cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d1tg6t
title: The Evolution of Function within the Nudix Superfamily: output final score S

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Output file for doi:10.6078/d1z593, with score S[final]
DOI: 10.6084/m9.figshare.28813374
title: Additional file 2 of Digital PCR-based genetic profiling from vitreous fluid as liquid biopsy for primary uveal melanoma: a proof-of-concept study

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.28813374.v1
title: Additional file 2 of Digital PCR-based genetic profiling from vitreous fluid as liquid biopsy for primary uveal melanoma: a proof-of-concept study

description: Supplementary Material 2
DOI: 10.6078/d1bc7t
title: The Evolution of Function within the Nudix Superfamily: genetic score

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Input file for doi:10.6078/d1kw28; derived from doi:10.6078/d1qp46
DOI: 10.6078/d1g59r
title: The Evolution of Function within the Nudix Superfamily: Biochem score

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Input file for doi:10.6078/d1kw28; derived from doi:10.6078/d1qp46
DOI: 10.6078/d1qp46
title: The Evolution of Function within the Nudix Superfamily: final score assignment

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: To describe confidence in function assignment of Nudix proteins, the two sheets "biochemical scores" and "genetic scores" combine all initial score assignments that belong to the two categories. Within the category, the maximum score of a given protein function was designated as Sbiochem and Sgenetic in the sheet "overall scores". The overall score was calculated by the equation: Soverall = 1 - (1 - Sgenetic) × (1 - Sbiochem). This score was adjusted to take into account the abundance of annotations for a given enzyme using an R script (explained below). The sheet "final scores" shows the score before (Soverall) and after the adjustment (Sfinal).
DOI: 10.6084/m9.figshare.28813375
title: Additional file 2 of The de novo DNA methyltransferase 3B is a novel epigenetic regulator of MYC in multiple myeloma, representing a promising therapeutic target to counter relapse

description: Supplementary Table 2
DOI: 10.6084/m9.figshare.28813375.v1
title: Additional file 2 of The de novo DNA methyltransferase 3B is a novel epigenetic regulator of MYC in multiple myeloma, representing a promising therapeutic target to counter relapse

description: Supplementary Table 2
DOI: 10.6084/m9.figshare.28813378.v1
title: Additional file 3 of The de novo DNA methyltransferase 3B is a novel epigenetic regulator of MYC in multiple myeloma, representing a promising therapeutic target to counter relapse

description: Supplementary Table 3
DOI: 10.6084/m9.figshare.28813381
title: Additional file 4 of The de novo DNA methyltransferase 3B is a novel epigenetic regulator of MYC in multiple myeloma, representing a promising therapeutic target to counter relapse

description: Supplementary Table 4
DOI: 10.6078/d1vc7g
title: The Evolution of Function within the Nudix Superfamily: initial score assignment

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: To describe confidence in function assignment of Nudix proteins, six evidence types were first classified as either biochemical or genetic, and biochemical evidence were further categorized into four subcategories: 1) kcat/Km, 2) pseudo kcat/Km (explained below), 3) relative activity, and 4) others (represented by five sheets of this file). All data points were assigned a score based on our scoring scheme (Table 4). In each sheets, the data and their corresponding scores are shown side-by-side. There is an additional sheet "kk used for pseudo kk", which contains a set of protein activities that had both their kcat/Km values and relative activities determined. In such cases, the kcat/Km value was used to approximate pseudo kcat/Km values for other relative activities in the same screening group.
DOI: 10.6084/m9.figshare.28813378
title: Additional file 3 of The de novo DNA methyltransferase 3B is a novel epigenetic regulator of MYC in multiple myeloma, representing a promising therapeutic target to counter relapse

description: Supplementary Table 3
DOI: 10.6084/m9.figshare.28813381.v1
title: Additional file 4 of The de novo DNA methyltransferase 3B is a novel epigenetic regulator of MYC in multiple myeloma, representing a promising therapeutic target to counter relapse

description: Supplementary Table 4
DOI: 10.6078/d1059d
title: The Evolution of Function within the Nudix Superfamily: Summary of Nudix enzyme’s functions:

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Summary of Nudix enzyme's functions collected from the literature. All experimental data for Nudix proteins were categorized into six different evidence types (represented by six sheets of this file): 1) kcat/Km, 2) kcat, 3) Km, 4) relative activity, 5) other biochemical activity (e.g. gel electrophoresis, HPLC, X-ray crystal structure), and 6) genetic evidence (e.g. knockouts, complementation). All data are compiled in a master sheet "all data" where each row corresponds to one protein activity pair. Additional rows are included where a given activity was investigated more than once. This file also has a sheet "GO terms" for all the Gene Ontology terms associated with at least one activity.
DOI: 10.6078/d17p4v
title: The Evolution of Function within the Nudix Superfamily: MySQL database

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: MySQL database dump file. The database contains experimental data on Nudix proteins with journal references. Refer to doi:10.6078/d13w2x for detailed information of its structure.
DOI: 10.7299/x7p84c1r
title: Archived Dataset metriocampa_allocerca
DOI: 10.15468/dl.k9375j
title: Occurrence Download

description: A dataset containing 265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rubus pseudojaponicus Koidz.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 265 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0204890-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cmpwz2
title: Occurrence Download

description: A dataset containing 445925 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is South America",
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Arthropoda"
 ]
}

 The dataset includes 445925 records from 320 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0284526-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5tnkfu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paeonia rotundiloba (D.Y.Hong) D.Y.Hong",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0199475-220831081235567/datasets/export for details.
DOI: 10.15468/dl.ryp3af
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helichrysum gloria-dei Chiov."
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238937-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11060149
title: FRACTESUS_VTT_73W_KJc_MCT_RR2_7

description: Fractesus project. Fracture test mini-CT. Raw data 73W. Framatome.
DOI: 10.5281/zenodo.11060150
title: FRACTESUS_VTT_73W_KJc_MCT_RR2_7

description: Fractesus project. Fracture test mini-CT. Raw data 73W. Framatome.
DOI: 10.15468/dl.3mxqsk
title: Occurrence Download

description: A dataset containing 471 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ixeris debilis (Thunb.) A.Gray",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 471 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0204914-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s92es6
title: Occurrence Download

description: A dataset containing 138871 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Year 2000-2011"
 ]
}

 The dataset includes 138871 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238912-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.brdwbk
title: Occurrence Download

description: A dataset containing 154190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plebejus argus (Linnaeus, 1758)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 154190 records from 665 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064285-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nf3yyt
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Impatiens gautieri Eb.Fisch. & Raheliv."
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0252365-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnnq72
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cirsium myokoense Kadota",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0204917-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.883uyh
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Impatiens fragicolor C.Marquand & Airy Shaw"
 ]
}

 The dataset includes 58 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0252349-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bf63us
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhus typhina L.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207831-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.