News

March 12, 2010

Several minor bug fixes applied.
InnateDB now considers pathway hierarchies from Reactome and INOH.
New gene list of curated genes playing a role in innate immune response.
New XML download file for curated interactions.
New data analysis feature: Upload a list of gene/protein identifiers using InnateDB-internal identifiers.
New data analysis feature: Downloadable results for predicted TF interactions now include cross-references for TFs.
Updated pathway data from Reactome (2009-Dec-15), KEGG (2010-Mar-10), and PID-NCI (2010-Mar-09).

A new XML file for InnateDB-curated interactions has been made available in order to fix the omission of approximately 600 interactions.

A variety of minor bug fixes.
New data analysis feature: Upload a list of gene/protein identifiers and view CisRed-predicted transcription factor interactions.
Perform analysis to identify transcription factor interactions that are over-represented in differentially expressed data.
New user interface for uploading gene/protein identifiers and specifying expression data.
Updated interactions from MINT (2009-July-29), IntAct (2009-Sept-24) and BioGRID (2009-Aug-31)
Updated pathway data from NetPath (2009-Jan-20), KEGG (2009-Oct-17), Reactome (2009-Sep-30), PID-NCI (2009-Oct-14) and PID-BioCarta (2009-Sept-09).
Updated gene and protein annotations based on Ensembl release 55 and UniProt.
Updated ortholog predictions based on Ortholuge analysis.
The InnateDB curation team has now contextually annotated more than 10,000 innate immunity relevant interactions. Thanks to everyone who has helped us achieve this goal.
New InnateDB annotation on the role of genes in innate immunity (~300 genes - ongoing).
New links to the Phosphosite database.
Updated XML download files.
InnateDB is now running on a 64-bit server with load-balancing and access to additional RAM for high-memory analyses.

Our review of systems-level approaches to investigating innate immunity is published in Trends in Immunology, June, 2009.

Upgraded to Cytoscape 2.6.2 on April 1, 2009. This fixes a bug that was causing an incompatibility with cerebral for Mac OS X users.

New Cytoscape version: 2.6.1
Updated database backbone based on Ensembl release 52.
Updated Interactions: new import process and updated datasets. InnateDB now contains 110,000+ interactions.
Updated pathways. New datasets and new dynamic links to KEGG from the ORA result page. InnateDB now contains 3100+ pathways.
Several minor bug fixes applied.

Important bug fix for interaction batch searches. An automated script introduced an bug on October 12th, causing data corruption in the interaction batch searches.

New Cytoscape plugin: CyOog. Enables power graph analysis of InnateDB interaction network data.
Improved gene batch search speeds by using large weekly updated concat tables of the database: now 4 to 5 times faster.
Interaction batch search can now be limited to return only interactions between genes in the uploaded file.
Solved issue with the export to Cerebral/Cytoscape for genes without gene symbols.
Complexes are now decomposed into their component interactions in Cerebral.
Fixed bug related to displayed columns when using multiple browser sessions simultaneously.
Several minor bug fixes applied.

Application code updated and now more resistant to Java null exceptions.
Improved interaction batch search speeds by using large weekly updated concat tables of the database. The 5,000 gene limit for batch searching interactions has been removed.
Solved issue with the export to Cerebral/Cytoscape for genes without gene symbols.
Fixed bug in alphanumeric sorting.
Solved issue with Cerebral/Cytoscape which would not open pathways with no annotated interactions. Now pathway will load with just the genes displayed if there are no interactions.