Lists

Lists allow you to manipulate sets of data at once. It is possible to upload your own lists of favourite contigs and save lists from results tables produced by searches. We have also created useful public lists that may be of general interest.

You can use the lists tab to:

• Combine lists to create a union of two lists,
• Get the intersection or differences between two lists
• use as input to our custom templates for searching the database
• use as input to our widgets to look for GO term or protein domain enrichment

See the lists section in our user manual for more information on generating and working with lists.

Templates

Templates provide predefined quick access to many of the useful search functions of planmine. We have preconfigured a number of forms allowing you to simply paste your input data (keyword, id, list) and query the database using various filters to give a results table.

Templates cover questions such as:

• Comparing Schmidtea assemblies: I have a dd_Smed contig id but what is the orthologous id in the ox_Smed assembly?
• Comparing Species: I’d like to find all contigs with a particular InterPro protein domain
• Comparing Functions: I’d like to find all Gene Ontology terms associated with a Contig ID
• Transcripts: I’d like the longest Open Reading Frame detected within a particular contig

For advanced searches the QueryBuilder tool is very powerful and for help with this see the section in our user manual.

MyMine

Mymine is the place to store your own personal

• queries and lists,
• modified query template searches
• mark favourite lists or templates to make them easier to find

The MyMine tab at the top of the page in the place to go for this functionality, but first you must create an account with use by providing and email address and password.

Learn about Planarians

The Species Pages provide background information on each species represented in PlanMine with a transcriptome. Information includes

• Pictures
• Background on the species' ecology and habitat
• Taxonomy references
• Distribution map (courtesy of Turbellarian database)
• Transcriptome stats

You can browse and access the species pages via the picture links on the home page.

Learn about gene functions

For each Smed transcript, the transcript pages give information on

• BLAST homologies in other species
• Domain predictions and GO term annotations
• Differential gene expression during regeneration, under different RNAi conditions or cell-type specific expression levels.
• Links to the publication describing the transcript, if any.
• Using the lists feature, you can analyze gene lists for GO term enrichment.

Differential gene expression data is currently only available for the dd_Smed assembly, utilizing published data sets. Access the transcript page by querying a specific transcript ID or clicking a transcript ID in a BLAST search results page.

Compare different Smed assemblies

No de novo assembled transcriptome is perfect. Transcript comparisons amongst the 5 independent Smed assemblies in PlanMine allow you to:

• Find orthologous transcripts in other assemblies
• Detect likely assembly mistakes (e.g., chimeras, fragmented transcripts)
• Find transcripts missing in a particular assembly
• Retrieve the longest ORF for a particular gene
• Assess assembly stats and download the individual transcriptomes.

Mine the unique pluripotent stem cell system of planarians

Planarians rely on abundant adult pluripotent stem cells to continuously renew all organismal cell types. PlanMine therefore offers a unique phylogenetic perspective on stem cell pluripotency. Salient features include:

• Minable lists of planarian stem cell and progeny enriched genes
• Differential gene expression data in stem cells, progeny and differentiated cells
• Differential gene expression data of radiation sensitive genes
• Easy Blast and annotation searches for identifying planarian orthologues of vertebrate stem cell genes

Probe the Planarian gene complement

Planarians are situated in a scarcely sampled corner of the tree of life. The planarian transcriptomes in PlanMine therefore provide a strategic resource for studying gene evolution. Useful features include:

• Easy search interface and comprehensive annotation of all transcriptomes
• Easy identification and downloading of complete gene families
• Orthologue information for planarian inter-species comparisons
• Thorough assembly reports and quality stats on each transcriptome
• Facile download options for transcriptomes and annotations