cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3643949_d1.v1
title: Additional file 10: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for extracting histone modification track signal near TSS for epigenetic modeling of gene expression method. Program written in R that calculates histone modification track signal in 100 bp bins spanning 1 kbp upstream and downstream of the TSS. Takes multiple .bigwig files of histone modification epigenomic tracks and the output of Additional file 9 as input. (R 5 kb)
DOI: 10.6084/m9.figshare.c.3643949_d4.v1
title: Additional file 16: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: HUVEC epigenetic modeling of gene expression dataset. Expression modeling dataset used for epigenetic modeling of gene expression analysis. Each row corresponds to a TSS and contains information on positions of PQS within 2 kbp of the TSS as well as â  bestbinâ   epigenomic track signals for DNase hypersensitivity and histone modifications. This file is an output of Additional file 11 and is taken as input by Additional file 19. (CSV 3089 kb)
DOI: 10.6084/m9.figshare.c.3643949_d6.v1
title: Additional file 4: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: Differentially expressed genes in Werner Syndrome. List of genes that are differentially expressed in human fibroblasts in Werner Syndrome. (CSV 116 kb)
DOI: 10.6084/m9.figshare.c.3643949_d7.v1
title: Additional file 8: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for mapping PQS to TSS for epigenetic modeling of gene expression method. Program written in R that identifies all PQS within 2 kbp of TSS, calculates relative distance between PQS and TSS, identifies whether PQS are located on sense or antisense strand. Takes Additional file 1 and the output of Additional file 8 as input. (R 13 kb)
DOI: 10.6084/m9.figshare.c.3643949_d9.v1
title: Additional file 2: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code used for mapping genomic PQS to known TSS. Program written in R, used for mapping PQS motifs to known TSS. Takes GENCODE annotations in .csv format and Additional file 1 as input. (R 7 kb)
DOI: 10.6084/m9.figshare.c.3643949_d10.v1
title: Additional file 7: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for CAGE data processing for epigenetic modeling of gene expression method. Program written in R that takes CAGE data in .gtf format and the output of Additional file 6 as input, merges rows with GENCODE annotation table (output of Additional file 6), calculates aggregate expression of all transcripts originating from a given TSS, and identifies TSS for each gene with the highest expression. (R 4 kb)
DOI: 10.6084/m9.figshare.c.3643949_d8.v1
title: Additional file 19: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for implementing epigenetic modeling of gene expression and analyzing PQS transcriptional effects. Program written in R that takes Additional files 12, 13, 14, 15, 16, 17, 18 as inputs and trains a Bayesian linear regression model upon epigenomic data to predict gene expression levels. Models are then applied to gene sets not used for training, and the subsequent sorting of modeling prediction errors by PQS position is used to calculate PQS transcriptional effects. Also conducts statistical bootstrapping simulations to estimate the FDR for this analysis. (R 44 kb)
DOI: 10.6084/m9.figshare.c.3643949_d13.v1
title: Additional file 14: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: HeLa-S3 epigenetic modeling of gene expression dataset. Expression modeling dataset used for epigenetic modeling of gene expression analysis. Each row corresponds to a TSS and contains information on positions of PQS within 2 kbp of the TSS as well as â  bestbinâ   epigenomic track signals for DNase hypersensitivity and histone modifications. This file is an output of Additional file 11 and is taken as input by Additional file 19. (CSV 4263 kb)
DOI: 10.6084/m9.figshare.c.3643949_d11.v1
title: Additional file 13: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: H1-hESC epigenetic modeling of gene expression dataset. Expression modeling dataset used for epigenetic modeling of gene expression analysis. Each row corresponds to a TSS and contains information on positions of PQS within 2 kbp of the TSS as well as â  bestbinâ   epigenomic track signals for DNase hypersensitivity and histone modifications. This file is an output of Additional file 11 and is taken as input by Additional file 19. (CSV 6250 kb)
DOI: 10.6084/m9.figshare.c.3643949_d12.v1
title: Additional file 21: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for PQS motif analysis in BS and WS differentially-expressed genes via SOM method. Program written in R for conducting self-organizing map classification of PQS motifs and analyzing enrichment of certain types of motifs in genes differentially expressed in BS and WS. (R 11 kb)
DOI: 10.6084/m9.figshare.c.3643949_d14.v1
title: Additional file 3: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: Mapped coordinates of all PQS within 2 kbp of known TSS. Genomic coordinates and gene localization of all PQS within 2 kbp of known TSS. Each row contains data on a PQS motif and its host gene. PQS entries are repeated multiple times if a given motif is within 2 kbp of multiple TSS. Genes without any PQS motifs are represented as single rows with missing PQS motif data. (ZIP 11660 kb)
DOI: 10.6084/m9.figshare.c.3643949_d15.v1
title: Additional file 22: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: PQS motif classifications from SOM method. PQS motif classifications from self-organizing map analysis. Number of nearest multidimensional cluster is given as the last column in the dataset. (CSV 8064 kb)
DOI: 10.6084/m9.figshare.c.3643949_d17.v1
title: Additional file 20: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for PQS feature analysis in BS and WS via ANOVA. Program written in R that analyses promoter-proximal PQS motif length, loop lengths, and base fraction in differentially expressed genes in BS and WS and compares the result to the genomic distribution. Takes Additional file 1 an Additional file 4 as input. (R 78 kb)
DOI: 10.6084/m9.figshare.c.3643949_d16.v1
title: Additional file 1: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: Genomic coordinates and motif features for all PQS. Reference coordinates from GRCh37 calculated using the Quadparser algorithm, and analysis of individual PQS sequence features including total length, loop lengths, number of G stacks, and base fractions of adenine, thymine, and cytosine. (ZIP 13239 kb)
DOI: 10.6084/m9.figshare.c.3643949_d18.v1
title: Additional file 15: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: HepG2 epigenetic modeling of gene expression dataset. Expression modeling dataset used for epigenetic modeling of gene expression analysis. Each row corresponds to a TSS and contains information on positions of PQS within 2 kbp of the TSS as well as â  bestbinâ   epigenomic track signals for DNase hypersensitivity and histone modifications. This file is an output of Additional file 11 and is taken as input by Additional file 19. (CSV 4911 kb)
DOI: 10.6084/m9.figshare.c.3643949_d20.v1
title: Additional file 12: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: GM12878 epigenetic modeling of gene expression dataset. Expression modeling dataset used for epigenetic modeling of gene expression analysis. Each row corresponds to a TSS and contains information on positions of PQS within 2 kbp of the TSS as well as â  bestbinâ   epigenomic track signals for DNase hypersensitivity and histone modifications. This file is an output of Additional file 11 and is taken as input by Additional file 19. (CSV 2493 kb)
DOI: 10.6084/m9.figshare.c.3643949_d19.v1
title: Additional file 6: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for GENCODE annotation processing protocol for epigenetic modeling of gene expression method. Program written in R for filtering low quality transcript annotations, assigning unique TSS numberings, and unique gene numberings. Takes GENCODE annotations in .gtf format as input. (R 3 kb)
DOI: 10.6084/m9.figshare.c.3643949_d21.v1
title: Additional file 11: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for determining optimal pseudocount and bin for epigenetic modeling of gene expression method. Program written in R that identifies optimal pseudocount and bin for calculating correlations of epigenomic track signals with gene expression. Takes output of Additional file 10 as input. (R 5 kb)
DOI: 10.6084/m9.figshare.c.3643949_d23.v1
title: Additional file 5: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for PQS abundance analysis in BS and WS differentially-expressed genes. Program written in R for analyzing differences in PQS abundance between BS/WS differentially-expressed genes and the rest of the genes in the genome. Takes Additional files 3 and 5 as input. (R 50 kb)
DOI: 10.6084/m9.figshare.c.3644063_d1.v1
title: Additional file 2: of TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

description: MS Excel spreadsheets containing 416 Bonferroni corrected t-tests conducted on all functionally confirmed consensus sequences in YEASTRACT database comparing the average information content obtained at the nucleobase level to that obtained at the phosphate linkage (i.e. backbone) level. An additional set of 416 tests were conducted on the 50 bp region flanking the confirmed consensus sites is included as well. (ZIP 13 kb)
DOI: 10.6084/m9.figshare.c.3644063_d2.v1
title: Additional file 3: of TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

description: TRX logo plots for general signatures ofÂ 16 transcription factor binding sites assembled fromÂ 416 Yeastract consensus sequences and collated according to JASPAR classification. (ZIP 1722 kb)
DOI: 10.6084/m9.figshare.c.3644063_d3.v1
title: Additional file 1: of TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

description: The TRX-LOGOS R module download complete with Perl wrapper scripts for batch processing and JASPAR query. Â Supporting files and documentation are also included. (ZIP 14 kb)
DOI: 10.6084/m9.figshare.c.3644072_d1.v1
title: Additional file 2: of Simulation study of activities of daily living functions using online computerized adaptive testing

description: A CAT module in MS Excel. (XLS 6542Â kb)
DOI: 10.6084/m9.figshare.c.3644072_d2.v1
title: Additional file 1: of Simulation study of activities of daily living functions using online computerized adaptive testing

description: The algorithm for determining Cutpoints and simulating data using MS Excel. (XLS 2362Â kb)
DOI: 10.6084/m9.figshare.c.3644072_d4.v1
title: Additional file 4: of Simulation study of activities of daily living functions using online computerized adaptive testing

description: The file layouts of data used for gathering feedback from patients using online CAT. (XLS 58Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d1.v1
title: Additional file 6: Table S6. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: This file contains ten tables: (1) Proteomics GO BP: GO Biological Pathways that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the proteomics results (using the top 25, 50, 100, or 283 genes with multiple comparison corrected significance); (2) Proteomics GO CC: GO Cellular Components that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the proteomics results; (3) Proteomics GO MF: GO Molecular Functions that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the proteomics results; (4) Proteomics MSigDB CP: MSigDB Canonical Pathways that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the proteomics results; (5) RNA-Seq GO BP: GO Biological Pathways that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the RNA-Seq results (using the top 25, 50, 100, 350, 600, 850, or 1095 genes with multiple comparison corrected significance); (6) RNA-Seq GO CC: GO Cellular Components that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the RNA-Seq results; (7) RNA-Seq GO MF: GO Molecular Functions that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the RNA-Seq results; (8) RNA-Seq MSigDB CP: MSigDB Canonical Pathways that showed an enrichment p-value smaller than 0.05 in any of the performed analyses for the RNA-Seq results; (9) Common Genes GO: GO terms that showed an enrichment p-value smaller than 0.05 in the 77 genes with common evidence in the RNA-Seq and proteomics results (multiple comparison corrected significance in one experiment and nominal significance in the other one); (10) Common Genes MSigDB CP: MSigDB Canonical Pathways that showed an enrichment p-value smaller than 0.05 in the 77 genes with common evidence in the RNA-Seq and Proteomics results. (XLSX 110Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d2.v1
title: Additional file 3: Table S3. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Results for the mRNA abundance comparison between 29 PD and 44 control samples for the 17,580 protein-coding genes from the RNA-Seq study. (XLSX 2337Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d3.v1
title: Additional file 4: Table S4. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Proteomics and RNA-Seq results for the 77 genes/proteins with common evidence (multiple comparison corrected significance in one of the experiments and nominal significance in the other). (XLSX 58Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d6.v1
title: Additional file 1: Table S1. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Detailed information for the entire set of 29 PD cases and 44 controls studied by MS3 proteomics, RNA-Seq, and expression microarray. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.c.3644078_d7.v1
title: Additional file 2: Table S2. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

description: Results for the protein abundance comparison between 12 PD and 12 control samples for the 3558 proteins from the MS3 proteomics study. (XLSX 336Â kb)
DOI: 10.6084/m9.figshare.c.3644168_d1.v1
title: MOESM1 of New perspectives on contributing factors to the monthly behavior of the aa geomagnetic index

description: Additional file 1. Time series of the aa index and moon luminosity from January 1868 through January 2015.
DOI: 10.6084/m9.figshare.c.3644252_d3.v1
title: Additional file 1: of Signature of microRNA expression during osteogenic differentiation of bone marrow MSCs reveals a putative role of miR-335-5p in osteoarthritis

description: Data analysis of the expression profile of miRNA sequences, from the Sanger miRBase v14 using the Taqman OpenArray MicroRNA pools A and B. (XLS 2463 kb)
DOI: 10.6084/m9.figshare.c.3644252_d5.v1
title: Additional file 6: of Signature of microRNA expression during osteogenic differentiation of bone marrow MSCs reveals a putative role of miR-335-5p in osteoarthritis

description: Extraction of all the experimentally validated microRNA-target interactions for hsa-miR-210 and hsa-miR-335-5p from the miRTarBase database. An extraction of miR-335 target genes related to the WNT pathway was also included. These belong to the Wnt signaling pathway, according to the enriched annotations provided in the Kyoto Encyclopedia of Genes and Genomes (KEGG) 04310. (XLS 2121 kb)
DOI: 10.6084/m9.figshare.c.3644255_d1.v1
title: Additional file 6: Table S3. of An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimer’s disease

description: IPA disease and/or function list for genes altered in glutamate versus glutamate + candesartan groups. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3644255_d3.v1
title: Additional file 11: Table S6. of An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimerâ  s disease

description: IPA of upstream regulators of genes preferentially expressed in cerebrovascular endothelial cells. Table S6 notes the upstream regulators of genes that are upregulated in Alzheimerâ  s disease and downregulated by candesartan in our neuronal cultures, and are of preferentially expressed in endothelial cells. (XLS 118 kb)
DOI: 10.6084/m9.figshare.c.3644255_d4.v1
title: Additional file 7: Table S4. of An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimer’s disease

description: List of upstream regulation analysis for genes differentially expressed between glutamate and glutamate + candesartan. (XLSX 200 kb)
DOI: 10.6084/m9.figshare.c.3644255_d5.v1
title: Additional file 2: Table S2. of An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimer’s disease

description: Differentially expressed genes in glutamate and glutamate + candesartan groups. Differentially expressed genes between glutamate versus glutamate + candesartan (spreadsheet #2) and between glutamate versus control (spreadsheet #3) and between candesartan versus control (spreadsheet #4). The common genes (spreadsheet #1) represent genes that are differentially expressed in both comparisons. There is a complete reversal of the effect of glutamate by candesartan on all the 501 genes in common. (XLSX 267 kb)
DOI: 10.6084/m9.figshare.c.3644255_d8.v1
title: Additional file 14: Table S8. of An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimerâ  s disease

description: IPA of upstream regulators of genes preferentially expressed in neurons. Table S8 notes the upstream regulators of genes that are downregulated in Alzheimerâ  s disease and upregulated by candesartan in our neuronal cultures, and are preferentially expressed in human neurons. (XLS 40 kb)
DOI: 10.6084/m9.figshare.c.3644255_d10.v1
title: Additional file 9: Table S9. of An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimer’s disease

description: Complete GSEA analysis output of CGCs treated with glutamate and glutamate + candesartan and several inflammatory gene signatures and gene signature from postmortem Alzheimer’s disease patient and a mouse model of Alzheimer’s disease. (XLSX 4051 kb)
DOI: 10.6084/m9.figshare.c.3644255_d13.v1
title: Additional file 12: Table S7. of An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimerâ  s disease

description: IPA of diseases and functions annotation of genes preferentially expressed in cerebrovascular endothelial cells. Table S7 notes the diseases and functions that are upregulated in Alzheimerâ  s disease and downregulated by candesartan and are preferentially expressed in cerebrovascular endothelial cells. (XLS 126 kb)
DOI: 10.6084/m9.figshare.28049906
title: Lilium henryi raw GC-MS files

description: Metabolite extraction from Lilium henryi leaf tissue
DOI: 10.6084/m9.figshare.28049906.v1
title: Lilium henryi raw GC-MS files

description: Metabolite extraction from Lilium henryi leaf tissue
DOI: 10.6084/m9.figshare.c.3644345_d1.v1
title: Additional file 1: Table S1. of Control of Caenorhabditis elegans germ-line stem-cell cycling speed meets requirements of design to minimize mutation accumulation

description: Full results of pedigree-depth optimizations. Asterisks: control points that are fixed to constant values; LX-D: cell cycle length at distal end of DMMZ at stage LX (from L2 to L4 + 3 days); LX-P: cell cycle length at proximal end of MMZ at stage LX; α LX: ratio of cycle lengths between distal DMMZ and proximal MMZ at larval stage LX; CI: 95 % credible interval derived from MCMC analysis. Further details of MCMC results are given in Figure S7. See Table 1 for abbreviated results and “Methods” for derivation details. (XLS 33 kb)
DOI: 10.6084/m9.figshare.c.3644351_d2.v1
title: Additional file 2: of Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes

description: List of all primers used in the paper. (XLSX 57Â kb)
DOI: 10.6084/m9.figshare.c.3644357_d1.v1
title: MOESM1 of Risk assessment of sheep welfare at small-scale slaughter in Nordic countries, comparing with large-scale slaughter

description: Additional file 1. Aggregated risk assessment data. Process steps, hazards and their estimated magnitudes and most-likely (ML) risks of poor sheep welfare at small-scale and large-scale slaughter in four Nordic countries; aggregated data from nine experts in 2012.
DOI: 10.6084/m9.figshare.c.3644354_d1.v1
title: Additional file 1 of Functional coherence metrics in protein families

description: Average similarity as measured by six different metrics for each of the discrete levels of noise. (XLS 50 kb)
DOI: 10.6084/m9.figshare.c.3644363_d3.v1
title: Additional file 4: of Implications of ethylene biosynthesis and signaling in soybean drought stress tolerance

description: Identification of cis -Acting Elements in Soybean Putative Gene Promoters (Table S9). In this table are shown the cis-acting elements present in the putative promoters of 176 analyzed genes. The analysis matrix was composed by 100 different elements, distributed in 29 families. Cells highlighted in different colors corresponding to elements in each promoter sequence identified, associated with the number of the identified elements. Thus, sequences with green and red cells respectively represent putative gene promoters in ethylene biosynthesis and signal transduction mediated by this plant hormone. All results are presented in three ways: the total number of matches for each cis-acting element in the matrix analyzed (column E); the number of different sequences of putative promoters that represent each cis-acting element that compose the matrix (column F); and, at last, the number of different sequences of putative promoters that represent each cis-acting element family (column G). These values are totaled, and the total number of matches identified in each sequence analyzed (line 107). (**) N.A. corresponds to not applicable. (XLSX 84Â kb)