dec 20.
PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions.
Qiao W1, Quon G, Csaszar E, Yu M, Morris Q, Zandstra PW.

DGEclust 20150607 – Hierarchical non-parametric Bayesian Clustering of Digital Expression data

DGEclust 20150607

:: DESCRIPTION

DGEclust is a program for clustering and differential expression analysis of expression data generated by next-generation sequencing assays, such as RNA-seq, CAGE and others.

::DEVELOPER

Computational Genomics Group, Department of Computer Science, University of Bristol, UK

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DGEclust 

:: MORE INFORMATION

Citation:

Genome Biol. 2015 Feb 20;16:39. doi: 10.1186/s13059-015-0604-6.
DGEclust: differential expression analysis of clustered count data.
Vavoulis DV, Francescatto M, Heutink P, Gough J.

PPIXpress 1.05 – Specific Protein Interaction Networks from Transcript Expression

PPIXpress 1.05

:: DESCRIPTION

PPIXpress exploits expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing.

::DEVELOPER

Thorsten Will  , Volkhard Helms

:: SCREENSHOTS

PPIXpress

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 PPIXpress

:: MORE INFORMATION

Citation

PPIXpress: construction of condition-specific protein interaction networks based on transcript expression.
Will T, Helms V.
Bioinformatics. 2015 Oct 27. pii: btv620.