Ontology highlight
ABSTRACT:
PROVIDER: PRJNA72139 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics. We develop this concept by investigating the molecular evolution of the shelterin complex, which protects telomeres, across 16 vertebrate species from zebrafish to humans covering 450 million years of evolution. Our phylointeractomics screen discovers previously unknown telomere-associated proteins and reveals how homologous proteins undergo functional evolution. For instance, we show that TERF1 evolved as a telomere-binding protein in the common stem lineage of marsupial and placental mammals. Phylointeractomics is a versatile and scalable approach to investigate evolutionary changes in protein function and thus can provide experimental evidence for phylogenomic relationships.
2017-02-15 | PXD005517 | Pride
Project description:Co-expression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting the functional roles of individual genes at a system-wide scale. To enable network reconstructions we built a large-scale gene expression atlas comprised of 62,547 mRNAs, 17,862 non-modified proteins, and 6,227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. There was little edge conservation in co-expression and GRNs reconstructed using transcriptome versus proteome data yet networks from either data type were enriched in ontological categories and effective in predicting known regulatory relationships. This integrated gene expression atlas provides a valuable community resource. The networks should facilitate plant biology research and they provide a conceptual framework for future systems biology studies highlighting the importance of studying gene regulation at several levels.
| MSV000079290 | MassIVE
Project description:Co-expression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting the functional roles of individual genes at a system-wide scale. To enable network reconstructions we built a large-scale gene expression atlas comprised of 62,547 mRNAs, 17,862 non-modified proteins, and 6,227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. There was little edge conservation in co-expression and GRNs reconstructed using transcriptome versus proteome data yet networks from either data type were enriched in ontological categories and effective in predicting known regulatory relationships. This integrated gene expression atlas provides a valuable community resource. The networks should facilitate plant biology research and they provide a conceptual framework for future systems biology studies highlighting the importance of studying gene regulation at several levels.
| MSV000079303 | MassIVE
Project description:Strains 2-22 (S. agalactiae ST261 isolated from fish) and A909 (ST7) were grown in TH medium, at 30C and harvested at OD 0.3-0.4. Please note: ST261 and ST7 refer to MLST types commonly used in S.agalactiae as a first approach for phylogenomic relationships (MLST is based on the sequence of 7 genes).
2013-03-01 | E-MEXP-3828 | biostudies-arrayexpress
Project description:Strains A909 (ST7 strain isolated from human) and CF01173 (ST7 strain isolated from fish) were grown in TH medium at 37C and harvested at OD 0.3-0.4. Please note: ST7 refers to MLST types commonly used in S.agalactiae as a first approach for phylogenomic relationships (MLST is based on the sequence of 7 genes).
2013-03-01 | E-MEXP-3830 | biostudies-arrayexpress
Project description:“phyloquant” to study the evolutionary relationships of organisms based on large scale quantitative protein expression
2021-09-09 | PXD017228 | Pride