Tools

Arachis Gene Expression Search Boxes

Arachis hypogaea Gene Expression at Arachismine

Expression plot in ArachisMine for genes from the in the Tifrunner.gnm2.ann2.
Prefixed gene ID:

Examples (include prefix; assembly 2): glyma.Wm82.gnm2.ann1.Glyma.15g026400 glyma.Wm82.gnm2.ann1.Glyma.12G040000
URL for the gene: https://mines.legumeinfo.org/glycinemine/gene:glyma.Wm82.gnm2.ann1.Glyma.15g026400

... or enter a gene in the Gene Search Tool, then choose the link to GlycineMine:

Examples (prefix optional; assembly 2): Glyma.15g026400 glyma.Wm82.gnm2.ann1.Glyma.12G040000

Arachis gene expression at CoNekT

Click for a description of the table, and credits and usage agreement

A toolkit to visualize co-expression of genes across species in selected datasets

The current version was built with a few species using the following annotations-- arahy.Tifrunner.gnm2.ann1, cicar.CDCFrontier.gnm1.ann1, glyma.Wm82.gnm2.ann1, phavu.G19833.gnm1.ann1, vigun.IT97K-499-35.gnm1.ann1 and accepts only those gene IDs. See below for the source of data.

Commonly Used Tools


Expression Profile of a Single Gene, Family Members and Profile Neighbors:

Paste & submit below an exact gene ID from the appropriate annotation to
(i) display its expression profile,
(ii) click the link for 'Phylogenetic Tree(s):' to display a comparative heatmap of the gene family members and
(iii) below it find similarly expressed genes(profile neighbors) in section 'Co-expression Networks' in the result page.

geneID (Full exact ID):
Examples:     arahy.Tifrunner.gnm2.ann1.0003EL     cicar.CDCFrontier.gnm1.ann1.Ca_06316      glyma.Wm82.gnm2.ann1.Glyma.06G321800     phavu.G19833.gnm1.ann1.Phvul.001G000500     vigun.IT97K-499-35.gnm1.ann1.Vigun06g115800
URL for the gene:

Compare Expression Profiles:

Compare the expression of up to 50 genes on the same graph in each experimental condition or tissue.

Gene Expression Heatmap:

Visualize gene expression of a list of genes as a heatmap. The expression of a list of genes can be compared within a species using the default tab or between species using the comparative tab as a heatmap. The between species comparison can accept a list of more than 50 genes but is limited in the number of conditions or tissues visualized-- only for those tissue groups common to multiple species.

Find Genes Specifically Expressed in a Given Tissue:

Using the form here genes can be found which are expressed specifically under a desired condition. Try SPM value 1.0 to list highly specific genes if exist.

Compare Specificity :

Find out which genes are expressed specifically in species and/or conditions and have homologs expressed in a different species and/or condition.

Expression of Gene Family Members:

Use the Advanced Search tool to choose a species and input the exact gene family ID (select the available method; do not disable). Search will list all the available genes in the given gene family with links to each of their expression profiles. Example grne family id: legfed_v1_0.L_D1KBMC


Source of Data

Arachis:
Josh Clevenger, Ye Chu, Brian Scheffler, Peggy Ozias-Akins, A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea, Front. Plant Sci. (2016)"(PRJNA291488)