cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3635801_d1
title: Additional file 1 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: PC-TraFF analysis with different distance constrains. Significant pairs found by PC-TraFF using different distance constrains in the sequences of human RefSeq genes. (XLS 13 kb)
DOI: 10.6084/m9.figshare.c.3635801_d2
title: Additional file 2 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Synthetic sequences. Synthetic sequences with USF-IRF1 binding sites. (FASTA 55 kb)
DOI: 10.6084/m9.figshare.c.3635801_d3
title: Additional file 7 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Breast cancer analysis in the context of miRNA genes. PC-TraFF significant pairs identified in the promoter sequences of breast cancer-associated miRNA genes. (XLS 13 kb)
DOI: 10.6084/m9.figshare.c.3635801_d4
title: Additional file 5 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Genome-wide analysis in the context of miRNA genes. PC-TraFF significant pairs identified in the genome-wide promoter sequences of miRNA genes. (XLS 3 kb)
DOI: 10.6084/m9.figshare.c.3635801_d5
title: Additional file 3 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Genome-wide analysis in the context of RefSeq genes. PC-TraFF significant pairs identified in the genome-wide promoter sequences of RefSeq genes. (XLS 4 kb)
DOI: 10.6084/m9.figshare.c.3635801_d6
title: Additional file 6 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Breast cancer analysis in the context of RefSeq genes. PC-TraFF significant pairs identified in the promoter sequences of breast cancer-associated RefSeq genes. (XLS 12 kb)
DOI: 10.6084/m9.figshare.c.3636047_d20
title: Additional file 19: Table S5. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Ribosome density calculations and comparisons. Sheet 1. Ribosome densities in procyclic forms. The average number of ribosomes per ORF was calculated as follows. First, we needed to correct the ribosome profiling results for the gene copy number in the genome assembly, since during the initial alignments, the reads had been spread out among all orthologues. Orthologue counts were taken from TritrypDB. Unexpected numbers were checked against our previous read alignment data [20], and in some cases manually. Read results for some gene families (such as amino acid transporters) are unreliable because related genes show different regulation. The orthologue counts used are in column D. All RPM were multiplied by the orthologue count (column H). Numbers of mRNAs per cell [16] were previously calculated assuming a total of 19,000 non-VSG mRNAs in bloodstream forms, and 43,000 non-EP-procyclin mRNAs/cell in procyclics [17]. There are about 275000 ribosomes per procyclic parasite and 125000 per bloodstream form [17]. The ribosome densities are calculated using these numbers. In practice, the densities are likely to be lower. About 5 % of ribosomes are likely to be on ORFs that were excluded from the analysis (Procyclin, VSG, ESAGs, and from repetitive elements). Approximately 70 % of all ribosomal RNA is in polysomes, 20 % is in monosomes and the rest is in subunits (our unpublished results); we do not know what proportion of the ribosomes in the monosomal fraction is engaged in translation. Sheet 2. Ribosome densities in bloodstream forms. Sheet 3. Ribosome densities and half-lives in procyclic forms, using only the “reliable” values that were chosen for modelling. Sheet 4. Ribosome densities and half-lives in bloodstream forms, using only the “reliable” values that were chosen for modelling. (XLSX 2688 kb)
DOI: 10.6084/m9.figshare.c.3636071_d1
title: Additional file 1: of Functional and regulatory profiling of energy metabolism in fission yeast

description: Supplementary tables. Table S1. Colony size ratios from nine genetic screens for respiratory mutants. Table S2. Results of RNA-seq analysis of transcriptomes of cells grown on glycerol versus glucose and selected groups of differentially expressed genes. Table S3. Relative expression data from microarray profiling after shift to respiratory medium and k-means gene clusters. Table S4. List of genes differentially expressed on YES + antimycin A relative to YES. Table S5. List of strains used in this study. (XLSX 1837 kb)
DOI: 10.6084/m9.figshare.c.3636077_d1
title: Additional file 11: Table S3. of Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

description: List of plasmid SNPs and indels observed in the Shigella strain used here that are different from the GenBank sequence of the Shigella flexneri 2a strain 301 virulence plasmid pCP301 (NC_004851). (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3636077_d4
title: Additional file 5: Table S4. of Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

description: Table listing tRNA genes and the number of insertions in each. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3636077_d6
title: Additional file 10: Table S2. of Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

description: List of chromosomal SNPs and indels observed in the Shigella strain used here that differ from the GenBank sequence NC004741. (TXT 4 kb)
DOI: 10.6084/m9.figshare.c.3636077_d12
title: Additional file 3: Table S1. of Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

description: Full table of gene characteristics and orthologue relationships used in the analyses. (TXT 411 kb)
DOI: 10.6084/m9.figshare.c.3636080_d1
title: Additional file 6: of Nilotinib (Tasignaâ ˘) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial

description: List of 106 pathways significantly downregulated in improvers post treatment (false discovery rate (FDR) &lt;5 %). The FDR is provided for each pathway. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3636080_d2
title: Additional file 4: of Nilotinib (Tasignaâ ˘) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial

description: Spearman correlation statistics (correlation coefficients and p values) for intrinsic subset assignment. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3636080_d4
title: Additional file 5: of Nilotinib (Tasignaâ ˘) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial

description: Detailed output for the 666 gene signature in improvers from Fig.Â  4b . For each gene in the improver gene signature, the following information is provided: where it is upregulated (baseline or post treatment), gene symbol, gene name, raw p value, false discovery rate (FDR)(BH), q value, fold change, baseline mean expression value and post-treatment mean expression value. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.c.3636167_d2
title: Additional file 1: of T-REx: Transcriptome analysis webserver for RNA-seq Expression data

description: Archive file containing all T-REx output files. (R 38 kb)
DOI: 10.6084/m9.figshare.c.3636167_d3
title: Additional file 6: of T-REx: Transcriptome analysis webserver for RNA-seq Expression data

description: T-REx R functions. (ZIP 179 kb)
DOI: 10.6084/m9.figshare.c.3636167_d4
title: Additional file 3: of T-REx: Transcriptome analysis webserver for RNA-seq Expression data

description: Figure S3; k-means clustering of differentially expressed genes in the mutants. (ZIP 31925 kb)
DOI: 10.6084/m9.figshare.c.3636167_d5
title: Additional file 4: of T-REx: Transcriptome analysis webserver for RNA-seq Expression data

description: Figures S4A and S4B; signal heatmaps of Class ‘Complex’ and Class ‘CodY’, respectively. (ZIP 1103 kb)
DOI: 10.6084/m9.figshare.c.3636167_d6
title: Additional file 2: of T-REx: Transcriptome analysis webserver for RNA-seq Expression data

description: Figures S2A - S2J; high resolution images of Figure 2 . (R 13 kb)
DOI: 10.6084/m9.figshare.c.3636197_d1
title: Additional file 1: of 
                     phoP, SPI1, SPI2 and aroA mutants of Salmonella Enteritidis induce a different immune response in chickens

description: List of primers used in real-time PCR. Primers used for the quantification of chicken gene expression by real time PCR are listed in this file.
DOI: 10.6084/m9.figshare.c.3636206_d1
title: Additional file 1: Appendix 1. of Geographical distribution of typhoid risk factors in low and middle income countries

description: Overdispersion. Appendix 2. Full specification of regression outputs. Appendix 3. TRF index (type 5) by sub-national boundary. Appendix 4. Final TRF index values by sub-national boundary. Appendix 5. TRF index in Bangladesh. (ZIP 1995Â kb)
DOI: 10.6084/m9.figshare.c.3636218_d1
title: Additional file 1: of The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression

description: Contains supplementary Tables S1-S21. Microsoft Excel Workbook containing twenty-one worksheets. Table S1: RNA-based sequence alignments against wheat and PST-130 reference genomes, using data from infection of wheat (Vuka) with PST 87/66. Table S2: Depth of coverage when RNA-seq data aligned to previously published PST-130 gene models. Table S3: Depth of coverage when RNA-seq data aligned to PST gene models generated herein. Table S4: Comparison of PST-130 gene models and those generated herein. Table S5: Wheat gene annotations. Table S6: 4,307 wheat triplets mined from Ensembl Plants Triticum aestivum portal. Table S7: 239 triplets identified as wheat core eukaryotic genes. Table S8: Mean correlation of expression vectors and mean relative difference comparing Cufflinks, RSEM, Salmon, and Kallisto. Table S9: Gene expression analysis of susceptible wheat cultivar Vuka infected with PST 87/66. Table S10: Gene expression analysis of a  resistant wheat line infected with PST 87/66. Table S11: Gene expression analysis of PST on Vuka . Table S12: KEGG pathway memberships displaying significant enrichment in each cluster for the 7 wheat clusters. Table S13: GO term annotations displaying significant enrichment for the 7 wheat clusters. Table S14: KEGG pathway memberships displaying significant enrichment for the 8 PST clusters. Table S15: GO term annotations displaying significant enrichment for the 8 PST clusters. Table S16: RNA-based sequence alignments against wheat and PST-130, using data from infection of wheat (Avocet line containing Yr5) with PST 87/66. Table S17: Transcripts per million (TPM) values for homologs of the defensome in a susceptible and resistant interaction with PST 87/66. Table S18: TPM values for PST vesicle trafficking components. Table S19: Summary of TPM values for PST vesicle trafficking components. Table S20: TPM values for host genes from a susceptible interaction with PST 87/66. Table S21: TPM values for host genes from a resistant interaction with PST 87/66. (XLSX 35.6 mb)
DOI: 10.6084/m9.figshare.c.3636218_d2
title: Additional file 2: of The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression

description: Annotation of updated PST gene models generated herein. (TSV 21048Â kb)
DOI: 10.15468/dl.feqt7c
title: Occurrence Download

description: A dataset containing 421 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-103.32621 20.62033,-103.29256 20.62033,-103.29256 20.63542,-103.32621 20.63542,-103.32621 20.62033))"
 ]
}

 The dataset includes 421 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033959-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t8t27r
title: Occurrence Download

description: A dataset listing the 22081 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 22081 records were derived from 382 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033949-241126133413365/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.3636335_d7
title: Additional file 1: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: Layout of the field experiment. Individual trees were planted in 2002 in a 3 × 3 m grid. Every fifth row in the field contained 5–19 trees (depending on the length of the rows) of the variety ‘Comum’, which is susceptible to WBD and serves as a natural and permanent inoculum source. Shade was provided using the traditional ‘cabruca’ system in which the trees are grown amongst the Atlantic Forest's native canopies. (XLS 97 kb)
DOI: 10.6084/m9.figshare.c.3636335_d12
title: Additional file 8: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: Phenotypic data of witches’ broom disease in MP01. (XLS 184 kb)
DOI: 10.6084/m9.figshare.c.3636341_d1
title: Additional file 1: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: Node support values and divergence time estimates for all phylogenetic analyses. Node numbers correspond to those on Fig.Â 1, 2, 3, and Additional file 2, 3, 4, 6, 7. Bold indicates an unsupported node. Asterix indicates the node is not represented in that topology. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3636335_d16
title: Additional file 3: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: Primer and probe sequences for candidate gene expression analysis. (XLS 35 kb)
DOI: 10.6084/m9.figshare.c.3636341_d5
title: Additional file 9: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of the 22 loci used in this study and primer information. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3636341_d6
title: Additional file 12: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of sequence length and loci coverage for samples in the mitochondrial dataset. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3636341_d8
title: Additional file 13: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of sequence characteristics per locus including length, variation, sample coverage and dataset. Site information and sample coverage represent Callicebus taxa only. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3636341_d7
title: Additional file 5: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: Divergence matrix for the cytochrome b locus for selected Callicebus species. Bold indicates distance valuesâ
DOI: 10.6084/m9.figshare.c.3636341_d10
title: Additional file 11: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of sequence length and loci coverage for samples in the combined and nuclear datasets. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3636341_d11
title: Additional file 10: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of the GenBank accession numbers for all sequences. In bold are the sequences newly generated for this study. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.c.3636341_d12
title: Additional file 8: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of genetic samples used in this study including ID, source and corresponding dataset. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.c.3636467_d2
title: Additional file 3: Table S3. of Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis

description: Marker genotypes of families of the mapping populations TC1966 Ă  NM92 and V2802 Ă  NM94 at bruchid resistance loci. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3636467_d4
title: Additional file 1: Table S1. of Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis

description: List of all SNPs that are homozygous in the mapping parents and map to chromosome 1â  11 of the mungbean reference sequence (Kang YJ, Kim SK, Kim MY, Lestari P, Kim KH, Ha BK, et al. Genome sequence of mungbean and insights into evolution within Vigna species. Nat Commun. 2014; doi: 10.1038/ncomms6443 ). (XLSX 343Â kb)
DOI: 10.6084/m9.figshare.c.3636485_d1
title: Additional file 1: of Design and rationale of the IN CONTROL trial: the effects of real-time continuous glucose monitoring on glycemia and quality of life in patients with type 1 diabetes mellitus and impaired awareness of hypoglycemia

description: Table S1. Overview of visits, telephone consultations and outcome assessments. (XLS 34 kb)
DOI: 10.6084/m9.figshare.c.3636566_d4
title: Additional file 3: Table S2. of Classification of low quality cells from single-cell RNA-seq data

description: P values of two-sided paired t-test comparing expression and noise level, between each type of low quality cell for different GO-terms (training mES dataset). (XLSX 2641Â kb)
DOI: 10.6084/m9.figshare.c.3636566_d5
title: Additional file 2: Table S1. of Classification of low quality cells from single-cell RNA-seq data

description: Quality annotation of cells for all tested datasets. (XLSX 146Â kb)
DOI: 10.6084/m9.figshare.c.3636566_d7
title: Additional file 4: Table S3. of Classification of low quality cells from single-cell RNA-seq data

description: P values of t-test comparing features between each type of low quality and high quality cells (training mES dataset). (TXT 1Â kb)
DOI: 10.6084/m9.figshare.c.3636581_d1
title: MOESM1 of Active acoustic tracking suggests that soft sediment fishes can show site attachment: a preliminary assessment of the movement patterns of the blue-spotted flathead (Platycephalus caeruleopunctatus)

description: Additional file 1: Table S1. Detailed quantitative summary of movement pattern metrics including final h values.
DOI: 10.6084/m9.figshare.c.3636590_d1
title: Additional file 10: Table S5. of The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp

description: A list of small secreted proteins (SSPs) of P. brassicae that contains potential RXLR motifs. Names displayed in bold are SSPs where the position of RXLR and EER motifs match the model described by Bhattacharjee et al. [59] and Win et al. [60]. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3636590_d5
title: Additional file 9: Table S4. of The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp

description: P. brassicae pathotype 3 predicted secreted proteins. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3636671_d10
title: Additional file 9: Table S3. of Transformation of enriched mammary cell populations with polyomavirus middle T antigen influences tumor subtype and metastatic potential

description: All differentially expressed genes in the luminal CD133â   tumor cluster compared with the mixed tumor cluster. Group 1 is the mixed tumor cluster, group 2 is the luminal CD133â   tumor cluster. A t test was performed on Benjaminiâ  Hochberg-corrected, log-transformed data. Table includes gene name, ratio, p value, and direction. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.c.3636671_d12
title: Additional file 8: Table S2. of Transformation of enriched mammary cell populations with polyomavirus middle T antigen influences tumor subtype and metastatic potential

description: Top 100 unique differentially expressed genes in the luminal CD133â   tumor cluster compared with the mixed tumor cluster. Group 1 is the mixed tumor cluster, and group 2 is the luminal CD133â   tumor cluster. A t test was performed on Benjaminiâ  Hochberg-corrected, log-transformed data. Table includes gene name, ratio, p value, and direction. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3636677_d1
title: MOESM1 of Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection

description: Additional file 1: Table S1. Summary of the downloaded chicken genome re-sequencing data. Description: The table provides sequencing depth and accession numbers from the downloaded chicken genome.
DOI: 10.6084/m9.figshare.c.3636677_d3
title: MOESM5 of Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection

description: Additional file 5: Table S4. GO analysis for all genes under selection in YNLC. The table provides the significantly overrepresented gene ontology (GO) terms among putatively selected genes in YNLC.
DOI: 10.6084/m9.figshare.c.3636677_d4
title: MOESM2 of Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection

description: Additional file 2: Table S2. Summary and annotation of SNPs in Xishuangbanna fighting chicken (YNLC) and Red Jungle Fowl (RJF).
DOI: 10.6084/m9.figshare.c.3636677_d5
title: MOESM3 of Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection

description: Additional file 3: Table S3. Putatively selected genes (top 5Â % level of $${\text{ZH}}_{\text{p}}$$ ZH p and $${\text{Z}}F_{\text{ST}}$$ Z F ST values) in the Xishuangbanna fighting chicken (YNLC).
DOI: 10.6084/m9.figshare.c.3636677_d6
title: MOESM6 of Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection

description: Additional file 6: Table S5. KEGG analysis for all genes under selection in YNLC. The table provides the significantly enriched KEGG pathways among putatively selected genes in YNLC.
DOI: 10.6084/m9.figshare.c.3636689_d1
title: Additional file 2 of Drug combinatorics and side effect estimation on the signed human drug-target network

description: Text file containing all drug pairs having synergistic scores a i (j)≥0.5 and a j (i)≥0.5. (TXT 1903 kb)
DOI: 10.6084/m9.figshare.c.3636689_d2
title: Additional file 7 of Drug combinatorics and side effect estimation on the signed human drug-target network

description: Text file containing all drug pairs having side effect scores b i (j)â Ľ0.5 but 0
DOI: 10.6084/m9.figshare.c.3636689_d3
title: Additional file 6 of Drug combinatorics and side effect estimation on the signed human drug-target network

description: Text file containing all drug pairs having side effect scores b i (j)≥0.5 and b j (i)≥0.5. (TXT 19 kb)