cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10311395
title: Table S3 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.15029821.v1
title: Identification of an epithelial-mesenchymal transition related long non-coding RNA (LncRNA) signature in Glioma

description: Epithelial–mesenchymal transition (EMT)-related long non-coding RNAs (lncRNAs) may be exploited as potential therapeutic targets in gliomas. However, the prognostic value of EMT-related lncRNAs in gliomas is unclear. We obtained lncRNAs from The Cancer Genome Atlas and constructed EMT-related lncRNA co-expression networks to identify EMT-related lncRNAs. The Chinese Glioma Genome Atlas (CGGA) was used for validation. Gene set enrichment and principal component analyses were used for functional annotation. The EMT–lncRNA co-expression networks were constructed. A real-time quantitative polymerase chain reaction assay was performed to validate the bioinformatics results. A nine-EMT-related lncRNAs (HAR1A, LINC00641, LINC00900, MIR210HG, MIR22HG, PVT1, SLC25A21-AS1, SNAI3-AS1, and SNHG18) signature was identified in patients with glioma. Patients in the low-risk group had a longer overall survival (OS) than those in the high-risk group (P &lt; 0.0001). Additionally, patients in the high-risk group showed no deletion of chromosomal arms 1p and/or 19q, isocitrate dehydrogenase wild type, and higher World Health Organization grade. Moreover, the signature was identified as an independent factor and was significantly associated with OS (P = 0.041, hazard ratio = 1.806). These findings were further validated using the CGGA dataset. The low- and high-risk groups showed different EMT statuses based on principal component analysis. To study the regulatory function of lncRNAs, a lncRNA-mediated ceRNA network was constructed, which showed that complex interactions of lncRNA–miRNA–mRNA may be a potential cause of EMT progression in gliomas. This study showed that the nine-EMT-related lncRNA signature has a prognostic value in gliomas.
DOI: 10.6084/m9.figshare.10311398.v1
title: Table S6 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.10311410
title: Table S1 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.10311416
title: Table S8 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.10311428
title: Table S7 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.10311428.v1
title: Table S7 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.12408674
title: Atmospheric factors controlling stable isotope variations in modern precipitation of the tropical region of Bangladesh

description: The study investigates the factors that control the isotopic composition of tropical precipitation in Bangladesh. Daily and monthly rainfall samples were collected from three stations from 2013 to 2015: (1) northern and moderately high altitude: Sylhet, (2) middle part of the country (close to Tropic of Cancer): Savar, and (3) southern coastal region: Barisal. To escape from the post-evaporation effect, proper care was adopted. This is supported by the fact that the local meteoric water lines (LMWLs) derived for the daily precipitations of all stations mostly follow the global meteoric water line (GMWL). The results exhibit a clear seasonal and spatial variation in both <i>δ</i><sup>18</sup>O and <i>δ</i><sup>2</sup>H of precipitation. <sup>18</sup>O is more depleted in samples collected during rainy (monsoon) seasons, while <sup>18</sup>O enrichment is associated to winter and summer (pre-monsoon) seasons. During rainy season, intra-seasonal variability of δ<sup>18</sup>O rainfall is clearly seen and remarkable depletion of <sup>18</sup>O is observed during the period of intense convective activity over the Bay of Bengal. This feature indicates that isotope variability in Bangladesh is controlled by large-scale convective activity rather than local rainfall amount.
DOI: 10.6084/m9.figshare.16602479.v1
title: Reliable Post-Signal Fault Diagnosis for Correlated High-Dimensional Data Streams

description: Rapid advance of sensor technology is facilitating the collection of high-dimensional data streams (HDS). Apart from real-time detection of potential out-of-control (OC) patterns, post-signal fault diagnosis of HDS is becoming increasingly important in the filed of statistical process control to isolate abnormal data streams. The major limitations of the existing methods on that topic include (i) they cannot achieve reliable diagnostic results in the sense that their performance is highly variable, and (ii) the informative correlation among different streams is often neglected by them. This article elaborates the problem of reliable fault diagnosis for monitoring correlated HDS using the large-scale multiple testing. Under the framework of hidden Markov model dependence, new diagnostic procedures are proposed, which can control the missed discovery exceedance (MDX) at a desired level. Extensive numerical studies along with some theoretical results show that the proposed procedures can control MDX properly, leading to diagnostics with high reliability and efficiency. Also, their diagnostic performance can be improved significantly by exploiting the dependence among different data streams, which is especially appealing in practice for identifying clustered OC streams.
DOI: 10.5281/zenodo.10679452
title: КОНЦЕПТ «HEAD/ГОЛОВА/БОШ» В АНГЛИЙСКОЙ , УЗБЕКСКОЙ И РУССКОЙ ЯЗЫКОВОЙ КАРТИНАХ МИРА
DOI: 10.5281/zenodo.10679453
title: КОНЦЕПТ «HEAD/ГОЛОВА/БОШ» В АНГЛИЙСКОЙ , УЗБЕКСКОЙ И РУССКОЙ ЯЗЫКОВОЙ КАРТИНАХ МИРА
DOI: 10.5281/zenodo.10679434
title: O'ZBEKISTONDA  BARQARORIQTISODIY O'SISH UCHUN INVESTITSIYA MUHITINI TA'MINLASH MASALALARI
DOI: 10.5281/zenodo.10679435
title: O'ZBEKISTONDA  BARQARORIQTISODIY O'SISH UCHUN INVESTITSIYA MUHITINI TA'MINLASH MASALALARI
DOI: 10.6084/m9.figshare.15029796
title: PAX6 upstream antisense RNA (PAUPAR) inhibits colorectal cancer progression through modulation of the microRNA (miR)-17-5p / zinc finger protein 750 (ZNF750) axis

description: Researchers have demonstrated that long non-coding RNAs (lncRNAs) are vital in colorectal cancer (CRC) progression. Here, we aimed to explore the function of lncRNA PAX6 upstream antisense RNA (PAUPAR) in the development of CRC. In the present study, PAUPAR and microRNA (miR)-17-5p expression levels in CRC tissues and cells were examined using quantitative real-time polymerase chain reaction (qRT-PCR). Western blot analysis was adopted to examine ZNF750 expression at the protein level in CRC cells. CRC cell proliferation was examined by colony formation experiment and 5-Bromo-2-deoxyUridine (BrdU) experiment. CRC cell migration and invasion were assessed by Transwell experiments. Apoptosis was measured using the TUNEL experiment. The targeting relationship between PAUPAR and miR-17-5p was confirmed using dual-luciferase reporter gene and RNA immunoprecipitation (RIP) experiments. We demonstrated that PAUPAR was markedly down-modulated in CRC, and its low expression was significantly related to increased T stage and local lymph node metastasis. Knockdown of PAUPAR enhanced CRC cell proliferation, migration and invasion, and restrained apoptosis relative to controls, whereas PAUPAR overexpression caused the opposite effects. Moreover, rescue experiments showed that miR-17-5p inhibitor could reverse the role of PAUPAR knockdown on the malignant phenotypes of CRC cells. Additionally, PAUPAR could positively regulate the expression of ZNF750 via repressing miR-17-5p. Taken together, these findings suggest that PAUPAR/miR-17-5p/ZNF750 axis is a novel mechanism implicated in CRC progression.
DOI: 10.6084/m9.figshare.21321541
title: Additional file 5 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 5. Initial predicted HLA-II binding epitopes.
DOI: 10.6084/m9.figshare.21321535.v1
title: Additional file 3 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 3. Linear B cell epitopes predicted by the ABCPred server.
DOI: 10.6084/m9.figshare.21321520
title: Additional file 15 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 15: Table S1. The initial result of the joint prediction using BepiPred-2.0 and ABCPred.
DOI: 10.6084/m9.figshare.21321541.v1
title: Additional file 5 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 5. Initial predicted HLA-II binding epitopes.
DOI: 10.6084/m9.figshare.19219194
title: Additional file 15 of Insights into glucosinolate accumulation and metabolic pathways in Isatis indigotica Fort.

description: Additional file 15: Table S5. Homologous sequences of AOP, GSL-OH, CYP79, CYP81F, CYP83, MAM and IPMS genes in 26 Brassicaceae species.
DOI: 10.6084/m9.figshare.21321547
title: Additional file 7 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 7. Initial predicted mouse MHC-II binding epitopes.
DOI: 10.6084/m9.figshare.21321547.v1
title: Additional file 7 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 7. Initial predicted mouse MHC-II binding epitopes.
DOI: 10.6084/m9.figshare.10311392.v1
title: Table S11 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.10311398
title: Table S6 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.