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79 results for “discriminant analysis”
Data to reproduce analysis in "Systematic analysis of transcriptional and epigenetic effects of genetic variation in Kupffer cells enables discrimination of cell intrinsic and environment-dependent mechanisms"
<p>Here you can find the datasets necessary to reproduce all analyses described in the Glass lab paper by <a href="https://www.biorxiv.org/content/10.1101/2022.09.22.509046v1">Bennett et al</a>. The python and R code for reproducing analysis and figures can be found on our linked <a href="https://github.com/HunterBennett/KupfferCell_NaturalGeneticVariation">github repository.</a></p> <p>Briefly, this paper explores the effect of natural genetic variation <em>in vivo</em>, using Kupffer cells as a model cell type. We collect and analyze transcriptional and epigenetic data (ATAC-seq, H3K27Ac ChIP-seq) to identify putative <em>trans</em> regulators driving differential gene expression across inbred strains of mice. Additionally, we provide evidence that <em>trans</em> effects control a majority of strain differential genes at homeostasis while <em>cis</em> effects dominate the transcriptional response to an external signal (lipopolysaccharide).</p> <p>References:</p> <p>Hunter Bennett, Ty D. Troutman, Enchen Zhou, Nathanael J. Spann, Verena M. Link, Jason S. Seidman, Christian K. Nickl, Yohei Abe, Mashito Sakai, Martina P. Pasillas, Justin M. Marlman, Carlos Guzman, Mojgan Hosseini, Bernd Schnabl, Christopher K. Glass bioRxiv 2022.09.22.509046; doi: <a href="https://doi.org/10.1101/2022.09.22.509046">https://doi.org/10.1101/2022.09.22.509046</a></p> <p> </p>
Figure 5. Ordinations and discriminant analysis. A in Morphometric analysis of Eocene nummulitids in western and central Cuba: taxonomy, biostratigraphy and evolutionary trends
Figure 5. Ordinations and discriminant analysis. A, two-dimensional ordination of studied specimens; genera are separated by different shapes (squares = Operculinoides; polygons = Palaeonummulites; triangles = Heterostegina). B, three-dimensional ordination of the studied specimens emphasizes the variation in the third component, highlighting the differentiation between Heterostegina sp. indet. and Operculinoides. C, discriminant analysis of Heterostegina species and Operculinoides or Palaeonummulites species; parameters are sorted in order of their importance as discriminators.
FIGURE 7. Age-specific discriminant analysis using all morphometric parameters for all sites. 7A in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?
FIGURE 7. Age-specific discriminant analysis using all morphometric parameters for all sites. 7A: Eocene. 7B: Oligocene. Triangles: Platanus neptuni. Squares: Eotrigonobalanus furcinervis. Circles: Daphnogene cinnamomifolia.
Fig. 8 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 8. PCA. Principal component scatter plot (PCA) conducted on the elliptic Fourier descriptions of denticles shapes using the first 10 harmonics; this figure shows the first two principal components (PC1 and PC2 are on the x and y-axes, respectively).
Fig. 9 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 9. Linear discriminant analysis (LDA) of Trichodina spp. using normalized elliptical Fourier descriptors. Percentages indicate the proportion of the trace captured in each LD component.
Fig. 4. Tree derived from a in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 4. Tree derived from a Maximum Likelihood (ML) analysis. The bootstrap consensus tree bases on ML inferred from 500 replicates. Bootstrap values for ML are given above nodes.
Fig. 2 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 2. Diagrammatic drawings of denticles of trichodinids. (A and B) Denticle of Trichodina bellotti n. sp. from Austrolebias bellottii. (C) Trichodina hypsilepis redrawn from Wellborn (1967). (D) Trichodina heterodentata redrawn from Duncan (1977). (E) Trichodina paraheterodentata redrawn from Tang and Zhao (2013). (F) Trichodina pseudoheterodentata redrawn from Tang et al. (2017).
Fig. 3 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 3. Phylogenetic tree based on 18S rDNA sequences by Bayesian Inference, with the model Trn + I + G applied in Mrbayes v.3.2.1. The new sequenced forms are in bold. Numbers given at nodes of branches are the posterior probability value.
Fig. 5 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 5. Denticles silhouettes utilized on Fourier analysis. Trichodina bellottii n. sp., Trichodina heterodentata redrawn from Duncan (1977); Albaladejo and Arthur, 1989; Bondad-Reantaso and Arthur, 1989; Van As and Basson, 1989; Basson and Van As, 1994; Al Rasheid et al., 2000; Asmat, 2004; Dove and O'Donoghue, 2005; Dias et al., 2009; Martins et al., 2010; Benites de Pádua et al., 2012; Miranda et al., 2012; Valladão et al., 2014. Trichodina paraheterodentata redrawn from Tang and Zhao (2013). Trichodina pseudoheterodentata redrawn from Tang et al. (2017).
Fig. 1 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 1. Microphotographs of Trichodina bellottii n. sp. from Austrolebias bellottii. (A–D) Adhesive disc after dry silver impregnation. E) Ciliature. (F) Macronucleus with methylene-blue staining. Scale bars: 20 μm.
Sex-dependent discrimination learning in lizards: a meta-analysis
<p>Raw data and R code used for analysis and to create plots</p>
Text-fig. 9. Sex estimation of Moča skull (Komárno district, southern Slovakia), linear discriminant analysis using Henke's Late Upper Palaeolithic and Mesolithic database (n = 129, f = 46, m = 83), as well as according to recent Howells's database (n = 2524, f = 1156, m = 1368) with variables M1 (GOL) and M45 (ZYB). in A Late Upper Palaeolithic Skull From Moča (The Slovak Republic) In The Context Of Central Europe
Text-fig. 9. Sex estimation of Moča skull (Komárno district, southern Slovakia), linear discriminant analysis using Henke's Late Upper Palaeolithic and Mesolithic database (n = 129, f = 46, m = 83), as well as according to recent Howells's database (n = 2524, f = 1156, m = 1368) with variables M1 (GOL) and M45 (ZYB).
Text-fig. 10. Regional affinity of the Moča skull (Komárno district, southern Slovakia), linear discriminant analysis using the Henke's Late Upper Palaeolithic and Mesolithic database (Europe, n = 76) with variables M1 (GOL), M5 (BNL), M8 (XCB), M40 (BPL), W – West Europe, CE – Central-East Europe, S – South Europe. in A Late Upper Palaeolithic Skull From Moča (The Slovak Republic) In The Context Of Central Europe
Text-fig. 10. Regional affinity of the Moča skull (Komárno district, southern Slovakia), linear discriminant analysis using the Henke's Late Upper Palaeolithic and Mesolithic database (Europe, n = 76) with variables M1 (GOL), M5 (BNL), M8 (XCB), M40 (BPL), W – West Europe, CE – Central-East Europe, S – South Europe.
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. 8 in Osteometric analysis of the scapula and humerus of Rangifer tarandus and Cervus elaphus: A contribution to the discrimination of Late Pleistocene cervids
Fig. 8. Morphological features distinguishing the distal portion of the humerus of Rangifer tarandus (A) and Cervus elaphus (B), in anterior (A1, B1), distal (A2,B2), and posterior (A3,B3) views (modified from Breda 2005).
Fig. 7 in Osteometric analysis of the scapula and humerus of Rangifer tarandus and Cervus elaphus: A contribution to the discrimination of Late Pleistocene cervids
Fig. 7. Morphological features distinguishing the proximal portion of the humerus of Rangifer tarandus (A) and Cervus elaphus (B) (modified from Pales and García 1981).
Fig. 6 in Osteometric analysis of the scapula and humerus of Rangifer tarandus and Cervus elaphus: A contribution to the discrimination of Late Pleistocene cervids
Fig. 6. Scatterplots of different combinations of scapular measurements and indices for Rangifer tarandus and Cervus elaphus from Kiputz IX (southern Pyrenees, Spain), Late Pleistocene. Abbreviations: GLP, greatest anteroposterior length of the glenoid process; LG, greatest anteroposterior length of the glenoid cavity; SLC, minimum diameter of the scapular neck.
Fig. 3 in Osteometric analysis of the scapula and humerus of Rangifer tarandus and Cervus elaphus: A contribution to the discrimination of Late Pleistocene cervids
Fig. 3. Osteological measurements of the scapula (A, B) and the humerus (C, D) (modified from Weinstock 2000a). All drawings are based on Rangifer tarandus.
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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.