PlantArrayNet

What is PlantArrayNet?

PlantArrayNet (PAN), the integrated version of RiceArrayNet, ArabidopsisNet, and RapaNet, provides co-expression information between genes in terms of correlation coefficients from accumulated microarray data of plants such as rice, Arabidopsis and Brassica rapa, respectively. Given the correlation of a gene pair, the degrees of closeness between gene expression profiling are calculated and are visualized in a relational tree and a relational network. In addition, PAN supports scatter plots of log ratios between genes and links them to pathway maps, while providing a common cis-element list of promoter regions that are involved.

What microarrays are used?

Rice 60k Microarray

Rice 60k Microarray contains 60,727 oligonucleotides that represent 58,417 genes, including those that are predicted. As of Dec. 2009, expression data from 183 microarrays.

Rice 300k Microarray

Rice 300k Microarray contains 392,714 oligonucleotides that represent 27,609 genes, including those that are predicted. As of Dec. 2009, expression data from 174 microarrays.

Brassica 300k Microarray

Brassica 300k Microarray contains 392,714 oligonucleotides that represent 47,548 genes, including those that are predicted. As of Dec. 2009, expression data from 143 microarrays.

Arabidopsis ATH1 Genome Array

Arabidopsis ATH1 Genome Array contains 507,495 oligonucleotides that represent 22,210 genes, including those that are predicted. As of Dec. 2010, expression data from 994 microarrays.

Release Notes

Jan. 10, 2017

RapaNet is opened to evalate expression reslationships between genes for Brassica rapa.

Jan. 10, 2011

Hierarchical clustering system is constructed.

Dec. 20, 2010

Arabidopsis ATH1 Array network DB is added to PAN.

Dec. 15, 2009

A new database, PlantArrayNet (PAN), based on RiceArrayNet, is constructed with brassca microarrays and newly designed rice microarrays.

Feb. 20, 2009

The network drawing function is added in order to show relations between genes with the network.

Jan. 29, 2009

The default tree viewer program is changed to ATV (A Tree Viewer).

Jan. 11, 2009

Two columns which contain the IRGSP gene name and the TIGR Locus name column respectively, are added in a spot information table.

Jan. 10, 2009

RiceArrayNet is opened to evalate expression reslationships between genes for Rice.

Reference to Papers

1. RiceArrayNet: Tae-Ho Lee, Yeon-Ki Kim, Thu Thi Minh Pham, Sang Ik Song, Ju-Kon Kim, Kyu Young Kang, Gynheung An, Ki-Hong Jung, David W. Galbraith, Minkyun Kim, Ung-Han Yoon and Baek Hie Nahm
RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice
Plant Physiology (2009) 151: 16-33.
2. RapaNet: Kim J, Jun KM, Kim JS, Chae S, Pahk YM, Lee TH, Sohn SI, Lee SI, Lim MH, Kim CK, Hur Y, Nahm BH, Kim YK
RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes
Evol Bioinform (2017) 13:1-11.
3. Kim Y-K, Chae S, Oh N-I, Nguyen NH and Cheong J-J
Recurrent Drought Conditions Enhance the Induction of Drought Stress Memory Genes in Glycine max L.
Front Genet (2020) 11:576086.

Contacting Information

Please send comments, corrections and requests for additional information to Yeon-Ki Kim