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1,297 results for “differential analysis”
Meta-analysis results of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
<p>Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (P<sub>Bonferroni</sub><1.06x10<sup>-7</sup>).</p>
Datasets, reproducible codes, and results for evaluating differential expression analysis methods on population-level RNA-seq data
<p>This upload contains the necessary R codes and data to reproduce the FDR and Power results described in our correspondence "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" to Li Y, Ge X, Peng F, Li W, Li JJ, Exaggerated false positives by popular differential expression methods when analyzing human population samples, <em>Genome Biology</em> 23, 79, 2022, DOI: 10.1186/s13059-022-02648-4.</p>
A Linked Application of Discrete Differential Evolution Algorithm Coupled with Simulation- Optimization Model and Comparative Analysis by Genetic Algorithm for Discrete Groundwater Management Problems
<p>Complete dataset of publication name as "The complete publication dataset is "A Discrete Differential Evolution- Linear Programming Algorithm for Groundwater Management Problems." You can find all the written codes in the zip file.</p>
Data from "Corset: enabling differential gene expression analysis for de novo assembled transcriptomes"
<p>This dataset contains de novo transcriptome assemblies for three publicly available RNA-seq dataset (SRA055442, SRR453566-SRR453571 and GSE37704 ). For each assembly we also provide a table with the read counts per contig, the output from corset (clusters and counts), and the results from a genome-based analysis. This dataset was used to assess the performance of the corset software. More detail is provided in the paper: Nadia M Davidson and Alicia Oshlack,<strong> </strong>Corset: enabling differential gene expression analysis for de novo assembled transcriptomes, <em>Genome Biology</em> 2014, <strong>15</strong>:410. http://genomebiology.com/2014/15/7/410/abstract</p>
Integrating differential expression and weighted correlation network analysis for identifying genes controlling shoot development in Sorghum bicolor
<p>Supplementery materials of journal article "Integrating differential expression and weighted correlation network analysis for identifying genes controlling shoot development in <em>Sorghum bicolor</em>"</p>
Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"
<p>This data set provides data files and R code to accompany the article <em>Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR</em> published by F1000Research.</p> <p>The data consists of Reduced Representation BS-seq methylation profiles of epithelial populations from the mouse mammary gland, with n=2 biological replicates for each of three cell populations.</p> <p>RNA-seq expression profiles of luminal and basal mammary epithelial populations are also provided.</p> <p>The R code undertakes an differential methylation analysis of the BS-seq profiles and demonstrates a strong negative correlation between the differential methylation and differential expression results.</p>
Pelagomonas calceolata gene expression levels in different nitrogen conditions and differential expression analysis.
<p>These files contains the expression levels and DESeq2 results of <em>Pelagomonas calceolata</em> genes cultivated with different nitrate conditions. Two strains of <em>P. calceolata </em>(RCC100 and RCC697) were cultivated and their RNAs reads were aligned on the predicted genes of <em>P. calceolata</em> RCC100 genome: <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download" rel="nofollow">https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download</a></p> <p>The following culture conditions were analysed :</p> <p>882 µM of Nitrate (RCC100 and RCC697) </p> <p>441 µM of Nitrate (RCC100)</p> <p>220 µM of Nitrate (RCC100 and RCC697)</p> <p>50 µM of Nitrate (RCC697)</p> <p>882 µM Cyanate (RCC100)</p> <p>882 µM Ammonia (RCC100)</p> <p>441 µM Urea (RCC100)</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv</a> : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_TPM.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC100-Nitrate_transcriptomes_TPM.tsv</a> : same data normalized in transcript per kb per million mapped reads (TPM).</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv</a> : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_TPM.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC697-Nitrate_transcriptomes_TPM.tsv</a> : same data normalized in transcript per kb per million mapped reads (TPM).</p> <p><span>Differential expression analysis (DESeq2) was performed by pairwise comparisons between the standard condition (882 µM nitrate) and low-nitrate conditions (50, 220 or 441 µM nitrate) or changing nitrogen sources (882 µM ammonium, 882 µM cyanate and 441 µM urea). Each DESeq-results_RCCxxx_xxx.tsv file contains 6 columns : <em>P.calceolata </em>gene name, base Mean, log2 Fold Change, standard error value (lfcSE), pvalue and adjusted pvalue (padj).<br></span></p>
Fig. 7 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 7. Alignment of the predicted amino acid sequences of the CYP307A1 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. We detected a sense amino acid mutation (14-threonine to serine).. This figure is shown in color in a supplementary document online as Suppl. Fig. 7 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 5 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 5. Alignment of the predicted amino acid sequences of CYP307A1 in Panonychus citribetween the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Only one amino acid mutation (278-lysine to glutamine) was detected.. This figure is shown in color in a supplementary document online as Suppl. Fig. 5 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 6 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 6. Nucleotide sequence comparison of CYP381A2 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Just one SNP site was detected. The nucleotide transition of A to T was at position 40.. This figure is shown in color in a supplementary document online as Suppl. Fig. 6 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 4 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 4. Nucleotide sequence comparison of the CYP307A1 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Three SNP sites were detected in all. The first nucleotide mutation (A to C) is located at 841, the second mutation is 1395-T to C, and the final mutation is 1491-T to C.. This figure is shown in color in a supplementary document online as Suppl. Fig. 4 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 3 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 3. Quantitative Real-time PCR analysis of CYPs in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. The numbers of genes down-regulated and up-regulated in the RR relative to the SS are indicated above or below the X axis. The light or dark gray was susceptible strain and resistant strain, respectively.
Fig. 1 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 1. Number, family and clan distribution of cytochrome P450 genes in Panonychus citri. The number shown along each column represents the P450 family and the number in parenthesis is the number of individual genes in the corresponding family. The P450 gene sequence information generated is from the VectorBase of the P. citri transcriptome sequence.
Fig. 2 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 2. Neighbor-joining phylogenetic analysis of cytochrome P450 from Panonychus citri and Tetranychus urticae. 4clans were observed. There are species (P. citri and T. urticae) in the phylogenetic tree. Only 10 sequences belong to T. urticae; A (Pc) before the CYP name denotes P. citri, a (Tu) before the CYP name denotes T. urticae. Numbers at nodes are bootstrap values.
Epigenome-wide analysis reveals specific DNA hypermethylation of T cells during human hematopoietic differentiation
<p>Epigenetic regulation plays an important role in cellular development and differentiation. A detailed map of the DNA methylation dynamics that occur during cell differentiation would contribute to decipher the molecular networks governing cell fate commitment. In this study we used the most recent Illumina MethylationEPIC Beadchip platform to describe the genome-wide DNA methylation changes observed throughout hematopoietic maturation by analyzing multiple hematopoietic cell types at different developmental stages.</p>
Feature count data for Love et al. 2019 analysis for "Using equivalence class counts for fast and accurate testing of differential transcript usage" paper
<p>Feature count data for Love et al. 2019 analysis used in the "Using equivalence class counts for fast and accurate testing of differential transcript usage" paper. For reproducing the analyses and figures using the <a href="https://github.com/Oshlack/ec-dtu-paper/">ec-dtu-paper</a> code.</p> <p>Contains:</p> <ul> <li>Equivalence class count matrix for all 24 samples (using counts from Salmon)</li> <li>Salmon quantification results for all 24 samples</li> <li>Exon counts for all 24 samples using DEXSeq-count</li> </ul>
Figure 3 in Application of multifactorial discriminant analysis in the morphostructural differentiation of wild and cultured populations of Vieja Azul (Andinoacara rivulatus)
Figure 3. Cluster from Mahalanobis distances for cultured and wild populations of both sexes. HP: Cultured females; HS: wild females; MP: cultures males; MS: wild males.
Figure 2 in Application of multifactorial discriminant analysis in the morphostructural differentiation of wild and cultured populations of Vieja Azul (Andinoacara rivulatus)
Figure 2. Plot of the individual observation discriminant scores obtained with the canonical discriminant function. HP: Cultured females; HS: wild females; MP: cultures males; MS: wild males.
Figure 1 in Application of multifactorial discriminant analysis in the morphostructural differentiation of wild and cultured populations of Vieja Azul (Andinoacara rivulatus)
Figure 1. (a) Location of 25 anatomic landmark points designed on the left-side view of Andinoacara rivulatus; (b) 32 truss characters making up a truss network. 1- Commissure of the mouth; 2- most cranial point of the upper premaxilla; 3- origin of pelvic fin; 4- origin of dorsal fin; 5- origin of anal fin; 6- most cranial point of the base of the tenth spine of the dorsal fin; 7- ending of anal fin; 8- ending of dorsal fin; 9- ventral origin of caudal fin; 10- dorsal origin of caudal fin; 11- most cranial point of caudal peduncle; 12- most caudal point of caudal peduncle; 13- ending of pectoral fin; 14- end of operculum; 15- cranial edge of the eye; 16- caudal edge of the eye; 17- preoccipital (most posterior aspect of neurocranium); 18- below operculum; 19- origin of pectoral fin; 20- lower end of the head; 21- anal opening; 22- most cranial point of the lower premaxilla; 23- ending of 1st dorsal fin ray; 24- ending of the last anal fin ray; 25- ending of the pelvic fin radius.
Fig. 1 in Differentiation of Trichuris species eggs from non-human primates by geometric morphometric analysis
Fig. 1. Trichuris sp. eggs collected from the samples. A. Macaque (Macaca sylvanus) B. Colobus (Colobus guereza kikuyensis). C. Grivet (Chlorocebus aethiops. D. Brazza's monkey (Cercopithecus neglectus). The bar represents 20 μm.
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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.