Announcing the two month old GeneMANIA release!
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Quaid Morris
Dec 20, 2012, 12:44:41 PM12/20/12
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Some of you probably noticed that about two months ago, the GeneMANIA website underwent a major user interface re-design and had added new search features. We hope these changes have improved your GeneMANIA experience but please provide us any feedback that you have about them.
The best way to find out about the changes is to try them out for yourself but here’s a quick summary:
We’ve made a number of improvements to the website interface:
i) The network view has been updated and new colours are used to improve contrast.
ii) Hovering over items in the Networks, Genes, and Functions tabs will now highlight neighbouring genes for easier visualization.
iii) Gene function is displayed using a new grid system which is condensed for quicker scanning and comparing of functions. You can access this when you click on a gene and hovering over a particular grid box will generate a pop-up description of its corresponding function.
iv) The number of genes and interactions are now displayed with each result.
v) The advanced options panel is faster.
vi) Performing a re-query will now use your changed query parameters rather than the parameters of the last query, and resetting the layout will set the nodes to their original positions.
We’ve also added new functionality to GeneMANIA: we’ve added “attributes” as a type of data that you can use to find related genes. Attributes are lists of genes with a shared feature. Right now, we’ve restricted the gene attributes to Interpro-derived protein domains but we have plans to add more attributes in the future (like mutant phenotypes and drug targets). GeneMANIA uses attributes to predict related genes in a similar manner as it does with networks and attribute weights have the same meaning as network weights -- if you use the default weighting scheme, attributes will receive high weight if there are enriched in your gene list (if you input a long gene list) or if they are predictive of Gene Ontology biological process (if you input a short gene list). In the GeneMANIA backend algorithm, each attribute is represented as a single network that contains a link between each pair of genes with that attribute but in the GeneMANIA display, attributes with non-zero weights will appear as a new attribute node (diamond) that will be linked to the genes that have that attribute. Because they are new and we are still investigating how useful they are, attributes are not enabled by default and you need to select them in the advanced options to use them in your queries.
Thanks and please send us feedback about the new version.
The GeneMANIA Team
--
Quaid Morris, PhD
Associate Professor, Banting and Best Department of Medical Research
Departments of Molecular Genetics and Computer Science
The Donnelly Centre, 160 College St, Rm 616
Toronto ON, M5S 3E1 Canada
http://morrislab.med.utoronto.ca
office: (416) 978 8568, cell: (416) 220 5796
The best way to find out about the changes is to try them out for yourself but here’s a quick summary:
We’ve made a number of improvements to the website interface:
i) The network view has been updated and new colours are used to improve contrast.
ii) Hovering over items in the Networks, Genes, and Functions tabs will now highlight neighbouring genes for easier visualization.
iii) Gene function is displayed using a new grid system which is condensed for quicker scanning and comparing of functions. You can access this when you click on a gene and hovering over a particular grid box will generate a pop-up description of its corresponding function.
iv) The number of genes and interactions are now displayed with each result.
v) The advanced options panel is faster.
vi) Performing a re-query will now use your changed query parameters rather than the parameters of the last query, and resetting the layout will set the nodes to their original positions.
We’ve also added new functionality to GeneMANIA: we’ve added “attributes” as a type of data that you can use to find related genes. Attributes are lists of genes with a shared feature. Right now, we’ve restricted the gene attributes to Interpro-derived protein domains but we have plans to add more attributes in the future (like mutant phenotypes and drug targets). GeneMANIA uses attributes to predict related genes in a similar manner as it does with networks and attribute weights have the same meaning as network weights -- if you use the default weighting scheme, attributes will receive high weight if there are enriched in your gene list (if you input a long gene list) or if they are predictive of Gene Ontology biological process (if you input a short gene list). In the GeneMANIA backend algorithm, each attribute is represented as a single network that contains a link between each pair of genes with that attribute but in the GeneMANIA display, attributes with non-zero weights will appear as a new attribute node (diamond) that will be linked to the genes that have that attribute. Because they are new and we are still investigating how useful they are, attributes are not enabled by default and you need to select them in the advanced options to use them in your queries.
Thanks and please send us feedback about the new version.
The GeneMANIA Team
Quaid Morris, PhD
Associate Professor, Banting and Best Department of Medical Research
Departments of Molecular Genetics and Computer Science
The Donnelly Centre, 160 College St, Rm 616
Toronto ON, M5S 3E1 Canada
http://morrislab.med.utoronto.ca
office: (416) 978 8568, cell: (416) 220 5796
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