PopGenIE (Populus Genome Integrative Explorer) is an integrated set of tools for exploring the

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

and

transcriptome The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The t ...

of the model plant system ''

Populus ''Populus'' is a genus of 25–30 species of deciduous flowering plants in the family Salicaceae, native to most of the Northern Hemisphere. English names variously applied to different species include poplar (), aspen, and cottonwood. The we ...

''. PopGenie is a

model organism A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workin ...

database which brings together the increasingly extensive collection of genetics and

genomics Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...

data created by the scientific community in a central resource. Such databases offer a single entry point to the collection of resources, typically including tools for exploring and querying those resources. PopGenIE contains an integrated set of tools including genome,

synteny In genetics, the term synteny refers to two related concepts: * In classical genetics, ''synteny'' describes the physical co-localization of genetic loci on the same chromosome within an individual or species. * In current biology, ''synteny'' mo ...

and

quantitative trait locus A quantitative trait locus (QTL) is a locus (section of DNA) that correlates with variation of a quantitative trait in the phenotype of a population of organisms. QTLs are mapped by identifying which molecular markers (such as SNPs or AFLPs) c ...

browsers for exploring genetic data. Expression tools include an electronic fluorescent pictograph browser, expression profile plots, co-regulation within collated

transcriptomics Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. He ...

data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are available in the browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. PopGenIE significantly increases accessibility to ''Populus'' genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. There are various tools (ePlant.eXplot, PopNet...) available in PopGenIE to analyse biological data. PopGenIE also archived their old versions. All tools are under MIT lLicence.

References

{{Reflist Biological databases