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Transcription factor expression is the main determinant of variability in gene co-activity
<p><strong>Summary</strong></p> <p>Co-activity scores for 343 GEUVADIS LCLs and ABC scores for 68 LCLs, of which 30 are contained in both.</p> <p><strong>Project abstract</strong></p> <p>Many genes are co-regulated and, when proximal, form domains of coordinated gene activity. However, the regulatory determinants of domain co-activity remain unclear. Here, we leverage human individual variation in gene expression to characterize the regulatory processes underlying the activities of such domains and systematically quantify their effect sizes. We employ transcriptional decomposition to extract from RNA expression data an expression component related to co-activity revealed by genomic positioning. This strategy reveals close to 1,500 domains of co-activity, covering most expressed genes, of which the large majority are invariable across individuals. Focusing specifically on domains with high variation in co-activity reveals that neighboring genes contained within variable co-activity domains have a higher sharing of eQTLs, a higher variability in enhancer interactions, and a specific enrichment of binding by variably expressed transcription factors. Through careful quantification of the relative contributions of regulatory activities underlying co-activity, we find transcription factor expression levels to be the main determinant of gene co-activity, indicating that distal <em>trans</em> effects contribute more than local genetic variation to individual variation in co-activity domains. </p> <p><strong>Included files</strong></p> <p>Co_activity_scores_343_individuals.tsv.zip - Contains co-activity scores for included individuals. Columns include chromosome, bin, start, end and one column per individual containing the co-activity score.</p> <p>ABC_scores_68_individuals.tsv.zip - Contains ABC scores for included individuals. Columns include chromosome, start of putative enhancer region, end of putative enhancer region, name of putative enhancer region, target gene, TSS of target gene, LCL identifier, ABC score</p>
Fig. 1 in Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?
Fig. 1. Ecological niche models (ENMs) estimated for each of the five species from present-day to Last Glacial Maximum, and climatic stability based on the ENM time series. Color coding uses "warm" colors to indicate areas of highest probability of occurrence, or highest climatic stability. Species names are abbreviated as follows: C.p. (Cryptocercus punctulatus), R.f. (Reticulitermes flavipes), O.d. (Odontotaenius disjunctus), S.s. (Scolopocryptops sexspinosus), and N.a. (Narceus americanus).
Fig. 4 in Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?
Fig. 4. Assessment of phylogeographic structure via comparison of FST (grey bars) versus Φ ST (black bars). All values represent mean differentiation across all pairs of BAPS clusters per species (i.e., "global" values). Species names are abbreviated as in Fig. 1.
Fig. 2 in Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?
Fig. 2. Unrooted dendrograms representing two competing hypotheses about key drivers of phylogeographic congruence among five saproxylic invertebrates: abiotic factors related to historical climatic stability (left) versus biotic factors related to ecological co-associations (right). Scale bars represent either the inverse of a measure of habitat overlap (1 – Schoener's D; left), or the cumulative dissimilarity score for species interactions based on trophic guild, timing of colonization during succession, frequency of syntopy, and presumed interaction type (right). Numbers on nodes for the biotic drivers scenario indicate the number of jackknife replicates (out of 4) that supported a given predicted partition. Species names are abbreviated as in Fig. 1.
Fig. 3 in Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?
Fig. 3. The number and distribution of spatial-genetic clusters, and phylogenetic relationships among mitochondrial DNA (mtDNA) haplotypes, for each of the five focal species. BAPS clusters were arbitrarily color-coded (alphabetic names are also shown), and spatial projections were based on membership of georeferenced individuals (Voronoї tessellations not shown). Grey shading identifies the "northern region" of the study area, referred to in the main text. Rooted phylogenetic trees (outgroup not shown) are simplified and color-coded corresponding to BAPS cluster membership of each mtDNA haplotype. Nodes with bootstrap support values>70% are marked by asterisks. Species names are abbreviated as in Fig. 1.
Summative evaluation of LIVE IT co-labs
<p>A report providing an overview of the co-labs procedures, data and results during the LIVE IT. Aggregated raw data is also included.</p>
Wells Fargo & Co. Diorama Team 2
Diorama for skills competition 2021 Source: Objaverse 1.0 / Sketchfab
FIGURE 16 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 16. Palearctic distribution of Tonnacypris stewarti, from Estonia to Mongolia. For references see text about geographical distribution. On the map, the populations are differentiated into asexual (just females; white circle) and sexual (females and males; black and white circle).
FIGURE 13 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 13. Valves of the first stages of development of T. stewarti from Nam Co (reference-ID NC18-S-37). They show a striated pattern on the surface of the valves. Right valve of juvenile A-5 and a close-up of center-dorsal of the valve (A). Right and left valves of juvenile A-6. Right and left valves of juvenile stage A-7, with a detail of the surface of the left valve (B). Arrow points to anterior.
FIGURE 10 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 10. Hemipenis and female genital lobes of T. stewarti from: A) Mang-tsa, Tibetan Plateau (TP) (reference-ID HNHM- IV-369, Daday 1908); B) Lake Band-e Amir, Afghanistan (reference-ID ZMH-27716, Hartmann 1964); and C) near Linzhi, TP (modified from Peng et al. 2021). Dorsal lobe (dl), lateral shield (ls), and medial shield (ms). Female genital lobes from: D) Mang-tsa, TP (reference-ID HNHM-IV-369); E) Lake Band-e Amir, Afghanistan (reference-ID ZMH-27716); F) Nam Co, TP (reference-ID NC-18-S-37); G) Peat near Taro Co, TP (reference-ID TIP11-105). The arrows indicates the intersection or a hook.
FIGURE 7 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 7. Tonnacypris stewarti (= E. afghanistanensis), male from Lake Band-e Amir, Afghanistan (reference-ID ZMHK27716). A) left A1, exterior view; B) right A2, interior view; C) right Md-coxa, exterior view; D) right Md-palp, interior view; E) upper lip and rake-like organ, F) right Mx1, interior view. (See Broodbakker & Danielopol (1982) for chaetotaxy.)
FIGURE 5 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 5. Tonnacypris stewarti, female from Nam Co (reference-ID NC18-S-37). A) left A1, exterior view; B) left A2, interior view; C) left Md coxa, exterior view; D) left Md-palp, interior view; E) upper lip; F) rake-like organ; G) right Mx1 with vibratory branchial plate, interior view. (See Broodbakker & Danielopol (1982) for chaetotaxy.)
FIGURE 4 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 4. Left valves of two individuals from Nam Co (A1‒A3) (reference-ID NC18-S-37). A2 and A4 indicate the inconspicuous anteroventral peg of each one. Left and right valves from Tangra Yum Co, TP (B1‒B2) (reference-ID TIP11-29); left valve of a female from Lake Band-e Amir, Afghanistan (C1) (reference-ID ZMH-K27716), with a close-up of anteroventral part (C2).
FIGURE 6 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 6. Tonnacypris stewarti, female from Nam Co (reference-ID NC18-S-37). A) left T1, exterior view; B) left T2, exterior view; C) left T3, exterior view; D) right CR with attachment and the female genital lobes. (See Broodbakker & Danielopol (1982) for chaetotaxy.)
FIGURE 3 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 3. Valve images of Tonnacypris stewarti (f = female, m = male): (A1) exterior view of left valve (LV) and (A2) right valve (RV); interior view (A3‒A4) of a female from Nam Co (reference-ID NC18-S-37). Exterior view of LV (B1) and RV (B2) of a female; interior view of RV (B3) and LV (B4) of male from Mang-tsa, Tibetan Plateau (TP) (Daday 1908; reference-ID HNHM-IV-369). Arrows above Figures A1‒A2 and B1‒B2 point to anterior end of the valve. Exterior view of LV (C1) and RV (C2); interior view (C3‒C4) of a female; exterior view of LV (D1) and RV (D2); interior view (D3‒D4) of a male from Lake Band-e Amir, Afghanistan (Hartmann 1964; reference-ID ZMH-K27716). (E1) shows the marginal pore canals in the anteroventral side in the right valve, and (E2) denotes the scars on the dorsal part of the left valve of T. stewarti.
FIGURE 1 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 1. Chronological overview of descriptions and synonyms for Tonnacypris stewarti since 1908. The green rectangle designates living specimens with preserved soft anatomical structures. The incorporation of two asterisks (*) further signifies the inclusion of male specimens exhibiting soft anatomical structures. The gray rectangle denotes scrutinized fossil and subfossil specimens.
FIGURE 2. Study area. A in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 2. Study area. A) Location of Nam Co on the Tibetan Plateau, and B) sampling sites according to the habitat type and abundances (living and sub-fossil organism (2 valves = 1 organism) per gram wet weight, org/g wet) of Tonnacypris stewarti (Daday 1908) in Nam Co. Abundance distribution was categorized into three distinct patterns: a complete circle (indicating low abundance), a cross-circle (indicating medium abundance), and a circle with a central line (indicating higher abundance). Sample numbers correspond to Table 2. The elevation bar corresponds to map B. Source: Esri, Maxar, GeoEye, Earthstar Geographics, CNES/Airbus DS, USDA, USGS, AeroGRID, IGN, and the GIS User Community.
FIGURE 12 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 12. Valves of an adult and juveniles (A-1 to A-4) of Tonnacypris stewarti from Nam Co (reference-ID NC18-S-37). Arrow points to anterior.
FIGURE 9 in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 9. Tonnacypris stewarti (= E. afghanistanensis); male from Lake Band-e Amir, Afghanistan (reference-ID ZMHK27716; Hartmann 1964), A) T1, B) Zenker organ, and C1–C2) hemipenis of male. Abbreviations: dorsal lobe (dl), lateral shield (ls), and medial shield (ms).
FIGURE 15. A in Taxonomy, ontogeny, and ecology of Tonnacypris stewarti (Daday 1908) comb. nov. (Ostracoda: Cyprididae) from Nam Co, Tibetan Plateau
FIGURE 15. A) Classification of samples according to associated environmental factors (water depth, electrical conductivity, water temperature, and pH). Group A contains samples from the open lake, group B those from shallow waters, open lagoons and embayments, group C those from rivers and confined lagoons. B) The boxplots below the dendrogram show mean values (x) and variance of Tonnacypris stewarti abundance within the three groups of habitat types. For means and ranges of environmental factors see Table 5.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.