cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5755824.v1
title: Additional file2: Table S2. of Analysis of microarrays of miR-34a and its identification of prospective target gene signature in hepatocellular carcinoma

description: GO enrichment analysis of miR-34a target genes. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.5755827
title: Additional file3: Table S3. of Analysis of microarrays of miR-34a and its identification of prospective target gene signature in hepatocellular carcinoma

description: Integrative-analysis of miR-34a target genes and the natural language processing (NLP) results. Twenty-four overlapping genes that are not only associated with the development and progression of HCC but also are the potential miR-34a target genes were obtained in this integrativeâ analysis (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.5755827.v1
title: Additional file3: Table S3. of Analysis of microarrays of miR-34a and its identification of prospective target gene signature in hepatocellular carcinoma

description: Integrative-analysis of miR-34a target genes and the natural language processing (NLP) results. Twenty-four overlapping genes that are not only associated with the development and progression of HCC but also are the potential miR-34a target genes were obtained in this integrativeâ analysis (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.5758866
title: Additional file 1: Table S1. of Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

description: Repeat Variable Di-residues (RVDs) of different groups of TALEs from X. citri strains sequenced using pacbio sequencing strategy including Xc-03-1638-1-1. The TALEs have been grouped in three types, pthA2/3 type, with two subgroups as pthA2 and pthA3; pthA4 type and pthA1 type. Note the residues highlighted for TALEs in Xc-03-1638-1-1 show chimeric version of pthA2/3 type upon comparing RVDs. (XLS 27 kb)
DOI: 10.6084/m9.figshare.5758866.v1
title: Additional file 1: Table S1. of Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

description: Repeat Variable Di-residues (RVDs) of different groups of TALEs from X. citri strains sequenced using pacbio sequencing strategy including Xc-03-1638-1-1. The TALEs have been grouped in three types, pthA2/3 type, with two subgroups as pthA2 and pthA3; pthA4 type and pthA1 type. Note the residues highlighted for TALEs in Xc-03-1638-1-1 show chimeric version of pthA2/3 type upon comparing RVDs. (XLS 27 kb)
DOI: 10.6084/m9.figshare.5758893
title: Additional file 2: Table S2. of Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

description: List of SNPs obtained upon comparing chromosomes of Xc-03-1638-1-1 and LM180. (XLS 44 kb)
DOI: 10.6084/m9.figshare.5758893.v1
title: Additional file 2: Table S2. of Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

description: List of SNPs obtained upon comparing chromosomes of Xc-03-1638-1-1 and LM180. (XLS 44 kb)
DOI: 10.6084/m9.figshare.5758917
title: Additional file 1: of Evaluation of a 27-gene inherited cancer panel across 630 consecutive patients referred for testing in a clinical diagnostic laboratory

description: Patient characteristics and variant listing among positive cases, Pathogenic and likely pathogenic variants detected in the study. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.5758917.v1
title: Additional file 1: of Evaluation of a 27-gene inherited cancer panel across 630 consecutive patients referred for testing in a clinical diagnostic laboratory

description: Patient characteristics and variant listing among positive cases, Pathogenic and likely pathogenic variants detected in the study. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.5759112
title: Additional file 1: of Dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs

description: Differentially expressed miRNAs and Correlation coefficient matrix. (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.5759112.v1
title: Additional file 1: of Dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs

description: Differentially expressed miRNAs and Correlation coefficient matrix. (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.5759403
title: TEAD4 promotes colorectal tumorigenesis via transcriptionally targeting YAP1

description: TEAD4 (TEA domain family member 4) was recently revealed as an oncogenic character in tumorigenesis. However, its role remains unclear in colorectal tumorigenesis. Here, we firstly found that the expression level of TEAD4 was significantly elevated in clinical samples of colorectal adenomas (CRA) and correlated with the size and histological type of CRA. Moreover, patients with higher TEAD4 expression in normal colon mucosa are more prone to be recurrent after polypectomy. TEAD4 knockdown significantly inhibited colorectal cell proliferation <i>in vitro</i> and suppressed tumor growth <i>in vivo</i>. RNA-seq and GSEA analysis reveals TEAD4 can probably regulate Hippo pathway and further experiment confirm the downstream target gene YAP1. The subsequent ChIP-qPCR and luciferase report assay indicated that TEAD4 regulated YAP1 by direct binding and transcriptional activation. In summary, our study reveals that TEAD4 plays an important tumor-promoting role in colorectal cancer by directly targeting the YAP1, thus we suggests TEAD4 may be used as a novel biomarker in colorectal tumorigenesis and provides TEAD4/YAP1 axis as a potential therapeutic option for colorectal cancer.
DOI: 10.6084/m9.figshare.5759403.v1
title: TEAD4 promotes colorectal tumorigenesis via transcriptionally targeting YAP1

description: TEAD4 (TEA domain family member 4) was recently revealed as an oncogenic character in tumorigenesis. However, its role remains unclear in colorectal tumorigenesis. Here, we firstly found that the expression level of TEAD4 was significantly elevated in clinical samples of colorectal adenomas (CRA) and correlated with the size and histological type of CRA. Moreover, patients with higher TEAD4 expression in normal colon mucosa are more prone to be recurrent after polypectomy. TEAD4 knockdown significantly inhibited colorectal cell proliferation <i>in vitro</i> and suppressed tumor growth <i>in vivo</i>. RNA-seq and GSEA analysis reveals TEAD4 can probably regulate Hippo pathway and further experiment confirm the downstream target gene YAP1. The subsequent ChIP-qPCR and luciferase report assay indicated that TEAD4 regulated YAP1 by direct binding and transcriptional activation. In summary, our study reveals that TEAD4 plays an important tumor-promoting role in colorectal cancer by directly targeting the YAP1, thus we suggests TEAD4 may be used as a novel biomarker in colorectal tumorigenesis and provides TEAD4/YAP1 axis as a potential therapeutic option for colorectal cancer.
DOI: 10.6084/m9.figshare.5759823
title: Individual human non-click data

description: These are the individual human data sets for non-click trials. Run the script EMREO_STATS_PNAS to re-create the summary statistics file using various processing options.
DOI: 10.6084/m9.figshare.5760273
title: Individual human click data

description: These are individual human subject data files for click trials.
DOI: 10.6084/m9.figshare.5760273.v1
title: Individual human click data

description: These are individual human subject data files for click trials.
DOI: 10.6084/m9.figshare.5764338
title: Fingerprint of Exhaust Gases and Database of Microbial Diversity During Silkworm Excrement Composting

description: Composting can convert silkworm excrement (SE) into good fertilizer, but the popularization of this practice is greatly hampered due to the strong odor produced. Determining the gas pollutants, the potential native aerogenic microorganisms and deodorant microorganism communities will lay foundations for developing good strategies to deal with malodor pollution from SE composting. This study qualitatively and quantitatively analyzed the exhaust gas and the microbial diversity. With a combination of solid-phase micro-extraction-gas chromatography tandem mass spectrometry technology and other methods of Chinese national standards, 43 odor pollutants from SE composting were identified and quantified. Ammonia, sulfur dioxide and hydrogen sulfide were the three major pollutants among the volatile inorganic compounds, with concentrations far exceeding the permissible standards for workplaces in China. 5-Ethyl-2,2,3-trimethyl-heptane, 2,2,4,6,6-5-methyl-heptane and 5-isobutyl-nonane accounted for 46.58% of volatile organic compounds. Using analysis of ribosome DNA sequences with Illumina Miseq PE 2 * 250, a next generation high-throughput sequencing technology, more than 694 bacteria (and actinomycetes) and more than 136 fungi were annotated, including groups of native aerogenic microorganisms and deodorant microorganisms. This study indicated a serious malodor problem and abundant microorganisms from SE composting and provided basic data not only for odor pollution control but also for future functional microorganism studies.
DOI: 10.6084/m9.figshare.5764338.v1
title: Fingerprint of Exhaust Gases and Database of Microbial Diversity During Silkworm Excrement Composting

description: Composting can convert silkworm excrement (SE) into good fertilizer, but the popularization of this practice is greatly hampered due to the strong odor produced. Determining the gas pollutants, the potential native aerogenic microorganisms and deodorant microorganism communities will lay foundations for developing good strategies to deal with malodor pollution from SE composting. This study qualitatively and quantitatively analyzed the exhaust gas and the microbial diversity. With a combination of solid-phase micro-extraction-gas chromatography tandem mass spectrometry technology and other methods of Chinese national standards, 43 odor pollutants from SE composting were identified and quantified. Ammonia, sulfur dioxide and hydrogen sulfide were the three major pollutants among the volatile inorganic compounds, with concentrations far exceeding the permissible standards for workplaces in China. 5-Ethyl-2,2,3-trimethyl-heptane, 2,2,4,6,6-5-methyl-heptane and 5-isobutyl-nonane accounted for 46.58% of volatile organic compounds. Using analysis of ribosome DNA sequences with Illumina Miseq PE 2 * 250, a next generation high-throughput sequencing technology, more than 694 bacteria (and actinomycetes) and more than 136 fungi were annotated, including groups of native aerogenic microorganisms and deodorant microorganisms. This study indicated a serious malodor problem and abundant microorganisms from SE composting and provided basic data not only for odor pollution control but also for future functional microorganism studies.
DOI: 10.6084/m9.figshare.5765019
title: Additional file 9: Dataset S1. of Chemical hybridizing agent SQ-1-induced male sterility in Triticum aestivum L.: a comparative analysis of the anther proteome

description: The relevant files of ClueGO results. (XLS 607Â kb)
DOI: 10.6084/m9.figshare.5765019.v1
title: Additional file 9: Dataset S1. of Chemical hybridizing agent SQ-1-induced male sterility in Triticum aestivum L.: a comparative analysis of the anther proteome

description: The relevant files of ClueGO results. (XLS 607Â kb)
DOI: 10.6084/m9.figshare.5765061
title: Additional file 2: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Annotation of interspersed repeats of P. tuoliensis genome. (XLSX 289 kb)
DOI: 10.6084/m9.figshare.5765061.v1
title: Additional file 2: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Annotation of interspersed repeats of P. tuoliensis genome. (XLSX 289 kb)
DOI: 10.6084/m9.figshare.5765070
title: Additional file 3: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Marker information of the genetic linkage and physical map. The table summarizes the information of markers mapped genetically and physically, including the positions on genetic linkage map and scaffolds. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.5765070.v1
title: Additional file 3: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Marker information of the genetic linkage and physical map. The table summarizes the information of markers mapped genetically and physically, including the positions on genetic linkage map and scaffolds. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.5765088
title: Additional file 4: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Markers mapped to LG1 of P. eryngii var. eryngii and their physical positions (Modified from Im et al., 2016). Primer sequences of markers were blasted to the whole genome sequence of ATCC90797 (JGI). Physical positions of markers were indicated as the start and end positions of the primers. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.5765088.v1
title: Additional file 4: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Markers mapped to LG1 of P. eryngii var. eryngii and their physical positions (Modified from Im et al., 2016). Primer sequences of markers were blasted to the whole genome sequence of ATCC90797 (JGI). Physical positions of markers were indicated as the start and end positions of the primers. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.5765121
title: Additional file 6: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Genes of the A mating type locus and the flanking regions. The table shows the genes used for the synteny comparison of the A mating type locus and the flanking region in P. tuoliensis (this study, 489P1) and P. eryngii var. eryngii (JGI, ATCC 90797). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5765121.v1
title: Additional file 6: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Genes of the A mating type locus and the flanking regions. The table shows the genes used for the synteny comparison of the A mating type locus and the flanking region in P. tuoliensis (this study, 489P1) and P. eryngii var. eryngii (JGI, ATCC 90797). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5765172
title: Additional file 9: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Recombination rates on a representative scaffold of each linkage group. Since several scaffolds were assigned to one LG (chromosome), we selected the longest scaffold (or a part of the scaffold for the ones divided into different LGs) as the representative. The physical positions of markers were plotted against the map positions, scatter plots were made for each linkage group. The red brackets indicate the physical positions of the high recombination rate suggesting the existence of recombination hotspots. The same scale was used for the X-axis in order to make the map distance of different LG more comparable. (ZIP 1562 kb)
DOI: 10.6084/m9.figshare.5765172.v1
title: Additional file 9: of A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci

description: Recombination rates on a representative scaffold of each linkage group. Since several scaffolds were assigned to one LG (chromosome), we selected the longest scaffold (or a part of the scaffold for the ones divided into different LGs) as the representative. The physical positions of markers were plotted against the map positions, scatter plots were made for each linkage group. The red brackets indicate the physical positions of the high recombination rate suggesting the existence of recombination hotspots. The same scale was used for the X-axis in order to make the map distance of different LG more comparable. (ZIP 1562 kb)
DOI: 10.6084/m9.figshare.5765229
title: Additional file 2: Table S1. of An epigenome-wide study of obesity in African American youth and young adults: novel findings, replication in neutrophils, and relationship with gene expression

description: CpG sites with p &lt; 1E−7 in this youth and young adult study. Table S2. Performance of the 55 CpG sites in neutrophils. Table S3. Association of the 55 CpG sites with cardiometabolic traits without adjustment of obesity/BMI. Table S4. The significant associations between CpG sites and metabolic traits after the adjustment of obesity/BMI. Table S5. DNA methylation, gene expression, and obesity. Table S6. Significantly enriched pathways (FDR &lt; 0.05). Table S7. Replication of previous reported CpG sites identified in middle-aged and elderly population. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.5765229.v1
title: Additional file 2: Table S1. of An epigenome-wide study of obesity in African American youth and young adults: novel findings, replication in neutrophils, and relationship with gene expression

description: CpG sites with p &lt; 1E−7 in this youth and young adult study. Table S2. Performance of the 55 CpG sites in neutrophils. Table S3. Association of the 55 CpG sites with cardiometabolic traits without adjustment of obesity/BMI. Table S4. The significant associations between CpG sites and metabolic traits after the adjustment of obesity/BMI. Table S5. DNA methylation, gene expression, and obesity. Table S6. Significantly enriched pathways (FDR &lt; 0.05). Table S7. Replication of previous reported CpG sites identified in middle-aged and elderly population. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.5765478
title: Human Control Data

description: These are the individual human subject data files for the control conditions (4 x plugged mic. "HP" and 1 x mic. in syringe "HS").
DOI: 10.6084/m9.figshare.5765496
title: Summary Data Files

description: These are the summary data files for both human and monkey data. See the user guide for individual descriptions.<br>Control data summaries can be generated with the scripts provided in this collection (see user guide).
DOI: 10.6084/m9.figshare.5765646
title: Additional file 1: Table S1. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: List of differentially expressed genes obtained from the RNA-Seq analysis of altered versus normal samples. (XLS 48Â kb)
DOI: 10.6084/m9.figshare.5765646.v1
title: Additional file 1: Table S1. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: List of differentially expressed genes obtained from the RNA-Seq analysis of altered versus normal samples. (XLS 48Â kb)
DOI: 10.6084/m9.figshare.5765649
title: Additional file 1: Table S1. of Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

description: Details of papaya tissues used for quantitative real-time PCR analysis. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5765649.v1
title: Additional file 1: Table S1. of Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

description: Details of papaya tissues used for quantitative real-time PCR analysis. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5765661
title: Additional file 2: Table S2. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: List of differentially expressed genes obtained from the RNA-Seq analysis of altered versus wild-type samples. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.5765661.v1
title: Additional file 2: Table S2. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: List of differentially expressed genes obtained from the RNA-Seq analysis of altered versus wild-type samples. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.5765664
title: Additional file 2: Table S2. of Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

description: Details of papaya tissues used for RNA-Seq library construction. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5765664.v1
title: Additional file 2: Table S2. of Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

description: Details of papaya tissues used for RNA-Seq library construction. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5765673
title: Additional file 3: Table S3. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: List of differentially expressed genes obtained from the RNA-Seq analysis of wild-type versus normal samples. (XLS 49Â kb)
DOI: 10.6084/m9.figshare.5765673.v1
title: Additional file 3: Table S3. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: List of differentially expressed genes obtained from the RNA-Seq analysis of wild-type versus normal samples. (XLS 49Â kb)
DOI: 10.6084/m9.figshare.5765679
title: Additional file 3: Table S3. of Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

description: Primers used for quantitative real-time PCR. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.5765679.v1
title: Additional file 3: Table S3. of Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

description: Primers used for quantitative real-time PCR. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.5765682
title: Additional file 4: Table S4. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: List of NRF2-AREs identified in the -5Â kb promoter regions of RAB6B, UCHL1 and TRIM16L genes. (XLS 38Â kb)
DOI: 10.6084/m9.figshare.5765682.v1
title: Additional file 4: Table S4. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: List of NRF2-AREs identified in the -5Â kb promoter regions of RAB6B, UCHL1 and TRIM16L genes. (XLS 38Â kb)
DOI: 10.6084/m9.figshare.5765691
title: Additional file 4: Table S4. of Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

description: List of species used for construction of the phylogenetic tree of subfamily III PLCP genes. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5765691.v1
title: Additional file 4: Table S4. of Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

description: List of species used for construction of the phylogenetic tree of subfamily III PLCP genes. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5765697
title: Additional file 5: Table S5. of Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

description: Multivariate analysis of 17-gene signature in 4 independent cohorts (XLS 25Â kb)