Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity

Simple item page
dc.contributor.authorKanapin, Alexanderen_ZA
dc.contributor.authorMulder, Nicolaen_ZA
dc.contributor.authorKuznetsov, Vladimiren_ZA
dc.date.accessioned2015-11-11T11:57:24Z
dc.date.available2015-11-11T11:57:24Z
dc.date.issued2010en_ZA
dc.description.abstractWe consider the problem of biological complexity via a projection of protein-coding genes of complex organisms onto the functional space of the proteome. The latter can be defined as a set of all functions committed by proteins of an organism. Alternative splicing (AS) allows an organism to generate diverse mature RNA transcripts from a single mRNA strand and thus it could be one of the key mechanisms of increasing of functional complexity of the organism's proteome and a driving force of biological evolution. Thus, the projection of transcription units (TU) and alternative splice-variant (SV) forms onto proteome functional space could generate new types of relational networks (e.g. SV-protein function networks, SFN) and lead to discoveries of novel evolutionarily conservative functional modules. Such types of networks might provide new reliable characteristics of organism complexity and a better understanding of the evolutionary integration and plasticity of interconnection of genome-transcriptome-proteome functions. RESULTS: We use the InterPro and UniProt databases to attribute descriptive features (keywords) to protein sequences. UniProt database includes a controlled and curated vocabulary of specific descriptors or keywords. The keywords have been assigned to a protein sequence via conserved domains or via similarity with annotated sequences. Then we consider the unique combinations of keywords as the protein functional labels (FL), which characterize the biological functions of the given protein and construct the contingency tables and graphs providing the projections of transcription units (TU) and alternative splice-variants (SV) onto all FL of the proteome of a given organism. We constructed SFNs for organisms with different evolutionary history and levels of complexity, and performed detailed statistical parameterization of the networks. CONCLUSIONS: The application of the algorithm to organisms with different evolutionary history and level of biological complexity (nematode, fruit fly, vertebrata) reveals that the parameters describing SFN correlate with the complexity of a given organism. Using statistical analysis of the links of the functional networks, we propose new features of evolution of protein function acquisition. We reveal a group of genes and corresponding functions, which could be attributed to an early conservative part of the cellular machinery essential for cell viability and survival. We identify and provide characteristics of functional switches in the polyform group of TUs in different organisms. Based on comparison of mouse and human SFNs, a role of alternative splicing as a necessary source of evolution towards more complex organisms is demonstrated.The entire set of FL across many organisms could be used as a draft of the catalogue of the functional space of the proteome world.en_ZA
dc.identifier.apacitationKanapin, A., Mulder, N., & Kuznetsov, V. (2010). Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity. <i>BMC Genomics</i>, http://hdl.handle.net/11427/14872en_ZA
dc.identifier.chicagocitationKanapin, Alexander, Nicola Mulder, and Vladimir Kuznetsov "Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity." <i>BMC Genomics</i> (2010) http://hdl.handle.net/11427/14872en_ZA
dc.identifier.citationKanapin, A. A., Mulder, N., & Kuznetsov, V. A. (2010). Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity. BMC genomics, 11(Suppl 1), S4.en_ZA
dc.identifier.ris TY - Journal Article AU - Kanapin, Alexander AU - Mulder, Nicola AU - Kuznetsov, Vladimir AB - We consider the problem of biological complexity via a projection of protein-coding genes of complex organisms onto the functional space of the proteome. The latter can be defined as a set of all functions committed by proteins of an organism. Alternative splicing (AS) allows an organism to generate diverse mature RNA transcripts from a single mRNA strand and thus it could be one of the key mechanisms of increasing of functional complexity of the organism's proteome and a driving force of biological evolution. Thus, the projection of transcription units (TU) and alternative splice-variant (SV) forms onto proteome functional space could generate new types of relational networks (e.g. SV-protein function networks, SFN) and lead to discoveries of novel evolutionarily conservative functional modules. Such types of networks might provide new reliable characteristics of organism complexity and a better understanding of the evolutionary integration and plasticity of interconnection of genome-transcriptome-proteome functions. RESULTS: We use the InterPro and UniProt databases to attribute descriptive features (keywords) to protein sequences. UniProt database includes a controlled and curated vocabulary of specific descriptors or keywords. The keywords have been assigned to a protein sequence via conserved domains or via similarity with annotated sequences. Then we consider the unique combinations of keywords as the protein functional labels (FL), which characterize the biological functions of the given protein and construct the contingency tables and graphs providing the projections of transcription units (TU) and alternative splice-variants (SV) onto all FL of the proteome of a given organism. We constructed SFNs for organisms with different evolutionary history and levels of complexity, and performed detailed statistical parameterization of the networks. CONCLUSIONS: The application of the algorithm to organisms with different evolutionary history and level of biological complexity (nematode, fruit fly, vertebrata) reveals that the parameters describing SFN correlate with the complexity of a given organism. Using statistical analysis of the links of the functional networks, we propose new features of evolution of protein function acquisition. We reveal a group of genes and corresponding functions, which could be attributed to an early conservative part of the cellular machinery essential for cell viability and survival. We identify and provide characteristics of functional switches in the polyform group of TUs in different organisms. Based on comparison of mouse and human SFNs, a role of alternative splicing as a necessary source of evolution towards more complex organisms is demonstrated.The entire set of FL across many organisms could be used as a draft of the catalogue of the functional space of the proteome world. DA - 2010 DB - OpenUCT DO - 10.1186/1471-2164-11-S1-S4 DP - University of Cape Town J1 - BMC Genomics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2010 T1 - Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity TI - Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity UR - http://hdl.handle.net/11427/14872 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/14872
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-11-S1-S4
dc.identifier.vancouvercitationKanapin A, Mulder N, Kuznetsov V. Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity. BMC Genomics. 2010; http://hdl.handle.net/11427/14872.en_ZA
dc.language.isoengen_ZA
dc.publisherBioMed Central Ltden_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Licenseen_ZA
dc.rights.holder2010 Kanapin et al; licensee BioMed Central Ltd.en_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en_ZA
dc.sourceBMC Genomicsen_ZA
dc.source.urihttp://www.biomedcentral.com/bmcgenomics/en_ZA
dc.subject.otherEvolution, Molecularen_ZA
dc.subject.otherGene Regulatory Networksen_ZA
dc.subject.otherProteomeen_ZA
dc.subject.otherTranscription, Geneticen_ZA
dc.titleProjection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexityen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Kanapin_Projection_of_gene_protein_networks_2010.pdf
Size:
1015.91 KB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Journal Articles