cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3716188_d1
title: Additional file 1: of Modern contraceptive utilization and associated factors among married pastoralist women in Bale eco-region, Bale Zone, South East Ethiopia

description: The SPSS datasets used or analysed during the current study. (SAV 175 kb)
DOI: 10.6084/m9.figshare.c.3716182_d3
title: Additional file 3 of Bicodon bias can determine the role of synonymous SNPs in human diseases

description: Table S1. Genetic diseases and sSNPs. The first column corresponds to the disease or genetic trait. The second and third columns correspond to the associated gene and SNP (where both can be more than one), respectively. Each SNP affects only one codon (third SNP row), but two bicodons, when the mutation is in the P-site (first SNP row), and when the mutation is in the A-site (second SNP row). Fourth, fifth, sixth and seventh columns, refer to the starting bicodon, list the bicodon sequence, the p-value, the residual score ( χ 2 = χ L 2 + χ H 2 $\chi ^{2}=\chi _{L}^{2}+ \chi _{H}^{2}$ ) and π value, respectively. The following four columns, refer to the resulting bicodon, list the bicodon sequence, the log-transformed p-value, the residual score and π value, respectively. The following three columns enumerate the relative p-value, the pause propensity variation, Δ π, and the corresponding Z-score due to the synonymous bicodon variant. The last two columns contain a summarized result of our analysis for each disease and the related references. (XLS 41 kb)
DOI: 10.6084/m9.figshare.c.3716182_d4.v1
title: Additional file 4 of Bicodon bias can determine the role of synonymous SNPs in human diseases

description: Table S2. Silent sSNPs. First and second columns correspond to benign sSNPs and their associated genes respectively. Each SNP affects only one codon (third SNP row), but two bicodons, when the mutation is in the P-site (first SNP row), and when the mutation is in the A-site (second SNP row), but only one codon (third SNP row). Third, fourth, fifth and sixth columns, refer to the starting bicodon, list the bicodon sequence, the p-value, the total residual score ( χ 2 = χ L 2 + χ H 2 $\chi ^{2}=\chi _{L}^{2}+ \chi _{H}^{2}$ ) and π value, respectively. The following four columns, refer to the resulting bicodon, list the bicodon sequence, the log-transformed p-value, the χ 2 score value and π value, respectively. The last three columns enumerate the relative p-value, the pause propensity variation, Δ π, and the corresponding Z-score due to the synonymous bicodon variant. (XLS 66 kb)
DOI: 10.6084/m9.figshare.c.3716182_d4
title: Additional file 4 of Bicodon bias can determine the role of synonymous SNPs in human diseases

description: Table S2. Silent sSNPs. First and second columns correspond to benign sSNPs and their associated genes respectively. Each SNP affects only one codon (third SNP row), but two bicodons, when the mutation is in the P-site (first SNP row), and when the mutation is in the A-site (second SNP row), but only one codon (third SNP row). Third, fourth, fifth and sixth columns, refer to the starting bicodon, list the bicodon sequence, the p-value, the total residual score ( χ 2 = χ L 2 + χ H 2 $\chi ^{2}=\chi _{L}^{2}+ \chi _{H}^{2}$ ) and π value, respectively. The following four columns, refer to the resulting bicodon, list the bicodon sequence, the log-transformed p-value, the χ 2 score value and π value, respectively. The last three columns enumerate the relative p-value, the pause propensity variation, Δ π, and the corresponding Z-score due to the synonymous bicodon variant. (XLS 66 kb)
DOI: 10.15468/dl.ax4vwy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Careproctus colletti Gilbert, 1896",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038380-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3717076_d1.v1
title: Additional file 1: Table S1. of Exaggerated CpH methylation in the autism-affected brain

description: Functional genomic region information. TableS2. Sample information. Table S3. Differentially methylated CpG sites (p
DOI: 10.6084/m9.figshare.c.3717091_d1.v1
title: Additional file 1: of Effect of modified graded recession and anteriorization on unilateral superior oblique palsy: a retrospective study

description: SOP Dataset (2006â  2015). SOP data of the 26 patients examined at our institution from 2006 to 2015. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3717076_d1
title: Additional file 1: Table S1. of Exaggerated CpH methylation in the autism-affected brain

description: Functional genomic region information. TableS2. Sample information. Table S3. Differentially methylated CpG sites (p
DOI: 10.6084/m9.figshare.c.3717064_d2.v1
title: MOESM2 of MicroRNA expression profiles in human CD3+ T cells following stimulation with anti-human CD3 antibodies

description: Additional file 2. RAR compressed file containg miRNA and qPCR raw data in GEO format.
DOI: 10.6084/m9.figshare.c.3717091_d1
title: Additional file 1: of Effect of modified graded recession and anteriorization on unilateral superior oblique palsy: a retrospective study

description: SOP Dataset (2006â  2015). SOP data of the 26 patients examined at our institution from 2006 to 2015. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3717064_d2
title: MOESM2 of MicroRNA expression profiles in human CD3+ T cells following stimulation with anti-human CD3 antibodies

description: Additional file 2. RAR compressed file containg miRNA and qPCR raw data in GEO format.
DOI: 10.6084/m9.figshare.c.3717109_d3.v1
title: Additional file 3: Table S1. of Functional analysis of fatty acid binding protein 7 and its effect on fatty acid of renal cell carcinoma cell lines

description: Fatty acid concentrations of TUHR14TKB transfectants. The concentrations of fatty acids accumulated by TUHR14TKB cells transfected with vectors expressing FABP7 or lacZ were assayed in four independent cultures. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.c.3717109_d3
title: Additional file 3: Table S1. of Functional analysis of fatty acid binding protein 7 and its effect on fatty acid of renal cell carcinoma cell lines

description: Fatty acid concentrations of TUHR14TKB transfectants. The concentrations of fatty acids accumulated by TUHR14TKB cells transfected with vectors expressing FABP7 or lacZ were assayed in four independent cultures. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.c.3717133_d1.v1
title: Additional file 1: of Glatiramer acetate treatment persistence - but not adherence - in multiple sclerosis patients is predicted by health-related quality of life and self-efficacy: a prospective web-based patient-centred study (CAIR study)

description: Data on adherence, persistence, self-efficacy, HRQoL, gender and disease duration. (XLSX 25 kb)
DOI: 10.15468/dl.82e23q
title: Occurrence Download

description: A dataset containing 353 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bombus bicoloratus Smith, 1879"
 ]
}

 The dataset includes 353 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038381-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3717160_d2.v1
title: Additional file 2: of Production of BP178, a derivative of the synthetic antibacterial peptide BP100, in the rice seed endosperm

description: Antibacterial, hemolytic and phytotoxic activity of antimicrobial peptides of interest in this study. (XLSX 12 kb)
DOI: 10.15468/dl.pxgvgg
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Careproctus cypselurus (Jordan & Gilbert, 1898)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038382-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3717160_d2
title: Additional file 2: of Production of BP178, a derivative of the synthetic antibacterial peptide BP100, in the rice seed endosperm

description: Antibacterial, hemolytic and phytotoxic activity of antimicrobial peptides of interest in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3717166_d2.v1
title: Additional file 2: Table S2. of Surveillance of avian influenza viruses in South Korea between 2012 and 2014

description: HA sequence information of H5 viruses for phylogenetic analysis. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3717160_d6.v1
title: Additional file 6: of Production of BP178, a derivative of the synthetic antibacterial peptide BP100, in the rice seed endosperm

description: Oligonucleotides used to amplify the rice seed promoter and its signal peptide coding region, the BP178 gene and the nopaline synthase terminator. (XLS 37 kb)
DOI: 10.6084/m9.figshare.c.3717166_d1.v1
title: Additional file 1: Table S1. of Surveillance of avian influenza viruses in South Korea between 2012 and 2014

description: National active surveillace plan for avian influenza in 2014 in South Korea. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3717160_d7.v1
title: Additional file 7: of Production of BP178, a derivative of the synthetic antibacterial peptide BP100, in the rice seed endosperm

description: Oligonucleotides used for quantitative polymerase chain reaction. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3717166_d1
title: Additional file 1: Table S1. of Surveillance of avian influenza viruses in South Korea between 2012 and 2014

description: National active surveillace plan for avian influenza in 2014 in South Korea. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3717160_d6
title: Additional file 6: of Production of BP178, a derivative of the synthetic antibacterial peptide BP100, in the rice seed endosperm

description: Oligonucleotides used to amplify the rice seed promoter and its signal peptide coding region, the BP178 gene and the nopaline synthase terminator. (XLS 37 kb)
DOI: 10.6084/m9.figshare.c.3717166_d2
title: Additional file 2: Table S2. of Surveillance of avian influenza viruses in South Korea between 2012 and 2014

description: HA sequence information of H5 viruses for phylogenetic analysis. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3717160_d7
title: Additional file 7: of Production of BP178, a derivative of the synthetic antibacterial peptide BP100, in the rice seed endosperm

description: Oligonucleotides used for quantitative polymerase chain reaction. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3717160_d8.v1
title: Additional file 8: of Production of BP178, a derivative of the synthetic antibacterial peptide BP100, in the rice seed endosperm

description: Selected transitions and parameters used in MS analysis of the BP178 peptide produced in rice seeds. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3717175_d4
title: Additional file 4: File S3. of MicroRNA categorization using sequence motifs and k-mers

description: PhyloXML formatted phylogenetic tree: This file can be directly uploaded to Itol or other phylogenetic tree viewers for further analysis. (TXT 7Â kb)
DOI: 10.6084/m9.figshare.c.3718198_d1.v1
title: Additional file 10 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S8. Validating coexpression patterns in 5,210 datasets. The descriptions and names of 5,210 datasets used to perform coexpression analysis are available as part of the online supplementary materials. SEEK sorted the datasets based on their coexpression score computed using the 113 genes from our extracellular matrix module. The AML-related datasets, highlighted in yellow, are frequent at the top of the list. The details of coexpression score and p-value computation are defined in the corresponding publication [44]. (XLS 1044 kb)
DOI: 10.6084/m9.figshare.c.3718198_d1
title: Additional file 10 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S8. Validating coexpression patterns in 5,210 datasets. The descriptions and names of 5,210 datasets used to perform coexpression analysis are available as part of the online supplementary materials. SEEK sorted the datasets based on their coexpression score computed using the 113 genes from our extracellular matrix module. The AML-related datasets, highlighted in yellow, are frequent at the top of the list. The details of coexpression score and p-value computation are defined in the corresponding publication [44]. (XLS 1044 kb)
DOI: 10.6084/m9.figshare.c.3718210_d1.v1
title: MOESM1 of Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae

description: Additional file 1: Table S1. Primer sequences, restriction sites, and DNA templates used for plasmid constructions in this study are summarized.
DOI: 10.6084/m9.figshare.c.3718210_d1
title: MOESM1 of Enzymatic improvement of mitochondrial thiol oxidase Erv1 for oxidized glutathione fermentation by Saccharomyces cerevisiae

description: Additional file 1: Table S1. Primer sequences, restriction sites, and DNA templates used for plasmid constructions in this study are summarized.
DOI: 10.6084/m9.figshare.c.3718198_d2.v1
title: Additional file 11 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S6. The cell cycle and translational control modules. Two modules with 319 and 193 genes were automatically selected by breast cancer survival analysis. In each sheet, gene symbols, Entrez IDs, and weights in the corresponding modules are reported. Genes are sorted based on their weights. (XLS 55 kb)
DOI: 10.6084/m9.figshare.c.3718198_d5.v1
title: Additional file 2 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S2. Overrepresented pathways. The canonical pathways that are overrepresented in the modules are available as part of the online supplementary materials. Each sheet in the excel file corresponds to a module. The statistics for each pathway (gene set) is reported on one row, in particular, the p-value of a hypergeometric test with the null hypothesis that the genes from the pathway were observed in the module by chance. The other columns include the name of the pathway (Set Name), the number of genes observed in the module (In Module), the number of the genes from the pathway that are present in our pool of 9,166 genes (Set Size), percentage of those genes that are in the module (% In Module), the name of the collection in MSIGDB [83] (Source), and a link to more information on the pathway (Description). There was no statistically significant pathway with p-value less than 10â  4 for the modules that are not included. (XLS 131 kb)
DOI: 10.6084/m9.figshare.c.3718225_d2.v1
title: Additional file 2: of Protein complex-based analysis is resistant to the obfuscating consequences of batch effects --- a case study in clinical proteomics

description: Simulated data D2.2H. (ZIP 3730Â kb)
DOI: 10.6084/m9.figshare.c.3718225_d2
title: Additional file 2: of Protein complex-based analysis is resistant to the obfuscating consequences of batch effects --- a case study in clinical proteomics

description: Simulated data D2.2H. (ZIP 3730Â kb)
DOI: 10.6084/m9.figshare.c.3718198_d5
title: Additional file 2 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S2. Overrepresented pathways. The canonical pathways that are overrepresented in the modules are available as part of the online supplementary materials. Each sheet in the excel file corresponds to a module. The statistics for each pathway (gene set) is reported on one row, in particular, the p-value of a hypergeometric test with the null hypothesis that the genes from the pathway were observed in the module by chance. The other columns include the name of the pathway (Set Name), the number of genes observed in the module (In Module), the number of the genes from the pathway that are present in our pool of 9,166 genes (Set Size), percentage of those genes that are in the module (% In Module), the name of the collection in MSIGDB [83] (Source), and a link to more information on the pathway (Description). There was no statistically significant pathway with p-value less than 10â  4 for the modules that are not included. (XLS 131 kb)
DOI: 10.15468/dl.c7ujc5
title: Occurrence Download

description: A dataset containing 313 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Careproctus dubius Zugmayer, 1911",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 313 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038383-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3718198_d6.v1
title: Additional file 3 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S1. Module assignments. The module assignments for all of the 9,166 genes are available as part of the online supplementary materials. The columns of the table include:   • Symbol: The gene name.   • ENTREZ ID: The gene ID in the Global Query Cross-Database Search System.   • Probe representative: The representative probe mapped to this gene.   • Adjusted p-value: For the null hypothesis that expression is similar in AML and MDS (Supplementary Note 2).   • Module ID: The assigned module.   • IMC: Intramodular connectivity.   • EMC: Extramodular connectivity.   • Rank: The rank of the gene in the module based on its intramodular connectivity.   • # of references The number of studies that reported the gene being relevant to AML according to Miller et al,. survey [81]. Intramodular and extramodular connectivities were computed by intramodularConnectivity() function from WGNCA package. They measure the overall correlation of the gene with other genes within and outside the module, respectively. The genes with the most connectivity in a module are considered as the “hubs” of that module [82]. See WGNCA manual for more information. (XLS 1618 kb)
DOI: 10.6084/m9.figshare.c.3718198_d6
title: Additional file 3 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S1. Module assignments. The module assignments for all of the 9,166 genes are available as part of the online supplementary materials. The columns of the table include:   • Symbol: The gene name.   • ENTREZ ID: The gene ID in the Global Query Cross-Database Search System.   • Probe representative: The representative probe mapped to this gene.   • Adjusted p-value: For the null hypothesis that expression is similar in AML and MDS (Supplementary Note 2).   • Module ID: The assigned module.   • IMC: Intramodular connectivity.   • EMC: Extramodular connectivity.   • Rank: The rank of the gene in the module based on its intramodular connectivity.   • # of references The number of studies that reported the gene being relevant to AML according to Miller et al,. survey [81]. Intramodular and extramodular connectivities were computed by intramodularConnectivity() function from WGNCA package. They measure the overall correlation of the gene with other genes within and outside the module, respectively. The genes with the most connectivity in a module are considered as the “hubs” of that module [82]. See WGNCA manual for more information. (XLS 1618 kb)
DOI: 10.6084/m9.figshare.c.3718228_d2.v1
title: Additional file 2: of SNP by SNP by environment interaction network of alcoholism

description: Table S1. This file provides the list of SNPs with CMH test p-value &lt; 0.0005. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.c.3718246_d4.v1
title: Additional file 4: of Visualization of consensus genome structure without using a reference genome

description: Table S2. 73 species Helicobacter pylori genome 469 information. (XLSX 42.5 kb)
DOI: 10.6084/m9.figshare.c.3718198_d10
title: Additional file 7 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S7. The extracellular matrix module. For each gene in the extracellular matrix module, the cellular component ontology (GO-CC) is available as part of the online supplementary materials. The genes are ordered according to their weight (also known as â  membershipâ   [85]) in the module eigengene, e.g., the first gene has the highest contribution to the eigengene. See the description of Additional file 2: Table S1 for the definition of other columns. (XLS 37 kb)
DOI: 10.6084/m9.figshare.c.3718198_d11.v1
title: Additional file 8 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S9. Biological processes. We used PANTHER (Version 10) [41] to identify the GO biological processes that are enriched in the 113 genes in our extracellular module. The columns of the resulting table include the name of GO biological process, the number of genes in the corresponding category (Homo sapiens), the number of overlapping genes, the expected overlap, the fold enrichment, and the Bonferroni-adjusted p-value. (XLS 20 kb)
DOI: 10.6084/m9.figshare.c.3718198_d11
title: Additional file 8 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

description: Table S9. Biological processes. We used PANTHER (Version 10) [41] to identify the GO biological processes that are enriched in the 113 genes in our extracellular module. The columns of the resulting table include the name of GO biological process, the number of genes in the corresponding category (Homo sapiens), the number of overlapping genes, the expected overlap, the fold enrichment, and the Bonferroni-adjusted p-value. (XLS 20 kb)
DOI: 10.6084/m9.figshare.c.3718246_d4
title: Additional file 4: of Visualization of consensus genome structure without using a reference genome

description: Table S2. 73 species Helicobacter pylori genome 469 information. (XLSX 42.5 kb)