- 26.08.2013 ConsensusPathDB version 27 has been released. A new data set has beed integrated into ConsensusPathDB: complex and binary protein interactions from the Protein Data Bank (PDB). Complex interactions are defined directly from the protein complexes found in PDB. Binary interactions are defined based on the direct contacts between proteins in PDB structures (data obtained from PDBsum).
- 11.05.2013 ConsensusPathDB version 26 has been released.
- 06.10.2012 ConsensusPathDB version 25 has been released. A new database has been integrated: ChEMBL contains drug-target interactions curated from the literature. In subsequent ConsensusPathDB releases, we will be filtering the data from ChEMBL based on identifyability of drugs and targets.
- 02.07.2012 ConsensusPathDB version 24 has been released. This build contains 215,541 interactions (5,260 new ones), 60,733 physical entities (4,059 new ones) and 4,601 pathways (1,264 new ones). We are happy to announce a new feature of the web interface: induced network module analysis (accessible via "gene set analysis" -> "induced network module"). This analysis allows you to upload a list of genes/proteins and view the functional connections between them. Optionally, intermediate nodes can be included (genes/proteins/metabolites/etc. that are not present in your input list of seed nodes, but have significantly many connections to the seed nodes). Expression (or other) values can be overlaid no the computed sub-networks. Moreover, we have scored binary protein-protein interactions in our database using an integrative confidence scoring method available through our tool IntScore.
- 06.04.2012 ConsensusPathDB version 23 has been released. This build contains 210,281 interactions (40,363 new ones), 56,674 physical entities (5,249 new ones) and 3,337 pathways (56 new ones). One new database has been integrated (contributing most of the new interactions): TTD (Therapeutic Target Database) contains thousands of drug-target interactions that have been imported into ConsensusPathDB. Furthermore, pathway over-representation and enrichment analysis with metabolites is now possible. This new feature aims to help you analyse metabolomics data on the pathway level.
- 15.01.2012 ConsensusPathDB version 22 has been released. This build contains 169,918 interactions (8,316 new ones), 51,425 physical entities (981 less than previous release) and 3,281 pathways (95 new ones). With the new year 2012, we have introduced a considerable amount of new data and features to ConsensusPathDB. Two new interaction types are now present in ConsensusPathDB: drug-target interactions and genetic interactions. Also, we have added two more resources: DrugBank (a database of drug-target interactions) and PIN (a database of protein complexes which we have used to define complex protein interactions). Over-representation and enrichment analyses now feature a fourth class of functional gene sets defined from protein complexes (over six thousand complexes are present in our meta-database). Last but not least, we have made essential changes in the accession number mapping module of ConsensusPathDB in the hope to increase even more the performance of over-representation and enrichment analysis. The reduced number of physical entities in this release is due to the fact that we no longer define a ConsensusPathDB entity for every gene that participates in a functional set, but rather define functional sets as lists of Entrez-gene identifiers.
- 11.10.2011 ConsensusPathDB version 21 has been released. This build contains 161,602 interactions (4,141 new ones), 52,406 physical entities (842 new ones) and 3,186 pathways (25 new ones). A resource for protein modification reactions, PhosphoSitePlus, was integrated into ConsensusPathDB.
- 17.07.2011 ConsensusPathDB version 20 has been released. This build contains 157,461 interactions (4,864 new ones), 51,564 physical entities (1,918 new ones) and 3,161 pathways (71 new ones).
- 28.06.2011 ConsensusPathDB version 19 has been released. This build contains 152,597 interactions (18,947 new ones), 49,646 physical entities (3,605 new ones) and 3,090 pathways (17 new ones). Three new databases have been integrated that contribute protein-protein interactions to ConsensusPathDB: BIND, InnateDB, and MatrixDB.
- 12.04.2011 ConsensusPathDB version 18 has been released. This build contains 133,650 interactions, 46,041 physical entities and 3,073 pathways. The decrease in the number of interactions is due to the fact that we do not import human protein interactions from the Pathogen Interaction Gateway (PIG) any more. The reason is mainly that the binary interactions in that meta-database originate from the decomposition of complex interactions (thus many of them are false), or from functional interactions taken from Reactome that constitute no physical interactions but pairs of proteins that catalyse successive metabolic reactions. Since PIG is constructed using some of the databases we integrate in ConsensusPathDB, the data are still present in our database in the form of complex interactions or metabolic reactions, respectively. Thus, in order to increase the quality of the protein interactome in ConsensusPathDB, from now on we only import host-pathogenic protein interactions from PIG.
Two new pathway databases have been integrated that contribute to the collection of curated pathways used for over-representation and enrichment analysis: SignaLink and SMPDB (small molecule pathway database).
- 10.01.2011 ConsensusPathDB version 17 has been released. This build contains 162,152 interactions (6,720 new ones), 43,512 physical entities (2,241 new ones) and 2,473 pathways (268 new ones). Three new databases have been integrated: PDZbase (biochemical reactions), PhosphoPOINT (protein interactions and biochemical reactions) and Wikipathways (pathway definitions to be used with the pathway analysis tools).
- 09.09.2010 ConsensusPathDB version 16 has been released. This build contains 155,432 interactions (3,372 new ones), 41,271 physical entities (2,017 new ones) and 2,205 pathways (67 new ones).
- 21.06.2010 ConsensusPathDB version 15 has been released. This build contains 152,060 interactions (7,493 new ones), 39,254 physical entities (1,464 new ones) and 2,138 pathways (12 new ones). In this release, we have integrated 5,238 physical interactions between human transcription factors published recently in Ravasi et al.: An atlas of combinatorial transcriptional regulation in mouse and man..
- 15.04.2010 ConsensusPathDB version 14 has been released. This build contains 144,567 interactions (6,631 new ones), 37,790 physical entities (2,322 new ones) and 2,126 pathways (10 new ones). In this release, the INOH, EHMN and MIPS-MPPI databases have been added. Moreover, Gene Ontology categories can be tested for enrichment in gene expression data, additionally to NESTs and pathways.
- 08.01.2010 ConsensusPathDB version 13 has been released. This build contains 137,936 interactions (712 new ones), 35,468 physical entities (1,934 new ones) and 2116 pathways (52 new ones). In this release, the CORUM list of human protein complexes has been added. Moreover, after assembling and visualizing a custom interaction network using the Java based visualization framework, it is possible to upload and overlay gene expression data on that network. To do that, simply click on Misc -> expression profile -> load expression profile.
- 09.10.2009 ConsensusPathDB version 12 has been released. This build contains 137,224 interactions (1,766 new ones), 33,534 physical entities (84 less due to increased mapping performance) and 2,064 pathways (107 new ones). In this release, the PharmGKB list of pathways has been added - although the pathways don't have defined interactions, they are useful for pathway over-representation and enrichment analysis. Also, a ConsensusPathDB instance for yeast has gone online. Although this instance is currelty a byproduct, we are planning to invest more efforts to integrate organism-pecific interaction databases (such as MIPS). Furthermore, the human protein interaction network is now available in PSI-MI format in the "data access" section.
- 26.08.2009 The protein interaction part of ConsensusPathDB is available for download. Just click on the "data access" link in the left-hand-side menu. Please consider that the interaction data are available under the licensing terms of the source databases.
- 08.07.2009 ConsensusPathDB version 11 has been released. This build contains 135,458 interactions (2,338 new ones), 33,534 physical entities (1,062 new ones) and 1,957 pathways (40 new ones). Highlight of this update is a new pathway analysis functionality based on the Wilcoxon signed-rank test. Read the documentation for more details. Furthermore, a new, Java-based graph visualization framework is vailable. While it is still under development, you can already benefit from some of the features of this visulization framework. Comments and bug reports are very welcome!
- 04.04.2009 ConsensusPathDB version 10 has been released. A new source database - the
Interaction Gateway (PIG) - has been added to ConsensusPathDB, and herewith an important class of protein interactions -
host-pathogenic protein interactions - have been introduced. PIG contains also human intraspecies interactions obtained from
other databases, some of which are already integrated in ConsensusPathDB (obvious from the big overlaps of PIG with the rest
of the protein interaction data sources). With PIG, 866 pathogen
species have been introduced into our database. Pathogen proteins are marked with a blue border in the visualization
Another important addition to ConsensusPathDB are the large-scale datasets from IntAct (the Ewing,
Rual and Stelzl datasets, combined into a dataset called "IntAct-LS" for "large-scale"). The small-scale part of IntAct
(previously called "IntAct" in ConsensusPathDB) has been renamed to "IntAct-SS".
Also, ConsensusPathDB has been updated with the newest versions of the rest of its source databases. Our database now
comprises 133,120 interactions (56,953
new ones), 32,472 physical entities (5,458 new ones) and 1,917 pathways (42 new ones). The source databases that have been updated
since the last ConsensusPathDB build are: Reactome, KEGG, HumanCyc, PID, IntAct, DIP,
MINT, BioGRID. The increased numbers of new interactions and entities are mostly due to the new
source database additions.
Moreover, we have optimized the over-representation analysis functionality. In short: The hypergeometric test strongly
depends on the background size. Before, there was a single background corresponding to the number of genes / proteins in the
whole ConsensusPathDB. Now, there are specific pre-calculated background sizes that correspond to the numbers of proteins
participating in at least one pathway / NEST and annotated with an identifier of the type used for the uploaded list.
Also, users can optionally upload their own background file (containing the IDs of all measured entities in their experiment).
For more details, please read the according
documentation. Note that the ORA results will now look somewhat different than
before because of these background optimizations.
- 08.01.2009 ConsensusPathDB has been updated with the newest versions of its source
databases. It now comprises 76,167 interactions (1,642 new ones), 27,014 physical
entities (500 new ones) and 1,875 pathways (119 new ones). The source databases that have been updated since the
last ConsensusPathDB build are: Reactome, KEGG, HumanCyc, PID, IntAct and BioGRID.
Furthermore, the database and the web interface have been improved in several ways: a (minor) bug in the Netpath
import script causing faulty protein mappings has been tracked and fixed; the graphical representation of protein
complexes has been improved; the information pages to graph nodes are even more informative now.
- 06.10.2008 ConsensusPathDB has been updated with the newest versions of its source
databases. It now comprises 74,525 interactions (236 new ones), 26,514 physical
entities (381 new ones) and 1,756 pathways (18 new ones). The source databases that have been updated since the
last ConsensusPathDB build are: Reactome, KEGG, PID, IntAct and BioGRID.
- 01.10.2008 Our paper describing ConsensusPathDB has been published in
Nucleic Acids Research(Database Issue).