Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus
Abstract Background The influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen. Results In this study, a data mining approach was employed to extract influenza-human Protein-Protein interactions (...
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| Format: | Article |
| Language: | English |
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BMC
2018-06-01
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| Series: | BMC Bioinformatics |
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| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2237-8 |
| _version_ | 1828391404529778688 |
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| author | Carlos A. García-Pérez Xianwu Guo Juan García Navarro Diego Alonso Gómez Aguilar Edgar E. Lara-Ramírez |
| author_facet | Carlos A. García-Pérez Xianwu Guo Juan García Navarro Diego Alonso Gómez Aguilar Edgar E. Lara-Ramírez |
| author_sort | Carlos A. García-Pérez |
| collection | DOAJ |
| description | Abstract Background The influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen. Results In this study, a data mining approach was employed to extract influenza-human Protein-Protein interactions (PPI) from VirusMentha,Virus MINT, IntAct, and Pfam databases, to mine motif-domain interactions (MDIs) stored as Regular Expressions (RegExp) in 3DID database. A total of 107 RegExp related to human MDIs were searched on 51,242 protein fragments from H1N1, H1N2, H2N2, H3N2 and H5N1 strains obtained from Virus Variation database. A total 46 MDIs were frequently mapped on the IAV proteins and shared between the different strains. IAV kept host-like MDIs that were associated with the virus survival, which could be related to essential biological process such as microtubule-based processes, regulation of cell cycle check point, regulation of replication and transcription of DNA, etc. in human cells. The amino acid motifs were searched for matches in the immune epitope database and it was found that some motifs are part of experimentally determined epitopes on IAV, implying that such interactions exist. Conclusion The directed data-mining method employed could be used to identify functional motifs in other viruses for envisioning new therapies. |
| first_indexed | 2024-12-10T07:01:16Z |
| format | Article |
| id | doaj.art-693ad9ee037a41d28c37f40e0a00b0e4 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T07:01:16Z |
| publishDate | 2018-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-693ad9ee037a41d28c37f40e0a00b0e42022-12-22T01:58:19ZengBMCBMC Bioinformatics1471-21052018-06-011911910.1186/s12859-018-2237-8Proteome-wide analysis of human motif-domain interactions mapped on influenza A virusCarlos A. García-Pérez0Xianwu Guo1Juan García Navarro2Diego Alonso Gómez Aguilar3Edgar E. Lara-Ramírez4Centro de Biotecnología Genómica, Instituto Politécnico NacionalCentro de Biotecnología Genómica, Instituto Politécnico NacionalOracle MDCCentro de Biotecnología Genómica, Instituto Politécnico NacionalUnidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro SocialAbstract Background The influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen. Results In this study, a data mining approach was employed to extract influenza-human Protein-Protein interactions (PPI) from VirusMentha,Virus MINT, IntAct, and Pfam databases, to mine motif-domain interactions (MDIs) stored as Regular Expressions (RegExp) in 3DID database. A total of 107 RegExp related to human MDIs were searched on 51,242 protein fragments from H1N1, H1N2, H2N2, H3N2 and H5N1 strains obtained from Virus Variation database. A total 46 MDIs were frequently mapped on the IAV proteins and shared between the different strains. IAV kept host-like MDIs that were associated with the virus survival, which could be related to essential biological process such as microtubule-based processes, regulation of cell cycle check point, regulation of replication and transcription of DNA, etc. in human cells. The amino acid motifs were searched for matches in the immune epitope database and it was found that some motifs are part of experimentally determined epitopes on IAV, implying that such interactions exist. Conclusion The directed data-mining method employed could be used to identify functional motifs in other viruses for envisioning new therapies.http://link.springer.com/article/10.1186/s12859-018-2237-8Motif-domain interactionsProtein-protein interactionsInfluenzaData-mining |
| spellingShingle | Carlos A. García-Pérez Xianwu Guo Juan García Navarro Diego Alonso Gómez Aguilar Edgar E. Lara-Ramírez Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus BMC Bioinformatics Motif-domain interactions Protein-protein interactions Influenza Data-mining |
| title | Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus |
| title_full | Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus |
| title_fullStr | Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus |
| title_full_unstemmed | Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus |
| title_short | Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus |
| title_sort | proteome wide analysis of human motif domain interactions mapped on influenza a virus |
| topic | Motif-domain interactions Protein-protein interactions Influenza Data-mining |
| url | http://link.springer.com/article/10.1186/s12859-018-2237-8 |
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