Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,818
datasets available to search
ShareScore release 0.9.0
Dataset results
3,818 results for “Differential Expression”
Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua
The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.
The differential inflammatory infiltration and gene expression in left and right atrium in patients with atrial fibrillation
<p><strong>Background: </strong>The difference between left and right atrium in Atrial fibrillation (AF) is still lacking. In the present study, we aimed to identify differences in immune infiltration and differentially expressed genes (DEGs) between atrial tissue in patients with AF and sinus rhythm (SR), and to compare the differences between left and right atrial tissues in AF.</p> <p><strong>Methods:</strong> The gene data of GSE79768, GSE115574, and GSE128188 from the Gene Expression Omnibus (GEO) database were retrieved. After merging all data and adjusting batch effect, DEGs were identified. Single-Sample Gene Set Enrichment Analysis (ssGESA), Functional enrichment analyses based on Gene Ontology (GO) resource, Kyoto Encyclopedia of Genes and Genomes (KEGG) resource, ESTIMATE algorithm were carried out to analyze the difference between AF and SR.</p> <p><strong>Results:</strong> In total, 105 atrial samples from 3 studies were included in the analysis. Compared with SR, AF tissue had more CD8 T cells (P = 0.039) and Th2 cells (P = 0.016), and it had fewer Th17 cells (P = 0.008), Tgd (P < 0.001) and NK CD56dim cells (P = 0.047). The differences between the left and right atrium in AF and SR were analyzed. In AF atrium tissue, a total of 88 DGEs (26 up-regulated, 61 down-regulated) were obtained. The enrichment signaling pathways and biological functions of DGEs were predicted.</p> <p><strong>Conclusions:</strong> The differing immune infiltrating cells and DEGs in left and right atrium indicate that there are different mechanisms for development remodeling and inflammatory environment of AF within the left and right atrium.</p>
Table S5. The differential expression of 5946 genes in cancer and normal tissues
<p>The file contains GeneID, GeneType, symbol, logFC, FDR, RCI, OverallSurv, DiseaseFreeSurv information for 5946 genomes. Among them, FDR indicates false discovery rate;RCI indicates the logarithm of the ratio of concentration to nucleus (Log<sub>2</sub>), positive value indicates distribution in cytoplasm, negative value indicates distribution in nucleus; 0 in OverallSurv and DiseaseFreeSurv indicates insignificant, 1 indicates significant.</p>
Supplementary information files: Gene co-expression network and differential expression analyses of subcutaneous white adipose tissue reveal novel insights into the pathological mechanisms underlying ketosis in dairy cows
<p>Supplementary information files: Gene co-expression network and differential expression analyses of subcutaneous white adipose tissue reveal novel insights into the pathological mechanisms underlying ketosis in dairy cows</p>
List of significantly differentially expressed genes (p.ajust < 0.01, |log2FC| > 0.3).
<p>DEGs were obtained by pair-wise differential expression analysis of <em>Lactobacillus johnsonii </em>N6.2 total lipid stimulation vs. the vehicle control. Table is provided as an xlsx file.</p>
Differential gene expression data from an experiment manipulating larval nutrition in female fruit flies (Drosophila melanogaster)
<p>This file contains data on differentially expressed genes, redundant GO terms, and overlapping genes from gene expression comparisons in Tables D1 - D8 as described in, "David H. Collins, David C. Prince, Jenny L. Donelan, Tracey Chapman, and Andrew F. G. Bourke. Developmental diet alters the fecundity-longevity relationship and age-related gene expression in <em>Drosophila melanogaste</em>r. The Journals of Gerontology: Series A. 2023."</p>
Fig. 7 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 7. Effects of control and drought stress on leaf microstructure of apricot. a, c, e, represent the leaf stomata, vertical section, and cuticle in the control group, respectively. b, d, f, represent the leaf stomata, vertical section, and cuticle in the drought stress group, respectively.
Fig. 4 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 4. KEGG enrichment of annotated DEGs in Treat versus Control. The Y-axis shows the KEGG pathway and the X-axis shows the Rich factor. This q value goes from purple to red, which means from 1 to 0. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 3. GO classifications of DEGs for Treat versus Control. The Y-axis represents the number of DEGs in a category. The BP, CC and MF represent biological process, cellular component and molecular function respectively.
Fig. 5. SSR motifs distribution. The X in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 5. SSR motifs distribution. The X-axis is SSR type, the Y-axis value is the coordinate, the specific number of repetitions should correspond to the legend according to the color, and the Z-axis is the number of SSR. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 1. Gene Function Classification of the assembled unigenes. Unigenes with BLAST hits were classified into three major categories and 56 sub-categories in GO. The Y-axis shows the number of genes in each sub-category.
Fig. 5. A in Differential expression after UV-B radiation and characterization of chalcone synthase from the Patagonian hairgrass Deschampsia antarctica
Fig. 5. A) Structural alignment between DaCHS (red) and crystal 4YJY (cyan). The RMSD value was 0.25 Å. B) Molecular dynamics simulation analysis. The MDS was carried out using NAMD software and the trajectory analysis was carried out by using VMD software. C) Proteins' structural stability in the function of RMSD, during 2 ns of MDS. RMSF plots of DaCHS (red) and 4YJY chain A (blue) during MD simulation are compared. The greatest fluctuations are found in the loops region of proteins.
Fig. 1 in Differential expression after UV-B radiation and characterization of chalcone synthase from the Patagonian hairgrass Deschampsia antarctica
Fig. 1. Multiple alignment of amino acids for monocotyledons sequences: H. vulgare HvCHS1 (ID: P26018.1), H. vulgare HvCHS2 (ID: Q96562.1), O. sativa subsp. japonica OsjCHS1(ID: XP_015618054.1), O. sativa subsp. japonica OsjCHS2(ID: XP_015646206.1), O. sativa subsp. indica OsiCHS1 (ID: A2ZEX7.1), Sorghum bicolor SbCHS1(ID: XP_002450874.1), S. bicolor SbCHS2(ID: XP_002450871.1), S. bicolor SbCHS3 (ID: XP_002450875.1), S. bicolor SbCHS4(ID: XP_002450870.1), S. bicolor SbCHS5(ID: XP_002449616.1), S. bicolor SbCHS6 (ID: XP_002450877.1), S. bicolor SbCHS7(ID: XP_002450876.1), Z. mays ZmCHS1 (ID: P24824.1), Z. mays ZmCHS2 (ID: NP_001142246.1). Arrows show active site residues, described for chalcone synthase (Cys 167, Phe 218, His 306 and Asn 339). N-terminal domain and Cterminal domain are shown.
Fig. 4 in Differential expression after UV-B radiation and characterization of chalcone synthase from the Patagonian hairgrass Deschampsia antarctica
Fig. 4. Lineal alignment and secondary structure comparison between DaCHS and the template (code 4YJY). Sequences have a high homology index (92% of sequence identity).
Fig. 3 in Differential expression after UV-B radiation and characterization of chalcone synthase from the Patagonian hairgrass Deschampsia antarctica
Fig. 3. Model of DaCHS structure. The 3D model structure of DaCHS shows 13 β sheets (yellow), 12 α helices (purple) and 8 α helices 310 (blue) and 23 loops. The center core is shown where catalytic residues are positioned. Enlargement of the active site shows the three catalytic residues (Cys 167, His 306 and Asn 339) and the two structural Phe residues (Phe 218, Phe 268). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Dataset from RNAseq analysis of differential gene expression among developmental stages of two non-marine ostracods
<p>Dataset comprising tree files and alignments used for phylogenetic validation of data, assemblies of reference transcriptomes and draft genomes, annotation of draft genomes, as well as supplementary tables.</p>
Study of Tamoxifen in Well Differentiated Neuroendocrine Tumors and Hormone Receptor Positive Expression
ClinicalTrials.gov study NCT03870399. IPD Sharing: NO. Countries: 2. Publications: 22.
The Relationship Between the Differential Expression of FosB Protein in Laryngeal Cancer Tissues and Clinical Prognosis
ClinicalTrials.gov study NCT06836765. IPD Sharing: NO. Countries: 1. Publications: 3.
Differential SERCA Expression in Laryngeal Muscles
ClinicalTrials.gov study NCT06837467. IPD Sharing: NO. Countries: 1. Publications: 2.
Differential Expression and Potential Value of c-MYC in Non-Invasive and Invasive Mammary Carcinoma
ClinicalTrials.gov study NCT06357338. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
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.