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75
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ShareScore release 0.9.0
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75 results for “gene expression evolution”
Data from: Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene
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Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua
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Data from: Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast‐Z effect in Heliconius
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Data from: Evolution of sex-biased gene expression and dosage compensation in the eye and brain of Heliconius butterflies
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Data from: Genetic accommodation in the wild: evolution of gene expression plasticity during character displacement
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Data from: NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss
Background: Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes is widely distributed across diverse lineages of photoautotrophic seed plants and mutants/transgenics lacking NDH function demonstrate little difference from wild type under non-stressed conditions. This study analyzes large transcriptomic and genomic datasets to evaluate the persistence and loss of NDH expression across plants. Results: Nuclear expression profiles showed accretion of the NDH gene complement at key transitions in land plant evolution, such as the transition to land and at the base of the angiosperm lineage. While detection of transcripts for a selection of non-NDH, photosynthesis related proteins was independent of the state of NDH, coordinate, lineage-specific loss of plastid NDH genes and expression of nuclear-encoded NDH subunits was documented in Pinaceae, gnetophytes, Orchidaceae and Geraniales confirming the independent and complete loss of NDH in these diverse seed plant taxa. Conclusion: The broad phylogenetic distribution of NDH loss and the subtle phenotypes of mutants suggest that the NDH complex is of limited biological significance in contemporary plants. While NDH activity appears dispensable under favorable conditions, there were likely sufficiently frequent episodes of abiotic stress affecting terrestrial habitats to allow the retention of NDH activity. These findings reveal genetic factors influencing plant/environment interactions in a changing climate through 450 million years of land plant evolution.
Data from: Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity
Background: Phosphodiesterase 6 (PDE6) is a protein complex that hydrolyses cGMP and acts as the effector of the vertebrate phototransduction cascade. The PDE6 holoenzyme consists of catalytic and inhibitory subunits belonging to two unrelated gene families. Rods and cones express distinct genes from both families: PDE6A and PDE6B code for the catalytic and PDE6G the inhibitory subunits in rods while PDE6C codes for the catalytic and PDE6H the inhibitory subunits in cones. We performed phylogenetic and comparative synteny analyses for both gene families in genomes from a broad range of animals. Furthermore, gene expression was investigated in zebrafish. Results: We found that both gene families expanded from one to three members in the two rounds of genome doubling (2R) that occurred at the base of vertebrate evolution. The PDE6 inhibitory subunit gene family appears to be unique to vertebrates and expanded further after the teleost-specific genome doubling (3R). We also describe a new family member that originated in 2R and has been lost in amniotes, which we have named pde6i. Zebrafish has retained two additional copies of the PDE6 inhibitory subunit genes after 3R that are highly conserved, have high amino acid sequence identity, are coexpressed in the same photoreceptor type as their amniote orthologs and, interestingly, show strikingly different daily oscillation in gene expression levels. Conclusions: Together, these data suggest specialisation related to the adaptation to different light intensities during the day-night cycle, most likely maintaining the regulatory function of the PDE inhibitory subunits in the phototransduction cascade.
Data from: Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife
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Data from: NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss
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Data from: Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity
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Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
GEO Series GSE46915. Caulobacter vibrioides. 15 samples. Type: Expression profiling by high throughput sequencing.
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
GEO Series GSE292756. Caenorhabditis briggsae; Caenorhabditis elegans. 14 samples. Type: Expression profiling by high throughput sequencing.
Mistranslation accelerates the evolution of antifungal drug resistance in Candida albicans [Gene expression]
GEO Series GSE60121. Candida albicans. 16 samples. Type: Expression profiling by array.
Expression evolution in gene groups: Inferring non-neutral regulatory change in pathways from transcriptional profiling data
GEO Series GSE38875. Saccharomyces mikatae; Saccharomyces cerevisiae x Saccharomyces bayanus; Saccharomyces bayanus; Saccharomyces cerevisiae; Saccharomyces cerevisiae x Saccharomyces mikatae; Saccharomyces paradoxus; Saccharomyces cerevisiae x Saccharomyces paradoxus. 18 samples. Type: Expression profiling by high throughput sequencing.
Evolution of Gene Expression in the Uterine Cervix related to Steroid Signaling: Conserved features in the regulation of cervical remodeling.
GEO Series GSE85815. Dasypus novemcinctus; Oryctolagus cuniculus; Mus musculus; Monodelphis domestica. 35 samples. Type: Expression profiling by high throughput sequencing.
Evolution of gene expression levels in Anopheles male reproductive organs
GEO Series GSE117656. Anopheles gambiae; Anopheles quadriannulatus; Anopheles coluzzii; Anopheles arabiensis; Anopheles merus. 30 samples. Type: Expression profiling by high throughput sequencing.
Evolution of gene expression across brain regions in behaviorally divergent deer mice
GEO Series GSE245182. Peromyscus maniculatus x Peromyscus polionotus; Peromyscus maniculatus; Peromyscus polionotus. 191 samples. Type: Expression profiling by high throughput sequencing.
Comparative epigenomic analyses of DNA methylomes and gene expression during ruminant evolution
GEO Series GSE211353. Ovis aries; Bos taurus; Capra hircus. 24 samples. Type: Methylation profiling by high throughput sequencing.
Gene Expression and evolution of antifungal drug resistance
GEO Series GSE12055. Saccharomyces cerevisiae. 46 samples. Type: Expression profiling by array.
Phylotranscriptomics reveals the convergent evolution of aggression is associated with both shared and unique patterns of gene expression evolution in cavity nesting songbirds
GEO Series GSE244480. Passer domesticus; Turdus migratorius; Troglodytes aedon; Thryothorus ludovicianus; Sialia sialis; Protonotaria citrea; Hirundo rustica; Passer montanus; Tachycineta bicolor; Setophaga petechia. 121 samples. Type: Expression profiling by high throughput sequencing.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.