Kristian Gray

Title

"New look HGNC gene families"

Home town

Handsworth, Sheffield

Where Benjamin Huntsman developed crucible steel

Highest degree

MSc in Bioinformatics from the University of Manchester

Previous teams

Cancer genome project and core software services team within the Sanger Institute

Current role

Scientific programmer within the HGNC

Unusual

Running 10K races and brewing all grain beer. One does not help the other ;-)

New look HGNC gene families

A whirlwind tour of our new gene family resource

Kristian Gray

What do we mean by gene families?

Biological dictionary: "A group of genes that have arisen by duplication of an ancestral gene. Such genes show similarities of nucleotide sequence ..." (Oxford Dictionary of Biology)
HGNC gene family: A group of genes that share important characteristics such as homology, work within a complex unit or participate in the same process

Old gene families

Family index

G protein-coupled receptors

Class B GPCRs, secretin-type

Index

Family with hierarchy

Family containing genes

Problems with the old version

Family data had to be added to multiple locations within Drupal and our MySQL DB.
Database schema wasn't designed to handle hierarchies or genes within multiple families.
Each page was created by hand and no defined template.
Pages could be more user friendly to navigate.
Users had to download each subset family to get all the genes associated to a family with a hierarchy
Pages containing many subset families were slow to load.
Difficult to visualise complex hierarchies
Couldn't search families effectively.

Family data had to be added to both Drupal and our MySQL DB, as well as separately adding the family to the index, which means a lot of time is spent adding family data to multiple locations.
The database schema wasn't designed to handle hierarchies or that a gene could have more than one family. The only place that had hierarchy data was Drupal and the only place that had gene data was the DB which was not ideal.
Each page was created by hand within Drupal by our curtors and didn't have a defined template.
And so were not friendly to navigate.
To download all the genes within a family containing a hierarcy, the user had to download a file for each subset family. In the case of the G protein coupled receptors that is a lot of downloading and file concatinations
Pages that contained many subsets were slow to load due to the module that creates the gene tables being called one after the other hitting the database many time before loadin the page.
Wasn't easy to visualise the hierarchy for a complex family such as G protein coupled receptors.
And users couldn't search families effectively.

Solution?

Rethink & redevelop a new gene families resource.

NEW HGNC gene families

Family index

Adhesion G protein-coupled receptors

Adhesion G protein-coupled receptors, subfamily C

Family index

Family containing sub-families - title

Family containing sub-families - map

Family containing sub-families - description & subsets

Family containing sub-families - genes within all subsets

Family containing sub-families - useful information and downloads

Sub family containing genes

Family without a hierarchy

New search with families

Search all pages

Search family pages

Kristian Gray

New look HGNC gene families

A whirlwind tour of our new gene family resource

What do we mean by gene families?

Old gene families

Index

Family with hierarchy

Family containing genes

Problems with the old version

Solution?

NEW HGNC gene families

Family index

Family containing sub-families - title

Family containing sub-families - map

Family containing sub-families - description & subsets

Family containing sub-families - genes within all subsets

Family containing sub-families - useful information and downloads

Sub family containing genes

Family without a hierarchy

New search with families

Search all example

Search families only

Coming soon

New HGNC BioMart server for genes and families

RESTful family API

Acknowledgments

Any questions?