PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology.
It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPI...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5638325?pdf=render |
| _version_ | 1819068266312630272 |
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| author | Aris Gioutlakis Maria I Klapa Nicholas K Moschonas |
| author_facet | Aris Gioutlakis Maria I Klapa Nicholas K Moschonas |
| author_sort | Aris Gioutlakis |
| collection | DOAJ |
| description | It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets. Moreover, the irreversible a priori normalization process hinders the identification of normalization artifacts in the integrated network, which originate from the nonlinearity characterizing the genetic information flow. PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. Its main novel feature over the existing meta-databases is its approach to primary PPI dataset integration via genetic information ontology. Building upon the PICKLE principles of using the reviewed human complete proteome (RHCP) of UniProtKB/Swiss-Prot as the reference protein interactor set, and filtering out protein interactions with low probability of being direct based on the available evidence, PICKLE 2.0 first assembles the RHCP genetic information ontology network by connecting the corresponding genes, nucleotide sequences (mRNAs) and proteins (UniProt entries) and then integrates PPI datasets by superimposing them on the ontology network without any a priori transformations. Importantly, this process allows the resulting heterogeneous integrated network to be reversibly normalized to any level of genetic reference without loss of the original information, the latter being used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. The PICKLE web-based interface (www.pickle.gr) allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes. |
| first_indexed | 2024-12-21T16:31:25Z |
| format | Article |
| id | doaj.art-b1f43378469a4b42bdefe29985a0d0f4 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T16:31:25Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-b1f43378469a4b42bdefe29985a0d0f42022-12-21T18:57:21ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-011210e018603910.1371/journal.pone.0186039PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology.Aris GioutlakisMaria I KlapaNicholas K MoschonasIt has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets. Moreover, the irreversible a priori normalization process hinders the identification of normalization artifacts in the integrated network, which originate from the nonlinearity characterizing the genetic information flow. PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. Its main novel feature over the existing meta-databases is its approach to primary PPI dataset integration via genetic information ontology. Building upon the PICKLE principles of using the reviewed human complete proteome (RHCP) of UniProtKB/Swiss-Prot as the reference protein interactor set, and filtering out protein interactions with low probability of being direct based on the available evidence, PICKLE 2.0 first assembles the RHCP genetic information ontology network by connecting the corresponding genes, nucleotide sequences (mRNAs) and proteins (UniProt entries) and then integrates PPI datasets by superimposing them on the ontology network without any a priori transformations. Importantly, this process allows the resulting heterogeneous integrated network to be reversibly normalized to any level of genetic reference without loss of the original information, the latter being used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. The PICKLE web-based interface (www.pickle.gr) allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes.http://europepmc.org/articles/PMC5638325?pdf=render |
| spellingShingle | Aris Gioutlakis Maria I Klapa Nicholas K Moschonas PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PLoS ONE |
| title | PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. |
| title_full | PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. |
| title_fullStr | PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. |
| title_full_unstemmed | PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. |
| title_short | PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. |
| title_sort | pickle 2 0 a human protein protein interaction meta database employing data integration via genetic information ontology |
| url | http://europepmc.org/articles/PMC5638325?pdf=render |
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