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41 results for “six genes”
Data from: Pleiotropy increases with gene age in six model multicellular eukaryotes
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Gene flow influences the genomic architecture of local adaptation in six riverine fish species
<p>Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from recombination and thus be selected for, but few studies have tested it with empirical data. Here, we used RADseq to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We used four differentiation-based outlier tests and three genotype-environment association analyses to define neutral SNPs and outlier SNPs that were putatively under selection. We then examined the distribution of outlier SNPs along the genome and investigated whether these SNPs were found in genomic islands of differentiation and inversions. We found that gene flow varied among species, and outlier SNPs were clustered more tightly in species with higher gene flow. The two species with the highest overall <em>F</em><sub>ST</sub> (0.0303 - 0.0720) and therefore lowest gene flow showed little evidence of clusters of outlier SNPs, with outlier SNPs in these species spreading uniformly across the genome. In contrast, nearly all outlier SNPs in the species with the lowest <em>F</em><sub>ST</sub> (0.0003) were found in a single large putative inversion. Two other species with intermediate gene flow (<em>F</em><sub>ST</sub> ~ 0.0025 - 0.0050) also showed clustered genomic architectures, with most islands of differentiation clustered on a few chromosomes. Our results provide important empirical evidence to support the hypothesis that increasingly clustered architectures of local adaptation are associated with high gene flow. </p>
Gene flow influences the genomic architecture of local adaptation in six riverine fish species
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FIGURE 3 in Phylogeny of pentatomomorphan bugs (Hemiptera-Heteroptera: Pentatomomorpha) based on six Hox gene fragments
FIGURE 3. Phylogeny of Pentatomomorpha based on six Hox gene fragments. The clades with morphological synapomorphies are illustrated by red lines. The support for each node is comprised of four values. The two numbers above each internode are the Bayesian posterior probability (BPP) while the two below are the bootstrap support (BS) of 100 replicates with maximum likelihood (ML) methods. Each number forward of the comma corresponds to the data matrix of amino acid (aa) sequences while each number behind corresponds to the data matrix of the first and second positions in the triplet codon of nucleotide (nt12) sequences. A dash stands for no support value for that node. The blue and green circles represent synapomorphy variants in C-terminal DFD 21 and 60, respectively. The lengths of the bugs are illustrated in proportion to their body sizes.
FIGURE 1 in Phylogeny of pentatomomorphan bugs (Hemiptera-Heteroptera: Pentatomomorpha) based on six Hox gene fragments
FIGURE 1. Summary of phylogenetic results of previous studies based on morphological characteristics, 18S rDNAs and mitochondrial genomes.
Data from: Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes
Background: Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be diverse transcriptional regulators, playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. Results: In this study, we identified 428 bZIP genes encoding 585 distinct proteins in six legumes, Glycine max, Medicago truncatula,Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Lotus japonicus. The legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. Four kinds of intron patterns (a–d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. We predicted the DNA-binding patterns and the dimerization properties, based on the characteristic features in the basic and hinge regions and the Leu zipper, respectively, which indicated that some highly conserved amino acid residues existed across each major group. The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. We also detected several key legume bZIP genes involved in drought- and salt-responses by comparing fold changes of expression values in drought-stressed or salt-stressed roots and leaves. Conclusions: In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses.
Data from: Mutation screening of 1,237 cancer genes across six model cell lines of basal-like breast cancer
Basal-like breast cancer is an aggressive subtype generally characterized as poor prognosis and lacking the expression of the three most important clinical biomarkers, estrogen receptor, progesterone receptor, and HER2. Cell lines serve as useful model systems to study cancer biology in vitro and in vivo. We performed mutational profiling of six basal-like breast cancer cell lines (HCC38, HCC1143, HCC1187, HCC1395, HCC1954, and HCC1937) and their matched normal lymphocyte DNA using targeted capture and next-generation sequencing of 1,237 cancer-associated genes, including all exons, UTRs and upstream flanking regions. In total, 658 somatic variants were identified, of which 378 were non-silent (average 63 per cell line, range 37–146) and 315 were novel (not present in the Catalogue of Somatic Mutations in Cancer database; COSMIC). 125 novel mutations were confirmed by Sanger sequencing (59 exonic, 48 3'UTR and 10 5'UTR, 1 splicing), with a validation rate of 94% of high confidence variants. Of 36 mutations previously reported for these cell lines but not detected in our exome data, 36% could not be detected by Sanger sequencing. The base replacements C/G>A/T, C/G>G/C, C/G>T/A and A/T>G/C were significantly more frequent in the coding regions compared to the non-coding regions (OR 3.2, 95% CI 2.0–5.3, P<0.0001; OR 4.3, 95% CI 2.9–6.6, P<0.0001; OR 2.4, 95% CI 1.8–3.1, P<0.0001; OR 1.8, 95% CI 1.2–2.7, P = 0.024, respectively). The single nucleotide variants within the context of T[C]T/A[G]A and T[C]A/T[G]A were more frequent in the coding than in the non-coding regions (OR 3.7, 95% CI 2.2–6.1, P<0.0001; OR 3.8, 95% CI 2.0–7.2, P = 0.001, respectively). Copy number estimations were derived from the targeted regions and correlated well to Affymetrix SNP array copy number data (Pearson correlation 0.82 to 0.96 for all compared cell lines; P<0.0001). These mutation calls across 1,237 cancer-associated genes and identification of novel variants will aid in the design and interpretation of biological experiments using these six basal-like breast cancer cell lines.
Data from: Mutation screening of 1,237 cancer genes across six model cell lines of basal-like breast cancer
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Data from: Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes
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ICH Induces Monocyte-Related Gene Expression Within Six Hours; A Study of Global Transcriptional Profiling in Swine ICH
GEO Series GSE124624. Sus scrofa. 20 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor
GEO Series GSE57268. Streptomyces coelicolor. 6 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profilling of six species of Brassica and early four generation of resynthesized B. napus (F1-F4)
GEO Series GSE43246. Brassica oleracea; Brassica juncea; Brassica napus; Brassica nigra; Brassica carinata; Brassica rapa. 10 samples. Type: Expression profiling by high throughput sequencing.
A six-gene prediction model for tumor response to induction chemotherapy in locoregionally advanced laryngo-hypopharyngeal carcinoma
GEO Series GSE184072. Homo sapiens. 54 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profiling of six MEF cell genotypes (wild type, β2SP+/-, β2SP-/-, SMAD3+/-, SMAD3-/-, and β2SP+/-; SMAD3+/-)
GEO Series GSE69750. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Intracerebral Hemorrhage Induces MicroRNA and Target Genes within Six Hours: An Integrated Analysis of miRNA-seq and mRNA-seq in Swine ICH
GEO Series GSE155242. Sus scrofa. 20 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [CGH]
GEO Series GSE40966. Homo sapiens. 463 samples. Type: Genome variation profiling by genome tiling array.
To identify differentially expressed genes in ventricular tissue between wildtype control and the 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish at six months.
GEO Series GSE269725. Danio rerio. 9 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profiles of cKit positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD
GEO Series GSE215369. Mus musculus. 54 samples. Type: Expression profiling by high throughput sequencing.
Comparative genomic analysis revealed twenty-six candidate genes involved in the air-breathing function of the broadhead catfish Clarias macrocephalus
GEO Series GSE151993. Clarias macrocephalus. 14 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide analysis of B and T cell gene expression during a six-week gluten challenge in patients with celiac disease
GEO Series GSE87629. Homo sapiens. 146 samples. Type: Expression profiling by array.
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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.