Table 1
Tools, URLs, and References
Methods
Tool
Web
Ref.
3.1 Genome
Browsers
Araport
https://www.araport.org/
[5]
1001 Genomes
https://1001genomes.org/
[11]
3.2 Precomputed
Gene Trees
Ensembl Plants Compara https://plants.ensembl.org/index.html
[12]
PLAZA
https://bioinformatics.psb.ugent.be/plaza/ [15]
PANTHER
http://www.pantherdb.org/
[84]
3.3 Epigenomic
Tools
EPIC-CoGe
https://genomevolution.org/CoGe/User.pl [18]
3.4 Expression
Analysis
eFP Browser/eFP-Seq
Browser
http://bar.utoronto.ca; http://bar.utoronto.
ca/eFP-Seq_Browser/
[24]
Genevestigator
www.genevestigator.com/gv/; https://
genevisible.com/search
[29]
TravaDB, NCBI
http://travadb.org
[28]
3.5 Coexpression
Tools
ATTED II
http://atted.jp
[32]
Expression Angler
http://bar.utoronto.ca
[30]
AraNet
https://www.inetbio.org/aranet
[85]
AtCAST
http://atpbsmd.yokohama-cu.ac.jp/cgi/
atcast/home.cgi
[86]
3.6 Promoter
Analysis
Cistome
http://bar.utoronto.ca/cistome/cgi-bin/
BAR_Cistome.cgi
[36]
ePlant
http://bar.utoronto.ca/eplant
[73]
MEME: FIMO and AME http://meme-suite.org/
[40, 41]
3.7 Functional
Classification
AgriGO
http://systemsbiology.cau.edu.cn/
agriGOv2/
[52]
AmiGO
http://amigo.geneontology.org/rte
[53]
Classification
SuperViewer
http://bar.utoronto.ca/ntools/cgi-bin/
ntools_classification_superviewer.cgi
[54]
3.8 Pathway
Visualization
AraCyc
www.plantcyc.org/
[55]
MapMan
http://mapman.gabipd.org/web/guest/
mapman-download
[51]
3.9 Protein
Information
SUBA Live
http://suba.live/
[57]
Cell eFP Browser
http://bar.utoronto.ca/cell_efp/cgi-bin/
cell_efp.cgi
[24]
P
3 DB—Plant Protein
Phosphorylation DB
http://p3db.org/index.php
[58–60]
Plant PTM Viewer
https://dev.bits.vib.be/ptm-viewer/index.
php
[62]
3.10 ProteinProtein
Interaction
Arabidopsis Interactions
Viewer 2
http://bar.utoronto.ca/interactions2/
[66]
3.11 Integrated
Tools
Virtual Plant
http://virtualplant.bio.nyu.edu/cgi-bin/
vpweb/
[68]
Gene Mania
http://genemania.org/
[87]
ePlant
http://bar.utoronto.ca
[73]
(continued)
Arabidopsis Bioinformatics
27