Regulatory element copy number differences shape primate expression profiles
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE33960
PROVIDER: PRJNA150543 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Regulatory element copy number differences shape primate expression profiles.
| PRJNA168156 | ENA
Project description:Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
2012-08-01 | GSE33960 | GEO
Project description:Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
2012-08-02 | GSE38572 | GEO
Project description:Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA. Gene expression patterns were compared between human, chimpanzee and rhesus macaque lymphoblastoid cell lines using RNA-Seq. Samples from 6 individuals of each species were used. The 6 human samples were previously published as a part of GEO record GSE19480 (samples GSM485426, GSM485428, GSM485468, GSM485410, GSM485413 and GSM485414). The 6 chimpanzee and 6 rhesus macaquesamples are included in the current record (GSE38572).
2012-08-02 | E-GEOD-38572 | biostudies-arrayexpress
Project description:Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across three primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs that were processed pseudogenes and some of which were expressed. Furthermore, there were copy number-different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
| S-EPMC3411951 | biostudies-literature
Project description:Evolution of transposable element copy number control in yeast
| PRJEB33725 | ENA
Project description:This set includes individuals from 10 different primate species whose genomic DNA was used in an array-based comparative genomic hybridization (aCGH)using human cDNA microarrays to detect gene copy number variation across 10 primate species. An organism part comparison experiment design type compares tissues, regions, organs within or between organisms. Keywords: organism_part_comparison_design, array CGH Computed
2012-02-24 | E-GEOD-9028 | biostudies-arrayexpress
Project description:This set includes individuals from 10 different primate species whose genomic DNA was used in an array-based comparative genomic hybridization (aCGH)using human cDNA microarrays to detect gene copy number variation across 10 primate species. An organism part comparison experiment design type compares tissues, regions, organs within or between organisms. Keywords: organism_part_comparison_design, array CGH
2012-02-24 | GSE9028 | GEO
Project description:Great Ape Copy Number Variation
| PRJNA144461 | ENA
Project description:Copy-number variants (CNVs) are large-scale amplifications or deletions of DNA that can drive rapid adaptive evolution and result in large-scale changes in gene expression. Whereas alterations in the copy number of one or more genes within a CNV can confer a selective advantage, other genes within a CNV can decrease fitness when their dosage is changed. Dosage compensation - in which the gene expression output from multiple gene copies is less than expected - is one means by which an organism can mitigate the fitness costs of deleterious gene amplification. Previous research has shown evidence for dosage compensation at both the transcriptional level and at the level of protein expression; however, the extent of compensation differs substantially between genes, strains, and studies. Here, we investigated sources of dosage compensation at multiple levels of gene expression regulation by defining the transcriptome, translatome and proteome of experimentally evolved yeast (Saccharomyces cerevisiae) strains containing adaptive CNVs.
2023-11-01 | PXD046587 | Pride