cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6600926.v1
title: Additional file 1: of Clinical trials involving positron emission tomography and prostate cancer: an analysis of the ClinicalTrials.gov database

description: Annotated Dataset. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6600908
title: Additional file 2 of DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

description: Parameter values. Reaction rates that were obtained by our automated database search for different metabolic systems. (XLSX 510 kb)
DOI: 10.6084/m9.figshare.6600908.v1
title: Additional file 2 of DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

description: Parameter values. Reaction rates that were obtained by our automated database search for different metabolic systems. (XLSX 510 kb)
DOI: 10.6084/m9.figshare.6600890
title: Additional file 3: of Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

description: List of selected genes validated by qPCR. The expression of 27 targeted genes and 2 references genes was studied using the SYBR green technology, while the expression of 7 targeted genes was studied using the TaqMan probe technology. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6600890.v1
title: Additional file 3: of Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

description: List of selected genes validated by qPCR. The expression of 27 targeted genes and 2 references genes was studied using the SYBR green technology, while the expression of 7 targeted genes was studied using the TaqMan probe technology. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6600878
title: Additional file 2: of Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

description: Metabolic pathways associated with the 207 differentially expressed genes. A KEGG analysis performed using Blast2GO identified 36 metabolic pathways. For each metabolic pathway, the number of genes either up- or down-regulated, as well as the corresponding number of encoded enzymes were determined. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6600878.v1
title: Additional file 2: of Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

description: Metabolic pathways associated with the 207 differentially expressed genes. A KEGG analysis performed using Blast2GO identified 36 metabolic pathways. For each metabolic pathway, the number of genes either up- or down-regulated, as well as the corresponding number of encoded enzymes were determined. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6600860
title: Additional file 1: of Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

description: Total for each sample of sequenced and mapped reads and the percentage of coverage quality. C for P. infestans without confrontationâ =â control, B for P. infestans with LBUM223, M for P. infestans with the mutant LBUM223phzC- and N for P. infestans with synthetic PCA. 1 was used for day 6, 2 for day 9, 3 for day 12. X, Y, Z are for the 3 replicates. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6600860.v1
title: Additional file 1: of Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

description: Total for each sample of sequenced and mapped reads and the percentage of coverage quality. C for P. infestans without confrontationâ =â control, B for P. infestans with LBUM223, M for P. infestans with the mutant LBUM223phzC- and N for P. infestans with synthetic PCA. 1 was used for day 6, 2 for day 9, 3 for day 12. X, Y, Z are for the 3 replicates. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6600824
title: Additional file 9: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of human specific motifs for motif lengths 6–10 from core, proximal, distal promoters and introns as compared to Denisovan. Statistically significant motifs of lengths 6–10 from core, proximal, and distal promoters as well as introns unique to modern humans are listed (and not found in Denisovan). These motifs were found in the corresponding genomic subregion in modern human, and the number of such human-unique motifs were listed for each gene variant. From these lists the top 100 genes were selected which had the highest number of human-unique motifs in their promoter/intron. Listed in tab “top genes (based on promoters)” are genes which were found in at least three top 100 lists. This was done separately for core, proximal, and distal promoters, and also for introns in the tab “top genes (based on introns)”. Fifty gene variants (38 genes) were found which both in the proximal and distal promoter sets appeared. One hundred four genes (their NP id, GeneCard name and annotation) were found which were listed in at least 3 top 100 gene lists whose introns contained statistically significant human-unique intron motifs. (XLSX 5181 kb)
DOI: 10.6084/m9.figshare.6600824.v1
title: Additional file 9: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of human specific motifs for motif lengths 6–10 from core, proximal, distal promoters and introns as compared to Denisovan. Statistically significant motifs of lengths 6–10 from core, proximal, and distal promoters as well as introns unique to modern humans are listed (and not found in Denisovan). These motifs were found in the corresponding genomic subregion in modern human, and the number of such human-unique motifs were listed for each gene variant. From these lists the top 100 genes were selected which had the highest number of human-unique motifs in their promoter/intron. Listed in tab “top genes (based on promoters)” are genes which were found in at least three top 100 lists. This was done separately for core, proximal, and distal promoters, and also for introns in the tab “top genes (based on introns)”. Fifty gene variants (38 genes) were found which both in the proximal and distal promoter sets appeared. One hundred four genes (their NP id, GeneCard name and annotation) were found which were listed in at least 3 top 100 gene lists whose introns contained statistically significant human-unique intron motifs. (XLSX 5181 kb)
DOI: 10.6084/m9.figshare.6600809
title: Additional file 8: of Motifome comparison between modern human, Neanderthal and Denisovan

description: Intergenic motifs in nCONDELs and dCONDELs. List of statistically significant motifs in nCONDELS and dCONDELs in Neanderthal and Denisovan. These are statistically significant whole genome motifs which were found in regions of the Neanderthal and Denisovan genomes which are missing from the genome of modern human. (XLSX 191Â kb)
DOI: 10.6084/m9.figshare.6600809.v1
title: Additional file 8: of Motifome comparison between modern human, Neanderthal and Denisovan

description: Intergenic motifs in nCONDELs and dCONDELs. List of statistically significant motifs in nCONDELS and dCONDELs in Neanderthal and Denisovan. These are statistically significant whole genome motifs which were found in regions of the Neanderthal and Denisovan genomes which are missing from the genome of modern human. (XLSX 191Â kb)
DOI: 10.6084/m9.figshare.6600791
title: Additional file 7: of Motifome comparison between modern human, Neanderthal and Denisovan

description: Results of GO analysis. A list of 82 statistically significant intron motifs from 20 intron HARs unique to human is provided. The list of 135 Uniprot IDs is listed as well as the 261 human genes that they correspond to. The results of the GO analysis for biological processes and cellular components are listed. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.6600791.v1
title: Additional file 7: of Motifome comparison between modern human, Neanderthal and Denisovan

description: Results of GO analysis. A list of 82 statistically significant intron motifs from 20 intron HARs unique to human is provided. The list of 135 Uniprot IDs is listed as well as the 261 human genes that they correspond to. The results of the GO analysis for biological processes and cellular components are listed. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.6600785
title: Additional file 3: of An efficient and improved method for virus-induced gene silencing in sorghum

description: Table S2. List of primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6600785.v1
title: Additional file 3: of An efficient and improved method for virus-induced gene silencing in sorghum

description: Table S2. List of primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6600776
title: Additional file 2: of An efficient and improved method for virus-induced gene silencing in sorghum

description: Table S1. List of sorghum genotypes/varieties showing BMV infection. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6600776.v1
title: Additional file 2: of An efficient and improved method for virus-induced gene silencing in sorghum

description: Table S1. List of sorghum genotypes/varieties showing BMV infection. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6600770
title: Additional file 6: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs in 49 HAR regions studied by Pollard et al., 2006 [23]. List of statistically significant genomic motifs found in 26 HARs in modern human, Neanderthal and Denisovan and in 20 intronic HARs in modern human, Neanderthal and Denisovan, as well as a list of the 82 intronic motifs unique to modern humans. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.6600770.v1
title: Additional file 6: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs in 49 HAR regions studied by Pollard et al., 2006 [23]. List of statistically significant genomic motifs found in 26 HARs in modern human, Neanderthal and Denisovan and in 20 intronic HARs in modern human, Neanderthal and Denisovan, as well as a list of the 82 intronic motifs unique to modern humans. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.6600761
title: Additional file 1: of MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-ÎşB

description: Supplemental Methods: Details an patient data, AAV vector production, shRNA vector design. Table S1. Primers used for qRT-PCR. Figure S1. Transduction of T-ALL with anti-MAP3K7 shRNA leads to an efficient knockdown. Figure S2. Plasmid map of pscAAV-CMV-GFP-U6-sh construct with anti-MAP3K7 shRNA. Figure S3. Transduction of T-ALL with anti-MAP3K7 shRNA induces apoptosis. (ZIP 3146 kb)
DOI: 10.6084/m9.figshare.6600761.v1
title: Additional file 1: of MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-ÎşB

description: Supplemental Methods: Details an patient data, AAV vector production, shRNA vector design. Table S1. Primers used for qRT-PCR. Figure S1. Transduction of T-ALL with anti-MAP3K7 shRNA leads to an efficient knockdown. Figure S2. Plasmid map of pscAAV-CMV-GFP-U6-sh construct with anti-MAP3K7 shRNA. Figure S3. Transduction of T-ALL with anti-MAP3K7 shRNA induces apoptosis. (ZIP 3146 kb)
DOI: 10.6084/m9.figshare.6600728
title: Additional file 2: of Age, sex, and the changing disability burden of compensated work-related musculoskeletal disorders in Canada and Australia

description: Supplementary results tables, including the annual number of time-loss claims by MSDs/Fractures/MSDs of the back by sex and age group, 2004â 13, Canada and Australia; annual number of time-loss years by MSDs by sex and age group, 2004â 13, Canada and Australia. (XLSX 111Â kb)
DOI: 10.6084/m9.figshare.6600728.v1
title: Additional file 2: of Age, sex, and the changing disability burden of compensated work-related musculoskeletal disorders in Canada and Australia

description: Supplementary results tables, including the annual number of time-loss claims by MSDs/Fractures/MSDs of the back by sex and age group, 2004â 13, Canada and Australia; annual number of time-loss years by MSDs by sex and age group, 2004â 13, Canada and Australia. (XLSX 111Â kb)
DOI: 10.6084/m9.figshare.6600710
title: Additional file 1: of Age, sex, and the changing disability burden of compensated work-related musculoskeletal disorders in Canada and Australia

description: Injury codes and descriptions used to identify similar injury claims in the Canadian and Australian workersâ compensation data, including Canadian Standards Association (CSA) Z785 nature of injury and part of body codes and Australian Type of Occurrence Classification System (TOOCS) nature of injury and disease, and bodily location codes. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.6600710.v1
title: Additional file 1: of Age, sex, and the changing disability burden of compensated work-related musculoskeletal disorders in Canada and Australia

description: Injury codes and descriptions used to identify similar injury claims in the Canadian and Australian workersâ compensation data, including Canadian Standards Association (CSA) Z785 nature of injury and part of body codes and Australian Type of Occurrence Classification System (TOOCS) nature of injury and disease, and bodily location codes. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.6600683
title: Additional file 3: of White-nose syndrome detected in bats over an extensive area of Russia

description: Table S2. Datasets used and analyzed during the current study and not included in Tables 1, 2 and 3. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6600683.v1
title: Additional file 3: of White-nose syndrome detected in bats over an extensive area of Russia

description: Table S2. Datasets used and analyzed during the current study and not included in Tables 1, 2 and 3. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6600671
title: Additional file 4: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs for mouse. The motif sequence, number of observed and expected occurrences as well as motif score are listed for motif lengths 6–10 in the whole genome, core, proximal, and distal promoters, as well as all introns, 5′ and 3’ UTRS, as well as average score and standard deviation for all motif lengths and genomic sub-regions. (XLSX 247147 kb)
DOI: 10.6084/m9.figshare.6600671.v1
title: Additional file 4: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs for mouse. The motif sequence, number of observed and expected occurrences as well as motif score are listed for motif lengths 6–10 in the whole genome, core, proximal, and distal promoters, as well as all introns, 5′ and 3’ UTRS, as well as average score and standard deviation for all motif lengths and genomic sub-regions. (XLSX 247147 kb)
DOI: 10.6084/m9.figshare.6600668
title: Additional file 2: of White-nose syndrome detected in bats over an extensive area of Russia

description: Table S1. Bat species from Palearctic and Nearctic regions with confirmed WNS or Pseudogymnoascus destructans infection. Summarized from [10, 16, 19, 21, 40, 47]. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6600668.v1
title: Additional file 2: of White-nose syndrome detected in bats over an extensive area of Russia

description: Table S1. Bat species from Palearctic and Nearctic regions with confirmed WNS or Pseudogymnoascus destructans infection. Summarized from [10, 16, 19, 21, 40, 47]. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6600617
title: Additional file 3: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs for Denisovan. The motif sequence, number of observed and expected occurrences as well as motif score are listed for motif lengths 6â 10 in the whole genome, core, proximal, and distal promoters, as well as all introns, as well as average score and standard deviation for all motif lengths and genomic sub-regions. (XLSX 191122Â kb)
DOI: 10.6084/m9.figshare.6600617.v1
title: Additional file 3: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs for Denisovan. The motif sequence, number of observed and expected occurrences as well as motif score are listed for motif lengths 6â 10 in the whole genome, core, proximal, and distal promoters, as well as all introns, as well as average score and standard deviation for all motif lengths and genomic sub-regions. (XLSX 191122Â kb)
DOI: 10.6084/m9.figshare.6600593
title: Additional file 2: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs for Neanderthal. The motif sequence, number of observed and expected occurrences as well as motif score are listed for motif lengths 6â 10 in the whole genome, as well as average score and standard deviation for all motif lengths. (XLSX 43083Â kb)
DOI: 10.6084/m9.figshare.6600593.v1
title: Additional file 2: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs for Neanderthal. The motif sequence, number of observed and expected occurrences as well as motif score are listed for motif lengths 6â 10 in the whole genome, as well as average score and standard deviation for all motif lengths. (XLSX 43083Â kb)
DOI: 10.6084/m9.figshare.6600542
title: Additional file 1 of Geometric characterisation of disease modules

description: Supplementary files. (ZIP 3154 kb)
DOI: 10.6084/m9.figshare.6600542.v1
title: Additional file 1 of Geometric characterisation of disease modules

description: Supplementary files. (ZIP 3154 kb)
DOI: 10.6084/m9.figshare.6600536
title: Additional file 4: of An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

description: UCSC track for eCpGs from MESA. (BED 8181 kb)
DOI: 10.6084/m9.figshare.6600536.v1
title: Additional file 4: of An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

description: UCSC track for eCpGs from MESA. (BED 8181 kb)
DOI: 10.6084/m9.figshare.6600524
title: Additional file 1: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs for modern human. The motif sequence, number of observed and expected occurrences as well as motif score are listed for motif lengths 6–10 in the whole genome, core, proximal, and distal promoters, as well as all introns, 5′ and 3’ UTRS, as well as average score and standard deviation for all motif lengths and genomic sub-regions. (XLSX 219664 kb)
DOI: 10.6084/m9.figshare.6600524.v1
title: Additional file 1: of Motifome comparison between modern human, Neanderthal and Denisovan

description: List of statistically significant motifs for modern human. The motif sequence, number of observed and expected occurrences as well as motif score are listed for motif lengths 6–10 in the whole genome, core, proximal, and distal promoters, as well as all introns, 5′ and 3’ UTRS, as well as average score and standard deviation for all motif lengths and genomic sub-regions. (XLSX 219664 kb)
DOI: 10.6084/m9.figshare.6600518
title: Additional file 3: of An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

description: UCSC track for eCpGs from GTP. (BED 2584 kb)
DOI: 10.6084/m9.figshare.6600518.v1
title: Additional file 3: of An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

description: UCSC track for eCpGs from GTP. (BED 2584 kb)
DOI: 10.6084/m9.figshare.6600497
title: Additional file 2: of An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

description: eCpG-transcript pairs, plus additional information for MESA. (TXT 44022 kb)
DOI: 10.6084/m9.figshare.6600497.v1
title: Additional file 2: of An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

description: eCpG-transcript pairs, plus additional information for MESA. (TXT 44022 kb)
DOI: 10.6084/m9.figshare.6600488
title: Additional file 1: of An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

description: eCpG-transcript pairs, plus additional information for GTP. (TXT 9056 kb)
DOI: 10.6084/m9.figshare.6600488.v1
title: Additional file 1: of An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

description: eCpG-transcript pairs, plus additional information for GTP. (TXT 9056 kb)
DOI: 10.6084/m9.figshare.6600482
title: Additional file 4: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

description: Fasta file of TE sequences generated in the TE annotation, with basic description of each TE sequence. (TXT 892 kb)
DOI: 10.6084/m9.figshare.6600482.v1
title: Additional file 4: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

description: Fasta file of TE sequences generated in the TE annotation, with basic description of each TE sequence. (TXT 892 kb)
DOI: 10.6084/m9.figshare.6600464
title: Additional file 3: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

description: TE insertion density per megabase (estimated from PopoolationTE2 output) for each TE order and each species analysed here. (TXT 166 kb)
DOI: 10.6084/m9.figshare.6600464.v1
title: Additional file 3: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

description: TE insertion density per megabase (estimated from PopoolationTE2 output) for each TE order and each species analysed here. (TXT 166 kb)
DOI: 10.6084/m9.figshare.6600455
title: Additional file 2: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

description: Table S1. D. pseudoobscura species group lines used in this study. Table S2. TEs found in D. obscura group. Sorted by if they are previously discovered or novel, then by Order and super family. Transmission states if the TE family is found to transfer between species. Table S3. Diagonal table showing the total number of TE families found in each species for comparison. In brackets, the number of novel TE families found shared between species. Table S4. Comparisons of dN/dS between TEs and nuclear genes. The dS values presented here are compared to the dS values of nuclear genes between the given species calculated previously. We considered a transfer event between two species to have occurred if the TE dS value is less than the 2.5th percentile for nuclear genes. For instances where no dS for nuclear comparisons are available, we used the dS between D. pseudoobscura and the species of interest. Table S5. Number of unique and shared polymorphic sites for each species comparison, for each TE family, used in the boxplots in Fig. 2e. (XLSX 153 kb)