Neo4j Browser

NEO4J Graph Database

Orthology between 5 Cephalopod and 3 other Mollusc species that have chromosomal genome assemblies:

Euprymna scolopes, Octopus sinensis, Nautilus pompilius, Doryteuthis pealeii, Octopus bimaculoides, Pecten maximus, Achatina fulica, and Anadara broughtonii.

You can investigate orthology between these species spanning 3 different levels: Chromosomes, Genes, and Conserved Noncoding Elements (CNEs). Note: CNE's for the last two species above are not integrated completely, yet

To access our database, please click here and on the new page that opens, click Connect without changing any settings.

Our database is built with NEO4J graph database management system which has its own query language called Cypher.

You can generate Cypher query commands for a few different types of interesting questions below.

First, fill in or choose the available options, then click Generate cypher code.

Next, you can simply select the whole code, and copy and paste it into NEO4J command line and run it.

Or you can click Download cypher code and then drag and drop the cypher file you've downloaded onto the NEO4J browser page.

You can then click Save to favorites and run it from favorites via the Star icon on left, or simply Paste to editor and run it from command line.

You can download the visualization of your orthology searches of interest using the download icon on the right top in various formats.

Note: If your search returns no matches, you will receive a "(no changes, no records)" message.

Shortcuts for Available Query Types

To view co-localized orthologous genes and CNE's click here, to filter that for a chromosome click here. and to filter it for a gene click here.

To show orthologous genes and CNEs located on orthologous chromosomes click here, for those on non-orthologous chromosomes click here.

To get the total counts of orthologous genes and CNEs located on orthologous chromosomes click here, for those on non-orthologous chromosomes click here.

For genes that are located in a region, to show the orthologous genes click here.

To see the orthologous gene of your gene of interest click here.

To see the orthologous chromosome of your chromosome of interest click here.

To get the total counts of Gene-CNE pairs where both orthologous genes and CNE’s are on orthologous chromosomes click here, for those with orthologous CNE's on non-orthologous chromosomes click here.

For genes that are located in a region, to show the orthologous genes in two other species click here, for the same thing for CNE's click here.

To calculate the average distances of orthologous gene and CNE pairs click here.

Cypher Query Generators for Neo4J

Query Type 1: Find orthologous genes and CNE's that are within a certain distance.

Get an immediate overview of co-localized CNEs and Genes where you can see which of them are on orthologous chromosomes and which had been moved to a different chromosome.

Query Type 2: Limit the Query Type 1 above for a single chromosome.

Please choose Species 1 as the species that you would like to filter your query for using a chromosome of your interest.

Query Type 3: Limit the Query Type 1 above for a single gene.

Please choose Species 1 as the species that you would like to filter your query for using the gene ID of your interest.

Query Type 4: Find the orthologous genes and CNEs of those on chromosome of Species 1 that are located on the orthologous chromosome(s) in the Species 2.

Please choose Species 1 as the species that you would like to query for the chromosome of your interest.

Query Type 5: Find the orthologous genes and CNEs of those on chromosome of Species 1 that are located on the NON-orthologous chromosomes in the Species 2.

Please choose Species 1 as the species that you would like to query for the chromosome of your interest.

Query Type 6: Get the counts of the orthologous genes and CNEs located on the same chromosomes of Species 1 that are located on an orthologous chromosome(s) in the Species 2.

Query Type 7: Get the counts of the orthologous genes and CNEs located on the same chromosomes of Species 1 that are located on the NON-orthologous chromosomes in the Species 2.

Query Type 8: For the genes that are located between two coordinates on a chromosome of Species 1, show the orthologous genes in Species 2.

Query Type 9: Find the orthologous gene of your gene of interest in another species.

Query Type 10: Total counts of Gene-CNE pairs in a bp distance in Species 1, where both Orthologous genes and Orthologous CNE’s are on Orthologous Chromosomes in Species 2.

Query Type 11: Total counts of Gene-CNE pairs in a bp distance in Species 1, where Orthologous genes are on Orthologous Chromosomes in Species 2 but Orthologous CNE’s are not.

Query Type 12: For the genes that are located between two coordinates on a chromosome of Species 1, show the orthologous genes in Species 2 and Species 3.

Query Type 13: For the CNEs that are located between two coordinates on a chromosome of Species 1, show the orthologous CNEs in Species 2 and Species 3.

Query Type 14: Generate a list of all pairs of genes or CNE's that also have an orthologous pair in the other species on the same chromosome and the average distances.