InterSPPI v1.3 – AraPathogen predicts PPIs between Arabidopsis thaliana and pathogens

InterSPPI v1.3

:: DESCRIPTION

InterSPPI is a web server that could predict protein-protein interactions (PPIs) between Arabidopsis thaliana and pathogens based on sequence and Arabidopsis thaliana intra-species PPI network (AraPPI) information.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

InterSPPI

:: MORE INFORMATION

Citation

Brief Bioinform. 2019 Jan 18;20(1):274-287. doi: 10.1093/bib/bbx123.
Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods.
Yang S, Li H, He H, Zhou Y, Zhang Z.

imiRTP 1.0 – Genome-scale Identification miRNA-target Interactions in Arabidopsis thaliana

imiRTP 1.0

:: DESCRIPTION

imiRTP is an intergrated miRNA-target interaction (MTI) prediction and analysis toolkit for Arabidopsis thaliana microRNAs.

::DEVELOPER

imiRTP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft .NET Framework 3.5 or higher

:: DOWNLOAD

 imiRTP

:: MORE INFORMATION

Citation:

BMC Genomics. 2012 Jun 11;13 Suppl 3:S3. doi: 10.1186/1471-2164-13-S3-S3.
Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.
Ding J1, Li D, Ohler U, Guan J, Zhou S.

arathGraphle – Functional Networks of Process, Tissue, and Developmental Stage Specific Interactions in Arabidopsis thaliana

arathGraphle

:: DESCRIPTION

ArathGraphle is an ensemble of genome-wide functional relationship networks predicted for A. thaliana using Bayesian integration of 60 experimental datasets. It is a hypothesis generation tool that integrates information from a variety of experiments to find consistent co-activities that might otherwise go unnoticed.

::DEVELOPER

Laboratory for Bioinformatics and Functional Genomics

:: SCREENSHOTS

ArathGraphle

:: REQUIREMENTS

  • Web Browser
  • Java

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2010 Dec 31;4:180. doi: 10.1186/1752-0509-4-180.
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.
Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG.

Diurnal 2.0 – Mining and Viewing Diurnal and Circadian Microarray data for Arabidopsis thaliana, poplar, and rice

Diurnal 2.0

:: DESCRIPTION

Diurnal is a web-based tool for accessing the diurnal and circadian genome-wide expression results of genes from several array experiments conducted on common model plants. The expression patterns of particular loci or array probes can be looked up under a variety of different conditions. For each condition, every expression pattern has been modeled using a periodic pattern, which has then been used to estimate the phase of peak expression.

::DEVELOPER

Mockler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J.
Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.