Plant Co-expression Annotation Resource

The Plant Co-expression Annotation Resource, or plantannot in short, is a system developed to find proteins that have no annotation or function assigned (PUFs, or Proteins of Unknown Function) and could be related to molecular mechanisms regarding abiotic stresses in plants. The systems aggregates orthology, coexpression networks and genomic data to filter the genomes of 53 plants (downloaded from Phytozome and NCBI) and select candidate proteins in that regard.

Methodology

As there are no information regarding the function of PUFs, one way to infer annotation is to link PUFs to other molecules by using ortholog groups in a guilt-by-association algorithm. In this way, members from a given ortholog group which already have annotation and/or have protein domains characterized, can be used as a proxy to infer function for the PUF co-members by association.

Furthermore, co-expression networks were constructed for four organisms Glycine max (Gma), Zea mays (Zma), Arabidopsis thaliana (Ath) and Oryza sativa (Osa), using RNA-seq information related to abiotic stresses (heat, cold, drought, dehydration and osmotic stress), downloaded from NCBI/GEO in a total of 30 different Series and 91 Samples. The RNA-seq data was used as input to the LSTrAP v1.3 software and groups of co-expression were created using the MCL software following the default instructions in LSTrAP.

Check Tables 1 and 2 for data information.

Whenever a given PUF is part of an ortholog group in which some member, necessarily one of Ath, Gma, Osa or Zma, have its mRNA composing a co-expression group, then by association, the initial PUF is supposedly also related to abiotic stresses in plants by inference.

Check the PUF annotation manual for more information.

Follow the tutorial below for more information on the system.

Tutorial

To see how many proteins, genes and organisms are loaded click on the Data Summary

To search all the data click on the blank Search box above

To make specific queries, fill the box with keywords, like this search example: kinase

To make queries on specific organisms (e.g. Oropetium thomaeum) click here to check it out.

To check how many PUFs Oropetium thomaueum has click here to check it out.

To check how many PUFs from Oropetium thomaueum participate in orthologous groups, click here to check it out.

To check how many PUFs from Oropetium thomaueum participate in orthologous groups, in which there are any mRNA that participate in any co-expression groups (which are all related to abiotic stress): click here to check it out.

API

Access PlantAnnot's API .

References

PlantAnnot's BMC Bioinformatics paper .

Machado's GigaScience paper .

New Version Available !

PlantAnnot Version 2.0 .