Plant Co-expression Annotation Resource

PlantAnnot aggregates orthology, co-expression networks and genomic data from 67 plant genomes to find and annotate Proteins of Unknown Function (PUFs) that may be involved in abiotic stress responses.

Or view the Data Summary for an overview of all loaded organisms.

What PlantAnnot Delivers

Functional clues for the proteins that no database annotates.

Guilt-by-Association Annotation

PUFs inherit functional clues from their orthogroup. Members that already carry annotation or characterised protein domains act as a proxy, so an uncharacterised co-member can be assigned a candidate function by association.

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Faceted PUF Search

Isolate candidates with stacked facets: organism, sequence ontology term, orthology, co-expression involvement, and the absence of DIAMOND or InterProScan matches that defines a PUF in the first place.

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67 Plant Genomes

Genomes downloaded from Phytozome and NCBI, including 14 added in v2 - among them Pearl millet and Populus simonii, both with characteristics of tolerance to abiotic stresses.

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Release Notes

Latest updates, improvements, and changes.

14 new genomes were added, including 2 with characteristics of tolerance to abiotic stresses: Pearl millet and Populus simonii. The RNA-seq basis is more diverse, covering new tissues, stages of development and additional sources of abiotic stress. Orthogroups are now built with OrthoFinder instead of OrthoMCL.
First public release of the Plant Co-expression Annotation Resource: orthology from OrthoMCL combined with LSTrAP and MCL co-expression networks for Arabidopsis thaliana, Glycine max, Oryza sativa and Zea mays, used to infer abiotic-stress involvement for Proteins of Unknown Function by guilt-by-association.

How PlantAnnot Works

From public genomes and stress RNA-seq to candidate stress-related proteins.

To check how many PUFs Oropetium thomaueum has click here.

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

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.

1

Aggregate Genomes and RNA-seq

67 plant genomes are collected from Phytozome and NCBI, alongside RNA-seq of abiotic stress - heat, cold, drought, dehydration and osmotic stress - drawn from NCBI/GEO across 44 Series and 154 Samples.

2

Build Orthogroups and Networks

OrthoFinder groups the proteins into orthogroups, while LSTrAP v1.3 and MCL build co-expression networks for four model organisms: Arabidopsis thaliana, Glycine max, Oryza sativa and Zea mays.

3

Infer and Explore

When a PUF shares an orthogroup with an Ath, Gma, Osa or Zma member whose mRNA belongs to a co-expression group, the PUF is flagged as a candidate for abiotic stress involvement - ready to explore through the search facets.

References

PlantAnnot: BMC Bioinformatics (2021), doi:10.1186/s12859-020-03792-z
Machado Genomics: GigaScience (2020), doi:10.1093/gigascience/giaa097