cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16940779
title: N<sup>6</sup>-Methyladenosine-regulated LINC00675 suppress the proliferation, migration and invasion of breast cancer cells via inhibiting miR-513b-5p

description: Breast cancer (BC) is the most common cancer among women. LINC00675 and miR-513b-5p has been reported to be abnormally expressed in multiple types of cancers and modulate malignant phenotypes of cancer cells. However, to date, the functional role and underlying regulatory mechanism of LINC00675 and miR-513b-5p in BC remains largely unknown. Here, we found that LINC00675 was significantly downregulated in BC tissues and cell lines. Decrease of LINC00675 expression associated with higher tumor grade, lymphovascular invasion and shorter survival in BC patients. Functional experiments demonstrated that overexpression of LINC00675 suppressed BC cell proliferation, migration and invasion, whereas depletion of LINC00675 exerted opposite effects. Mechanistically, LINC00675 functioned as a competing endogenous RNA (ceRNA) to interact with miR-513b-5p and suppress its expression. Moreover, METTL3 increased the m<sup>6</sup>A methylation of LINC00675, which enhanced the association between LINC00675 and miR-513b-5p. Collectively, the central findings of our study suggest that LINC00675 represses BC progression through the inhibition of miR-513b-5p in a m<sup>6</sup>A-dependent manner.
DOI: 10.6084/m9.figshare.13265862
title: Additional file 2 of Phylogenetic analysis and clinical characteristics of the co-occurring mutations in HA and NA genes of influenza A(H1N1)pdm09 viruses during 2015–2017 in Beijing, China

description: Additional file 2: Table 2. Amino acid similarity of HA genes compared to vaccine strains.
DOI: 10.6084/m9.figshare.16940890
title: Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence

description: Bladder cancer (BLCA) is one of the most common cancers worldwide with high recurrence rate. Hence, we intended to establish a recurrence-related long non-coding RNA (lncRNA) model of BLCA as a potential biomarker based on multi-omics analysis. Multi-omics data including copy number variation (CNV) data, mutation annotation files, RNA expression profiles and clinical data of The Cancer Genome Atlas (TCGA) BLCA cohort (303 cases) and GSE31684 (93 cases) were downloaded from public database. With multi-omics analysis, twenty lncRNAs were identified as the candidates related with BLCA recurrence, CNVs and mutations in training set. Ten-lncRNA signature were established using least absolute shrinkage and selection operation (LASSO) and Cox regression. Then, various survival analysis was used to assess the power of lncRNA model in predicting BLCA recurrence. The results showed that the recurrence-free survival time of high-risk group was significantly shorter than that of low-risk group in training and testing sets, and the predictive value of ten-lncRNA signature was robust and independent of other clinical variables. Gene Set Enrichment Analysis (GSEA) showed this signature were associated with immune disorders, indicating this signature may be involved in tumor immunology. After compared with the other reported lncRNA signatures, ten-lncRNA signature was validated as a superior prognostic model in predicting the recurrence of BLCA. The effectiveness of the model was also evaluated in bladder cancer samples via qRT-PCR. Thus, the novel ten-lncRNA signature, constructed based on multi-omics data, had robust prognostic power in predicting the recurrence of BLCA and potential clinical implications as biomarkers.
DOI: 10.6084/m9.figshare.16940892
title: A comprehensive genome-wide analysis of long non-coding RNA and mRNA expression profiles of JAK2V617F-positive classical myeloproliferative neoplasms

description: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in the progression of myeloid neoplasms, but the role of lncRNAs in the JAK2V617F-positive subtype of classical myeloproliferative neoplasms (cMPNs) remains unclear. This study was conducted to clarify the expression and regulation patterns of lncRNAs in JAK2V617F-positive cMPNs, and to explore new potential carcinogenic factors of cMPNs. Bioinformatics analysis of microarray detection and wet testing verification were performed to study the expression and regulation signature of differentially expressed lncRNAs (DELs) and related genes (DEGs) in cMPNs. The expression of lncRNAs and mRNAs were observed to significantly dysregulated in JAK2V617F-positive cMPN patients compared with the normal controls. Co-expression analysis indicated that there were significant differences of the co-expression pattern of lncRNAs and mRNAs in JAK2V617F-positive cMPN patients compared to normal controls. GO and KEGG pathway analysis of DEGs and DELs showed the involvement of several pathways previously reported to regulate the pathogenesis of leukemia and cMPNs. Cis- and trans-regulation analysis of lncRNAs showed that ZNF141, DHX29, NOC2L, MAS1L, AFAP1L1, and CPN2 were significantly cis-regulated by lncRNA ENST00000356347, ENST00000456816, hsa-mir-449c, NR_026874, TCONS_00012136, uc003lqp.2, and ENST00000456816, respectively, and DELs were mostly correlated with transcription factors including CTBP2, SUZ12, REST, STAT2, and GATA4 to jointly regulate multiple target genes. In summary, expression profiles of lncRNAs and mRNAs were significantly altered in JAK2V617F-positive cMPNs, the relative signaling pathway, co-expression, cis- and trans-regulation were regulated by dysregulation of lncRNAs and several important genes, such as ITGB3, which may act as a promising carcinogenic factor, warrant further investigation.
DOI: 10.5522/04/22183891
title: MAGICC vertex-level gene expression data

description: Vertex-level expression data from the Multiscale Atlas of Gene Expression for Integrative Cortical CartographyFiles include:Template cortical surface meshes for flat, inflated and very_inflated surfaces with 32k verticesfs_LR.32k.L.flat.surf.giifs_LR.32k.L.inflated.surf.giifs_LR.32k.L.very_inflated.surf.giiGlasser_2016.32k.L.label.gii - parcellation of fs_LR 32k surface according to Glasser et al., 2016 Nature.<br>ahba_vertex.npy - Atlas of cortical gene expression for 20,781 genes at 32k vertex locationsahba_vertex_gradients.npy - Atlas of cortical gene expression gradients for 20,781 genes at 32k vertex locationsSuppTable2.csv - Gene-level characterisations for 20,781 in the same order as the above files. Includes gene symbol, alongside many other annotations described in the manuscript.Example to code to analyse these data can be found at:<br>https://github.com/kwagstyl/magicc
DOI: 10.5522/04/22183891.v1
title: MAGICC vertex-level gene expression data

description: Vertex-level expression data from the Multiscale Atlas of Gene Expression for Integrative Cortical CartographyFiles include:Template cortical surface meshes for flat, inflated and very_inflated surfaces with 32k verticesfs_LR.32k.L.flat.surf.giifs_LR.32k.L.inflated.surf.giifs_LR.32k.L.very_inflated.surf.giiGlasser_2016.32k.L.label.gii - parcellation of fs_LR 32k surface according to Glasser et al., 2016 Nature.<br>ahba_vertex.npy - Atlas of cortical gene expression for 20,781 genes at 32k vertex locationsahba_vertex_gradients.npy - Atlas of cortical gene expression gradients for 20,781 genes at 32k vertex locationsSuppTable2.csv - Gene-level characterisations for 20,781 in the same order as the above files. Includes gene symbol, alongside many other annotations described in the manuscript.Example to code to analyse these data can be found at:<br>https://github.com/kwagstyl/magicc
DOI: 10.6084/m9.figshare.16941032
title: Abdominal obesity increases the risk of reflux esophagitis: a systematic review and meta-analysis

description: The association between abdominal obesity and reflux esophagitis (RE) has been extensively evaluated, but the current findings are mixed and more convincing epidemiological evidence urgently needs to be established. To thoroughly explore this relationship, we summarized the latest studies, performed an updated meta-analysis, and examined the dose–response relationship. We performed a systematic search of PubMed, Web of Science, and Embase up to 28 March 2021, using prespecified terms to identify studies investigating the association between abdominal obesity and RE. Odds ratios (ORs) with 95% confidence intervals (CIs), mean differences (MDs) or standardized mean differences (SMDs) with 95% CIs were taken as effect-size estimates. Forty-two observational studies, including 11 cohort studies, were meta-analyzed. Overall, a statistically significant association was observed between abdominal obesity and RE, by both the pooled OR (adjusted OR = 1.51, 95% CI: 1.37–1.66, <i>p</i> &lt; .001) and the pooled SMD (SMD = 0.36, 95% CI: 0.30–0.42, <i>p</i> &lt; .001). Moreover, this significant relationship persisted with subgroup stratification. In subgroup analyses, we found that study design, abdominal obesity measurement, adjustment for covariates and sex were possible sources of between-study heterogeneity. For the dose–response analyses, the risk of RE increased with the degree of abdominal obesity, and the increasing trend accelerated when waist circumference (WC) reached 87.0 cm. This meta-analysis indicated a significant association between abdominal obesity and RE, and the risk of RE increased with abdominal obesity especially when the WC was over 87.0 cm.
DOI: 10.6084/m9.figshare.13266008.v1
title: Additional file 2 of Polymorphisms in the airway epithelium related genes CDHR3 and EMSY are associated with asthma susceptibility

description: Additional file 2.
DOI: 10.6084/m9.figshare.14724652.v1
title: Supplementary Files S1 It contains the RepeatMasker annotation of the six avian genomes. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.19556241
title: Additional file 2 of Exogenous proline mitigates toxic effects of cadmium via the decrease of cadmium accumulation and reestablishment of redox homeostasis in Brassica juncea

description: Additional file 2: Fig. S2. Effects of exogenous proline on contents of PCs in leaves (A) and roots (B) of Brassica juncea seedlings under normal growth (Control), 80 µM Cd treatment (Cd), 60 mg/L proline treatment (Pro), and 80 µM Cd + 60 mg/L proline treatment (Cd + Pro). All the analyses were performed with three replicates. Error bars represent the standard deviations (SD). The different letters in the group indicate significantly different values between treatments (P &lt; 0.05). PCs, phytochelatins.
DOI: 10.6084/m9.figshare.14319818
title: Table S2: Geomorphology and geochemistry of the late Cenozoic volcanoes in the Halaha River-Chaoer River volcanic fields, western Greater Hinggan Mountain Range, NE China

description: Table providing data on the geomorphology of volcanoes
DOI: 10.6084/m9.figshare.7504070.v1
title: Additional file 1: of Comparative transcriptomics identifies patterns of selection in roses

description: Table S1. BUSCO analysis of the assemblies and coreset1. C, S, D, F, and M represent the proportion of the complete, the complete and single-copy, the complete and duplicated, the fragmented, and the missing BUSCO transcripts, respectively. (XLSX 128 kb)
DOI: 10.6084/m9.figshare.14319818.v1
title: Table S2: Geomorphology and geochemistry of the late Cenozoic volcanoes in the Halaha River-Chaoer River volcanic fields, western Greater Hinggan Mountain Range, NE China

description: Table providing data on the geomorphology of volcanoes
DOI: 10.6084/m9.figshare.14319821
title: Table S1: Geomorphology and geochemistry of the late Cenozoic volcanoes in the Halaha River-Chaoer River volcanic fields, western Greater Hinggan Mountain Range, NE China

description: Table providing data on the geomorphology of volcanoes
DOI: 10.6084/m9.figshare.14319821.v1
title: Table S1: Geomorphology and geochemistry of the late Cenozoic volcanoes in the Halaha River-Chaoer River volcanic fields, western Greater Hinggan Mountain Range, NE China

description: Table providing data on the geomorphology of volcanoes
DOI: 10.6084/m9.figshare.14319821.v2
title: Table S1: Geomorphology and geochemistry of the late Cenozoic volcanoes in the Halaha River-Chaoer River volcanic fields, western Greater Hinggan Mountain Range, NE China

description: Table providing data on the geomorphology of volcanoes
DOI: 10.6084/m9.figshare.14724658.v1
title: Supplementary Figure This file contains Figure S1. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.23751803.v1
title: Additional file 8 of CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes

description: Additional file 8: Table S7. Co-expressed PCG.
DOI: 10.6084/m9.figshare.23751791.v1
title: Additional file 4 of CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes

description: Additional file 4: Table S3. Disease Enrichment Noncoding.
DOI: 10.6084/m9.figshare.19556238
title: Additional file 1 of Exogenous proline mitigates toxic effects of cadmium via the decrease of cadmium accumulation and reestablishment of redox homeostasis in Brassica juncea

description: Additional file 1: Fig. S1. The plant height (A), root length (B), shoot dry weight (C), and root dry weight (D) of Brassica juncea under normal growth (Control), 80 µM Cd treatment (Cd), 60 mg/L proline treatment (Pro), and 80 µM Cd + 60 mg/L proline treatment (Cd + Pro). All the analyses were performed with three replicates. Error bars represent the standard deviations (SD). The different letters in the group indicate significantly different values between treatments (P &lt; 0.05).
DOI: 10.6084/m9.figshare.23751791
title: Additional file 4 of CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes

description: Additional file 4: Table S3. Disease Enrichment Noncoding.
DOI: 10.6084/m9.figshare.19556244
title: Additional file 3 of Exogenous proline mitigates toxic effects of cadmium via the decrease of cadmium accumulation and reestablishment of redox homeostasis in Brassica juncea

description: Additional file 3: Fig. S3. Effects of exogenous proline on GR activity in leaves (A) and roots (B) of Brassica juncea seedlings under Cd stress. All the analyses were performed with three replicates. Error bars represent the standard deviations (SD). The different letters in the group indicate significantly different values between treatments (P &lt; 0.05). GR, glutathione reductase.
DOI: 10.6084/m9.figshare.19556238.v1
title: Additional file 1 of Exogenous proline mitigates toxic effects of cadmium via the decrease of cadmium accumulation and reestablishment of redox homeostasis in Brassica juncea

description: Additional file 1: Fig. S1. The plant height (A), root length (B), shoot dry weight (C), and root dry weight (D) of Brassica juncea under normal growth (Control), 80 µM Cd treatment (Cd), 60 mg/L proline treatment (Pro), and 80 µM Cd + 60 mg/L proline treatment (Cd + Pro). All the analyses were performed with three replicates. Error bars represent the standard deviations (SD). The different letters in the group indicate significantly different values between treatments (P &lt; 0.05).
DOI: 10.6084/m9.figshare.19556337.v1
title: Additional file 4 of Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system

description: Additional file 4. Statistics analysis example in R language.
DOI: 10.6084/m9.figshare.23751785
title: Additional file 2 of CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes

description: Additional file 2: Table S1. Disease Enrichment Protein Coding.
DOI: 10.6084/m9.figshare.23751797
title: Additional file 6 of CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes

description: Additional file 6: Table S5. SNPs Per GWAS.
DOI: 10.6084/m9.figshare.23751794.v1
title: Additional file 5 of CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes

description: Additional file 5: Table S4. Tested Noncoding RNAs.
DOI: 10.6084/m9.figshare.23751836.v1
title: Additional file 1 of Integration of single-cell regulon atlas and multi-omics data for prognostic stratification and personalized treatment prediction in human lung adenocarcinoma

description: Additional file 1: Table S1. Basic information of included datasets. Table S2. Identification of prognostic regulons. Table S3. LPRI of all included datasets.
DOI: 10.6084/m9.figshare.23751836
title: Additional file 1 of Integration of single-cell regulon atlas and multi-omics data for prognostic stratification and personalized treatment prediction in human lung adenocarcinoma

description: Additional file 1: Table S1. Basic information of included datasets. Table S2. Identification of prognostic regulons. Table S3. LPRI of all included datasets.
DOI: 10.6084/m9.figshare.24084567
title: numr-1/2 and ETPs

description: Numerical data for manuscript
DOI: 10.6084/m9.figshare.24084567.v2
title: numr-1/2 and ETPs

description: Numerical data for manuscript
DOI: 10.6084/m9.figshare.24084567.v1
title: numr-1/2 and ETPs

description: Numerical data for manuscript
DOI: 10.6084/m9.figshare.8028872
title: Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples

description: The study of gene expression quantitative trait loci (eQTL) is an effective approach to illuminate the functional roles of genetic variants. Computational methods have been developed for eQTL mapping using gene expression data from microarray or RNA-seq technology. Application of these methods for eQTL mapping in tumor tissues is problematic because tumor tissues are composed of both tumor and infiltrating normal cells (e.g., immune cells) and eQTL effects may vary between tumor and infiltrating normal cells. To address this challenge, we have developed a new method for eQTL mapping using RNA-seq data from tumor samples. Our method separately estimates the eQTL effects in tumor and infiltrating normal cells using both total expression and allele-specific expression (ASE). We demonstrate that our method controls Type I error rate and has higher power than some alternative approaches. We applied our method to study RNA-seq data from The Cancer Genome Atlas and illustrated the similarities and differences of eQTL effects in tumor and normal cells. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.24281953
title: Supplementary data for the manuscript: Exploring the causal effects and potential mechanisms affecting plasma low-density lipoprotein cholesterol levels: a multiomics Mendelian randomization study

description: This dataset contains data about the causal effects and potential mechanisms affecting plasma LDL-C levels.
DOI: 10.6084/m9.figshare.13266090
title: Additional file 18 of Tumor-derived exosomal miR-934 induces macrophage M2 polarization to promote liver metastasis of colorectal cancer

description: Additional file 18: Table S3. Deregulated miRNA between stage I and stage IV colon cancer from TCGA data set.
DOI: 10.6084/m9.figshare.13266090.v1
title: Additional file 18 of Tumor-derived exosomal miR-934 induces macrophage M2 polarization to promote liver metastasis of colorectal cancer

description: Additional file 18: Table S3. Deregulated miRNA between stage I and stage IV colon cancer from TCGA data set.
DOI: 10.13012/b2idb-0365076_v1
title: Data for little brown occupancy and associated landcover data from McHenry County, Illinois

description: Mist netting data for little brown bats (Myotis lucifugus) in McHenry County, Illinois and output of acoustic data processed using Kaleidoscope (Version 5.1.9, Bats of North America 5.1.0; Wildlife Acoustics) auto-identification software. Associated survey metadata and landcover metrics calculated using Fragstats included.
DOI: 10.6084/m9.figshare.23751817
title: Additional file 11 of The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

description: Additional file 11: Table S9. DEGs participating in cell division.
DOI: 10.6084/m9.figshare.23751814.v1
title: Additional file 10 of The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

description: Additional file 10: Table S8. DEGs consistent with the change of phytohormones.