CoNekT@LIS : Co-expression Network Toolkit at LIS

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.

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)
Cicer:
Singh, V.K., Garg, R. and Jain, M. (2013), A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnol J, 11: 691-701 (PRJNA182724)
Glycine:
Libault M et al., An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants., Plant J, 2010 Apr 7;63(1):86-99
Phaseolus:
O'Rourke JA, Iniguez LP, Fu F, Bucciarelli B, Miller SS, Jackson SA, McClean PE, Li J, Dai X, Zhao PX, Hernandez G, Vance CP. An RNA-Seq based gene expression atlas of the common bean. BMC Genomics. 2014 Oct 6;15:866. (PRJNA210619)
Vigna:
The Vigna unguiculata Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data provides insights into seed maturation mechanisms (PRJNA389300)

About CoNekT

This is an instance of CoNekT (Coexpression Network Toolkit) at LIS, The Legume Information System.

It is work in progress at LIS and only some functionalities of CoNekT have been implimented here so far.

Publication for CoNekT:
CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses (Proost and Mutwil, NAR 2018).

More information about CoNekT is available at GitHub(the original version) and more recently at https://github.com/sepro/CoNekT.