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One of the outputs of the Tomato Expression Atlas is the Expression Cube which displays a list of genes grouped by their similarity in expression profiles. Co-expressed genes tend to participate in the same biological processes and therefore this co-expression tool can be used to reveal new genes potentially involved in similar processes as the query gene. As explained in previous sections, pasting the query gene ID into the input box named By Gene ID and clicking on Get Expression will display the expression values from the query gene and a list of candidates genes with correlated expression profiles.

4.1 Example: Identification of candidate genes involved in vascular tissue development

As an example, we will use the gene Solyc04g080940, with the description "Noduline-like protein", as a query gene. This gene is homolog of the Medicago truncatula gene "nodulin 21", which is upregulated in Rhizobium-induced Medicago nodules (Ranocha et al. 2013), and to the Arabidopsis thaliana gene AT1G75500, "Walls are thin 1" (WAT1), a member of the plant drug/metabolite exporter (P-DME) family. WAT1 is preferentially expressed in vascular tissues, including developing xylem vessels and fibers (Ranocha et al. 2010), and WAT1 mutants show defects in cell elongation, a dwarfed phenotype and little to no secondary cell walls in stem fibers (Ranocha et al. 2010). WAT1 has also been shown to act as a vacuolar auxin transport facilitator required for auxin homoeostasis and involved in regulating fibre cell wall thickness (Ranocha et al. 2013).

The tomato WAT homolog, Solyc04g080940 (Figure 1) is highly expressed in the pericarp vascular tissue during cell expansion, from 5 days post anthesis (DPA) to the mature green stage.
The list of genes co-expressed with Solyc04g080940 suggests genes with functions related to WAT1 in vascular tissue development and hormone/amino acids transport. Particularly interesting are Solyc01g100920 and Solyc03g005480, which are also described as "Noduline-like proteins" (table 1, in yellow): and homologs to arabidopsis genes encoding amino acids transporters (TAIR). Other genes involved on vascular tissue development (xylem/phloem) that are shown in the co-expression cube are the genes Solyc03g111810, Solyc05g013850 and Solyc05g013870 (table 1, in gray). These genes are homolog of AT3G01680, which encodes a structural protein found in phloem sieve elements (Anstead et al. 2012, Ruping et al. 2010).

The list of co-expressed genes in the expression cube can indicate candidate genes potentially involved in the same biological process or pathway, including transcription factors that may regulate their expression, and that can then be selected for experimental validation.

Figure 1. Expression Cube output for Solyc04g080940.

Table 1. Genes co-expressed with Solyc04g080940 on the expression cube.

Gene ID	Description	Correlation val.	Ath Homolog	Ath Gene Name
Solyc04g080940	Nodulin-like protein	1	AT1G75500	WAT1/UMAMIT5
Solyc02g061990	Basic leucine zipper transcription factor	0.91	AT2G17770	ATBZIP27
Solyc01g066860	Unknown Protein	0.9	AT1G63310
Solyc03g095490	Receptor like kinase, RLK	0.9	AT5G58300
Solyc03g111810	Sieve element-occluding protein 3	0.9	AT3G01680	AtSEOR1
Solyc04g072030	Interferon-induced GTP-binding protein Mx	0.9	AT1G60500	DRP4C
Solyc05g006830	Thioredoxin H	0.9	AT5G39950	ATTRX2
Solyc05g013850	Sieve element-occluding protein 3	0.9	AT3G01680	AtSEOR1
Solyc05g013870	Sieve element-occluding protein 3	0.9	AT3G01680	AtSEOR1
Solyc06g083080	Unknown Protein	0.9	AT5G48500
Solyc11g011890	Zinc finger protein 7	0.9	AT1G66140	ZFP4
Solyc01g100920	Nodulin-like protein	0.89	AT1G09380	UMAMIT25
Solyc05g010400	Receptor like kinase, RLK	0.89	AT5G16000	ATNIK1
Solyc08g066490	Receptor like kinase, RLK	0.89	AT2G25790	SKM1
Solyc08g075880	Metal ion binding protein	0.89	AT2G18196
Solyc09g009830	Carbonic anhydrase (Carbonate dehydratase)	0.89
Solyc11g011920	Glutamate decarboxylase	0.89
Solyc11g069570	Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG	0.89
Solyc01g101120	Glucan endo-1 3-beta-glucosidase 1	0.88
Solyc02g076690	Cathepsin B-like cysteine proteinase	0.88
Solyc02g080900	Genomic DNA chromosome 5 TAC clone K6A12	0.88
Solyc03g005480	Nodulin-like protein	0.88	AT2G39510	UMAMIT14

References

Anstead et al. 2012	Arabidopsis P-Protein Filament Formation Requires Both AtSEOR1 and AtSEOR2
Ranocha et al. 2010	Walls are thin 1 (WAT1), an Arabidopsis homolog of Medicago truncatula NODULIN21, is a tonoplast-localized protein required for secondary wall formation in fibers
Ranocha et al. 2013	Arabidopsis WAT1 is a vacuolar auxin transport facilitator required for auxin homoeostasis
Ruping et al. 2010	Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants