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1,123 results for “Cis”
aFCn for independent cis-eQTLs across 49 tissues in the GTEx v8 release
<p>The aFC-n model is the multi-variant generalization of the aFC approach (<a href="https://github.com/secastel/aFC">https://github.com/secastel/aFC</a>), to estimate the <i>cis</i>-regulatory effect size in genes associated with multiple conditionally independent eQTLs. Notably, aFC-n is the first method that allows for predicting genetically regulated gene expression in a haplotype-specific fashion, paving the way for a future class of genome association studies that can systematically incorporate allele dosage effects.</p><p>This dataset is generated using aFC-n software package (<a href="https://doi.org/10.5281/zenodo.8412460">10.5281/zenodo.8412460</a>) to calculate effect sizes for ~half a million independent <i>cis</i>-eQTLs across 49 tissues in the GTEx v8 release as described in the <a href="https://www.biorxiv.org/content/10.1101/2022.01.28.478116v1">manuscript</a>.</p><p>GTEx_v8_aFCn contains:</p><ul><li>gene_id : Ensembl gene ID</li><li>variant_id : eQTL ID associated to the gene</li><li>log2_aFC : The log2 of eQTL effect sizes measured as allelic Fold Change (aFC).</li><li>log2_aFC_min_95_interv : Lower bound 95% confidence interval</li><li>log2_aFC_plus_95_interv: Upper bound 95% confidence interval</li></ul><p>GTEx_v8<i>_</i>aFCn<i>_</i>combined contains:</p><ul><li>gene_id : Ensembl gene ID</li><li>variant_id : eQTL ID associated to the gene</li><li>rest of the columns : The log2 of eQTL effect sizes measured as allelic Fold Change (aFC) in the tissue specified by the column label capped at ±log2(100) <ul><li>nan = The variant is not an eQTL for the tissue / the effect size is not calculated for variants on chrX</li></ul></li></ul><p> </p>
Data for "A combined experimental and computational exploration of heteroleptic cis-Pd2L2L'2 nanocages through geometric complementarity"
<div>In the following subdirectories are the input and output of GFN2-xTB and DFT calculations for this publication:</div> <div> </div> <div>chemrxiv: <strong><em><a href="https://doi.org/10.26434/chemrxiv-2024-s0mmw">https://doi.org/10.26434/chemrxiv-2024-s0mmw</a></em></strong></div> <div> </div> <div>Published: <strong><em><a href="https://doi.org/10.1002/chem.202403336">https://doi.org/10.1002/chem.202403336</a></em></strong></div> <div> </div> <div>Code repository: <a href="https://github.com/andrewtarzia/simple_het_construction">github.com/andrewtarzia/simple_het_construction</a></div> <div>Zenodo code DOI: <a href="https://doi.org/10.5281/zenodo.13649229">10.5281/zenodo.13649229</a></div> <div> </div> <div>data directory:</div> <div> <ul> <li>a spreadsheet with all final energy values and exchange energy calculations</li> <li>CSD Survey data, NPd_survey_data_261119.csv, for Pd centres</li> </ul> </div> <div>Naming convention for file conversions:</div> <div> <ul> <li>l1: 1DBF</li> <li>l2: 1Ph</li> <li>l3: 1Th</li> <li>la: 2DBF</li> <li>lb: 2Py</li> <li>lc: 2Ph</li> <li>ld: 2Th</li> </ul> </div> <div>Structure naming convention: </div> <div> <ul> <li> <em><strong>mX</strong></em> indicates a homoleptic cage with <em><strong>X</strong></em> Pd atoms, <strong><em>cis</em></strong>/<strong><em>trans</em></strong> are the cis/trans heteroleptic cages, respectively</li> </ul> </div> <div> <p> </p> <p>structures/xtb directory:</p> </div> <div> <ul> <li>contains the structures from GFN2-xTB/ALPB(DMSO) optimisations of stk-generated structures </li> </ul> </div> <div> </div> <div>structures/opt_*METHOD*_SP_*METHOD*_06-02-2024 directories:</div> <div> <ul> <li>All DFT was run by Victor Posligua</li> <li>contains the input files (.com), output files (.log) and structure files (.xyz/.mol) of DFT optimisations and single point energy calculations with each method</li> <li>When the opt method and SP method are the same, the final structure is included in .mol and .xyz formats</li> <li>However, if opt method is different from the SP method, the final structure is not included because only a single-point energy calculation was run. </li> <li>For example, there are no .mol or .xyz files for 'opt_PBE0_SP_B3LYP_06-02-2024’ since the structure is already in 'opt_PBE0_SP_PBE0_06-02-2024’.</li> <li>you’ll find 8 different folders:<br> <ul> <li>opt_PBE0_SP_PBE0_06-02-2024</li> <li>opt_PBE0_SP_B3LYP_06-02-2024</li> <li>opt_PBE0_SP_B97D3_06-02-2024</li> <li>opt_PBE0_SP_HSE_06-02-2024</li> <li>opt_B3LYP_SP_B3LYP_06-02-2024</li> <li>opt_B97D3_SP_B97D3_06-02-2024</li> <li>opt_HSE_SP_HSE_06-02-2024</li> <li>opt_GFN2-xTB_SP_PBE0_06-02-2024</li> </ul> </li> </ul> </div>
Constructing CIs for 'the' Generalization Error
<p>This data contains information that is too large to be included in our GitHub repository: https://github.com/slds-lmu/paper_2023_ci_for_ge.<br><br>After downloading the data you need to first extract/decompress it.<br><br>The files are:<br><br>* results - Result datasets that need to be moved into the the GitHub repository in order to reproduce the analysis from the paper. Both the raw and processed datasets are contained.<br>* figures-granular - additional figures on a very granular level<br><br>The folders also contain READMEs describing the datasets and figures.<br><br>If you want to work with the datasets (all in .rds format) but don't want to work in R, you can simply load them in R (using readRDS(<path>)) and then convert them e.g. to csv using the write.csv function.</p>
OPT data from: A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint
<p><span>The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however, knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of <em>Nkx3.2</em> that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish <em>Danio rerio</em>, and was thus designated as <em>jaw joint regulatory sequence 1</em> (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of <em>Nkx3.2</em> and leads to transient jaw joint deformation and partial fusion. The emergence of this <em>Nkx3.2 </em>enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.</span></p>
Artificial selection on cis-element of Abl contributes cocoon yield increase in domestic silkworm
<p><span>The silkworm (</span><em><span>Bombyx mori</span></em><span>) is an important silk-producing domestic insect.</span><span> The quality and yield of the silk produced by <em>B. mori </em>exceeds that of its ancestor, the wild silkworm <em>B. mandarina</em>. However, to date little is known about the molecular mechanisms underlying domestication-related increases in silk yield. Here, we identified a gene associated with both domestication and silk-related quantitative trait locus (QTL): Abelson tyrosine protein kinase (<em>Abl</em>). </span><span>Population genomic data for <em>B. mori</em> and <em>B. mandarina</em> identified obvious signatures of artificial selection in the genomic region bearing the <em>Abl</em></span><span><em> </em>gene. T</span><span>here were two fixed nucleotide substitutions (−244 and −1311) in the </span><span>tran</span><span>scription factor binding motif of the upstream regulatory region of <em>B. mori Abl</em>.</span> <span>Compared to <em>Abl </em>in the wild silkworm <em>B. mandarina</em>, <em>B. mori Abl</em> exhibited significantly greater promoter activity and was upregulated in the silk gland from the last day of the 5<sup>th</sup> larval instar to pupal stage (P0). Compared to the wild type, CRISPR/Cas9-generated <em>Abl </em>loss-of-function mutants </span><span>exhibited a higher sensitivity to diseases, shorter developmental duration, and reductions in economically important silk traits, including cocoon weight, pupal weight, and cocoon layer thickness. Comparison of silk-gland transcriptomes between the wild type and the mutant indicated that genes enriched in ribosome biosynthesis, splicing, RNA transport, and the carbon metabolism were significantly downregulated in the mutants. Weighted gene co-expression network analysis (WGCNA) confirmed that genes related to ribosome biosynthesis were pivotal, driving the significant differentiation in silk yield between <em>B. mori</em> and <em>B. mandarina</em>. Here, we demonstrated that artificial selection acts on the cis-elements of silk-trait QTL gene <em>Abl </em>in a novel case (the domestic silkworm), and that this selection pressure increased <em>Abl </em>promoter activity and expression level. By promoting protein translation and synthesis, artificial selection further enhanced the robustness of silkworm larvae and improved cocoon silk synthesis.</span></p>
CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues
<p>Cis-regulatory elements (CREs) play a pivotal role in gene expression regulation, allowing cells to serve diverse functions and respond to external stimuli. To address this gap, we have created CREdb, a comprehensive database of over 10 million human regulatory elements across 1,058 cell types and 315 tissues. Data from 11 sources were curated and mapped to standard ontological terms. 11,223,434 combined elements are present in the final database, and these were merged into 5,666,240 consensus elements representing the combined ranges of the individual elements informed by their overlap. Each consensus element contains metadata including the number of elements supporting it and a hash linking to the source databases. The inferred activity of each consensus element in various cell-type and tissue context is also provided.</p>
Fig. 1 in Una nueva especie del género Cis Latreille, 1796 de la comarca de Osona, Cataluña, España (Coleoptera: Tenebrionoidea: Ciidae).
Fig. 1.- Holotypus ♂ de Cis onyosi n. sp., de Sant Bartomeu del Grau, Barcelona. Escala = 0,5 mm.
Fig. 1 in Presencia de Cis bilamellatus (Wood, 1884) en la Península Ibérica (Coleoptera: Ciidae)
Fig. 1.- Piptoporus betulinus sobre abedul muerto. Foto de Pablo Bahillo.
Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [Microscope images - Oct4 KDs]
<p>Microscope images related to Figure 2 in Schwämmle et al. 2025. </p> <p>The cells are undifferentiated or day 2 differentiated TX1072 XX SP427 mESCs with (or without) Oct4 knockdown in the indicated media.</p> <p>Exonic Xist is stained using Cy5 Stellaris probes. The nuclei are stained using DAPI.</p> <p>These files were used to manually count Xist clouds (see fish_sgOct4_manual.txt for counts). For code to visualize the results see https://github.com/EddaSchulz/TFiScreen_Paper. RA samples relate only to the biorXiv release of the manuscript (https://doi.org/10.1101/2024.10.08.617282).</p>
Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [FACS + BAMs + tables]
<div>FACS data related to Figures 1 and 4 in Schwämmle et al. 2025. </div> <div>Also include BAM files of published data and other files needed to replicate analyses included in https://github.com/EddaSchulz/TFiScreen_Paper. </div>
(TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep1)
<p><strong>Title</strong>: (TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep1)</p> <p><strong>Description</strong>: Simulation of a POPC membrane containing ten LAPTM4B-TM3_D2A peptides using charmm36 at 310K. (TM3_D2A peptides have cis peptides bonds by mistake)</p> <p><strong>MD engine</strong>: gromacs 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310K</p> <p><strong>Simulation time</strong>: 1000ns</p> <p><strong>Saving frequency</strong>: 100ps</p> <p><strong>Molecular content</strong>:<br> TM3_D2A 10<br> POPC 512<br> SOL 20470<br> NA 55<br> CL 55</p> <p><strong>Other information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * The peptide presents the D202A mutation.<br> * 5 peptides pointing up/ 5 peptides pointing down.<br> <br> - Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep2)
<p>System description<br> -------------------<br> - Title: (TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep2)</p> <p>- Description: Simulation of a POPC membrane containing ten LAPTM4B-TM3_D2A peptides using charmm36 at 310K. (TM3_D2A peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 2016.1</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 1000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3_D2A 10<br> POPC 512<br> SOL 20470<br> NA 55<br> CL 55</p> <p>- Other information:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * The peptide presents the D202A mutation.<br> * 5 peptides pointing up/ 5 peptides pointing down.<br> <br> - Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K membrane
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K membrane</p> <p>- Description: Simulation of a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.4</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 2000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> SOL 20470<br> NA 65<br> CL 55</p> <p>- Other information:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * 5 peptides pointing up/ 5 peptides pointing down</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep3)
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep3)</p> <p>- Description: Simulation intake nine ceramides (CER16) to a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.1.2</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 5000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p>- Other information:<br> * Simulations containing 9 CER16 in the water phase initially.<br> * Membrane containing LAPTM4B TM3 peptides.</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3_ASPH-CIS) POPC_512_TM3_ASPH_10_5up_5down_NaCl_150mM_310K
<p>System description<br> -------------------<br> - Title: (TM3_ASPH-CIS) Simulation POPC_512_TM3_ASPH_10_5up_5down_NaCl_150mM_310K membrane</p> <p>- Description: Simulation of a POPC membrane containing ten LAPTM4B-TM3_ASPH peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.4</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 2000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3_ASPH 10<br> POPC 512<br> SOL 20480<br> NA 55<br> CL 55</p> <p>- Other information:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * ASP 202 is in protonated form<br> * 5 peptides pointing up/ 5 peptides pointing down</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)</p> <p>- Description: Simulation intake nine ceramides (CER16) to a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.5-dev-20150319-0bec922</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 4000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p>- Other information:<br> * Simulations containing 9 CER16 in the water phase initially.<br> * Membrane containing LAPTM4B TM3 peptides.</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)</p> <p>- Description: Simulation intake nine ceramides (CER16) to a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.5-dev-20150319-0bec922</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 1000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p>- Other information:<br> * Simulations containing 9 CER16 in the water phase initially.<br> * Membrane containing LAPTM4B TM3 peptides.</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3_ASPH-CIS) Simulation CER160_9_POPC_512_TM3_ASPH_10_5up_5down_NaCl_150mM_310K
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation CER160_9_POPC_512_TM3_ASPH_10_5up_5down_NaCl_150mM_310K</p> <p>- Description: Simulation intake nine ceramides (CER16) to a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.5-dev-20150319-0bec922</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 4000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3_ASPH 10<br> POPC 512<br> CER160 9<br> SOL 34258<br> NA 92<br> CL 92</p> <p>- Other information:<br> * Simulations containing 9 CER16 in the water phase initially.<br> * Membrane containing LAPTM4B TM3 peptides.<br> * ASP 202 is in protonated form<br> * 5 peptides pointing up/ 5 peptides pointing down</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
<p>ATAC-seq peaks are in narrowPeak format. RNA-seq results are organized according to cell type. The normalized RPKM is reported for each gene in GENCODE 19. All data was mapped to hg19.</p>
Fig. 2 in A new species of Todites (Pteridophyta) with in situ spores from the Upper Permian of Pechora Cis-Urals (Russia)
Fig. 2. Stratigraphical column of the locality studied.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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