cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3820321_d6.v1
title: Additional file 6 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: Chromosomal locations: Chromosomal locations of arrestin genes. Table of chromosomal locations of arrestin genes in species with genomes assembled on chromosome-level. The columns â  SAG(a)â   contain the location of SAG for non-duplicated species (SAGb does not exist) or of SAGa for teleosts. This applies to all columns. Note that ARR3 is located on the sex chromosome X in all mammals. SDP ARR0: SDPs distinguishing ARR0.1 from sea urchin ARR0.2 and other ARR0. The classification is based on unsupervised multi-correspondence analysis of all ARR0 with S3det. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARRB1 are listed. SDP SAG: SDPs distinguishing SAGa and SAGb in teleosts. The classification is based on unsupervised MCA of all filtered teleost SAG with S3det. During filtering, SAGb from pufferfish and stickleback were excluded due to sequence coverage &lt; 70%. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine SAG are listed. SDP ARRB2: SDPs distinguishing ARRB2a and ARRB2b in teleosts. The classification was given in supervised MCA of all filtered teleost ARRB2. Due to redundancy &gt; 98%, ARRB2a of platyfish (Xiphophorus maculatus), pufferfish and medaka were excluded from the analysis. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARRB2 are listed. SDP ARR3: SDPs distinguishing ARR3a and ARR3b in teleosts. The classification is based on unsupervised MCA of all teleost ARR3 with S3det. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARR3 are listed. Codeml: Analysis of positive selection after arrestin duplication. Specific branches within the arrestin gene tree were tested for positive selection using the branch-site model of codeml, part of the PAML program. The null-hypothesis assumes purifying or neutral selection on the foreground and background branches, while the alternative model allows for positive selection on the foreground branch. Fractions of sites are given, that are predicted to belong to the respective classes (p) together with their dN/dS ratios (w). If the null hypothesis was rejected, sites that were under positive selection under BEB were mapped onto the respective bovine ortholog. (XLSX 44.5 kb)
DOI: 10.6084/m9.figshare.c.3820321_d6
title: Additional file 6 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: Chromosomal locations: Chromosomal locations of arrestin genes. Table of chromosomal locations of arrestin genes in species with genomes assembled on chromosome-level. The columns â  SAG(a)â   contain the location of SAG for non-duplicated species (SAGb does not exist) or of SAGa for teleosts. This applies to all columns. Note that ARR3 is located on the sex chromosome X in all mammals. SDP ARR0: SDPs distinguishing ARR0.1 from sea urchin ARR0.2 and other ARR0. The classification is based on unsupervised multi-correspondence analysis of all ARR0 with S3det. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARRB1 are listed. SDP SAG: SDPs distinguishing SAGa and SAGb in teleosts. The classification is based on unsupervised MCA of all filtered teleost SAG with S3det. During filtering, SAGb from pufferfish and stickleback were excluded due to sequence coverage &lt; 70%. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine SAG are listed. SDP ARRB2: SDPs distinguishing ARRB2a and ARRB2b in teleosts. The classification was given in supervised MCA of all filtered teleost ARRB2. Due to redundancy &gt; 98%, ARRB2a of platyfish (Xiphophorus maculatus), pufferfish and medaka were excluded from the analysis. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARRB2 are listed. SDP ARR3: SDPs distinguishing ARR3a and ARR3b in teleosts. The classification is based on unsupervised MCA of all teleost ARR3 with S3det. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARR3 are listed. Codeml: Analysis of positive selection after arrestin duplication. Specific branches within the arrestin gene tree were tested for positive selection using the branch-site model of codeml, part of the PAML program. The null-hypothesis assumes purifying or neutral selection on the foreground and background branches, while the alternative model allows for positive selection on the foreground branch. Fractions of sites are given, that are predicted to belong to the respective classes (p) together with their dN/dS ratios (w). If the null hypothesis was rejected, sites that were under positive selection under BEB were mapped onto the respective bovine ortholog. (XLSX 44.5 kb)
DOI: 10.6084/m9.figshare.c.3820321_d7
title: Additional file 7 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: Alignment of deuterostome arrestins with functional annotation known from experimental studies of arrestins in mammals. Note that the naming differs from the naming used throughout the manuscript with ARR1, ARR2, ARR3 and ARR4 used instead of SAG, ARRB1, ARRB2 and ARR3, respectively. Please load alignment with annotation file (provided at http://dx.doi.org/10.5281/zenodo.820866 ) in Jalview alignment viewer. (FA 44.5 kb)
DOI: 10.6084/m9.figshare.c.3820321_d5.v1
title: Additional file 5 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: ML tree of arrestins excluding columns known to confer receptor binding. The tree was constructed from the same alignment as Additional file 3 deleting the columns known to confer receptor specificity according to [2, 17, 19, 23, 31â  33] (model JTT+G+I with Îą 1.05, p-invariable 0.05, 200x bootstrapping). The tree can be visualized with a tree viewer, e.g. Dendroscope [115]. (NW 7.42 kb)
DOI: 10.6084/m9.figshare.c.3820321_d4.v1
title: Additional file 4 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: Maximum clade credibility tree of arrestins. Starting from the same alignment as used for Additional file 3, we constructed a phylogenetic tree with BEAST2 [94] under the Birth Death model with a relaxed molecular clock (log normal) using the gamma site model (JTT+G+I with Îą 1.04, p-invariable 0.05). The tree can be visualized with a tree viewer, e.g. Figtree [99]. (TREE 253 kb)
DOI: 10.6084/m9.figshare.c.3820321_d5
title: Additional file 5 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: ML tree of arrestins excluding columns known to confer receptor binding. The tree was constructed from the same alignment as Additional file 3 deleting the columns known to confer receptor specificity according to [2, 17, 19, 23, 31â  33] (model JTT+G+I with Îą 1.05, p-invariable 0.05, 200x bootstrapping). The tree can be visualized with a tree viewer, e.g. Dendroscope [115]. (NW 7.42 kb)
DOI: 10.6084/m9.figshare.c.3820321_d4
title: Additional file 4 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: Maximum clade credibility tree of arrestins. Starting from the same alignment as used for Additional file 3, we constructed a phylogenetic tree with BEAST2 [94] under the Birth Death model with a relaxed molecular clock (log normal) using the gamma site model (JTT+G+I with Îą 1.04, p-invariable 0.05). The tree can be visualized with a tree viewer, e.g. Figtree [99]. (TREE 253 kb)
DOI: 10.6084/m9.figshare.c.3820321_d3.v1
title: Additional file 3 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: ML tree of arrestins (depicted in Fig. 4). Starting information for tree reconstruction was an alignment of arrestins investigated in this study, for which sequence information was close to complete. Sequences derived from genomic annotations were substituted by sequences with experimental evidence available if these were more complete. The tree was constructed using PhyML from the amino acid sequences of arrestin paralogs from an alignment of nucleotide sequences aligned with MACSE (model JTT+G+I with Îą 1.04, p-invariable 0.05, 200x bootstrapping). The tree can be visualized with a tree viewer, e.g. Dendroscope [115]. (NW 1340 kb)
DOI: 10.6084/m9.figshare.c.3820321_d3
title: Additional file 3 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: ML tree of arrestins (depicted in Fig. 4). Starting information for tree reconstruction was an alignment of arrestins investigated in this study, for which sequence information was close to complete. Sequences derived from genomic annotations were substituted by sequences with experimental evidence available if these were more complete. The tree was constructed using PhyML from the amino acid sequences of arrestin paralogs from an alignment of nucleotide sequences aligned with MACSE (model JTT+G+I with Îą 1.04, p-invariable 0.05, 200x bootstrapping). The tree can be visualized with a tree viewer, e.g. Dendroscope [115]. (NW 1340 kb)
DOI: 10.6084/m9.figshare.c.3820351_d1
title: Additional file 1: of Preparation and evaluation of goose reovirus inactivated vaccine

description: Alignment data of the sequence among JS-01 strain and other reovirus strains. (TXT 61 kb)
DOI: 10.6084/m9.figshare.c.3820351_d1.v1
title: Additional file 1: of Preparation and evaluation of goose reovirus inactivated vaccine

description: Alignment data of the sequence among JS-01 strain and other reovirus strains. (TXT 61 kb)
DOI: 10.6084/m9.figshare.c.3820324_d4
title: Additional file 4:Table S4. of VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

description: Information about the 2,657 top-scoring predicted viral contigs assembled from 78 human gut microbiome samples from the liver cirrhosis study of Qin et al. 2014. (XLSX 520Â kb)
DOI: 10.6084/m9.figshare.c.3820324_d4.v1
title: Additional file 4:Table S4. of VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

description: Information about the 2,657 top-scoring predicted viral contigs assembled from 78 human gut microbiome samples from the liver cirrhosis study of Qin et al. 2014. (XLSX 520Â kb)
DOI: 10.15468/dl.7sw8cp
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Ailurus fulgens F.G.Cuvier, 1825",
 "Year 2000-2024"
 ]
}

 The dataset includes 14 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035796-241126133413365/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.3820321_d2.v1
title: Additional file 2 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: Approximate ML tree of the arrestin fold family as extracted from UniProtKB (depicted in Additional file 1: Figure S1). Hits were assigned to the arrestin fold family if they contained at least one arrestin_N or arrestin_C domain (see Methods). The tree was generated with the FastTree software and bootstrapping was performed 1000 times with SeqBoot [119]. The tree can be visualized with a tree viewer, e.g. Dendroscope [115]. (TREE 78.3 kb)
DOI: 10.6084/m9.figshare.c.3820324_d3.v1
title: Additional file 3: Table S3. of VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

description: The virus and prokaryotic species abundance profile used for the simulation of metagenomic samples.(XLSX 164Â kb)
DOI: 10.6084/m9.figshare.c.3820321_d2
title: Additional file 2 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

description: Approximate ML tree of the arrestin fold family as extracted from UniProtKB (depicted in Additional file 1: Figure S1). Hits were assigned to the arrestin fold family if they contained at least one arrestin_N or arrestin_C domain (see Methods). The tree was generated with the FastTree software and bootstrapping was performed 1000 times with SeqBoot [119]. The tree can be visualized with a tree viewer, e.g. Dendroscope [115]. (TREE 78.3 kb)
DOI: 10.6084/m9.figshare.c.3820324_d3
title: Additional file 3: Table S3. of VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

description: The virus and prokaryotic species abundance profile used for the simulation of metagenomic samples.(XLSX 164Â kb)
DOI: 10.6084/m9.figshare.28031957
title: COMPANY PROFILE JOURNAL.pdf

description: This study explores the development of a company profile website for small businesses using the Waterfall method. Each phase of the methodology—from requirements analysis to maintenance—is meticulously executed, ensuring a clear development path. The website is built using <b>Next.js</b> for optimized performance and <b>Tailwind CSS</b> for responsive and efficient UI design. Key features include an interactive homepage, a product showcase, and integrated contact functionality. Despite challenges like limited resources and maintaining responsive design, the outcome is a user-friendly, professional website tailored to business needs. The deployment strategy and SEO optimization are also discussed to enhance visibility and user engagement.
DOI: 10.6084/m9.figshare.28031957.v3
title: COMPANY PROFILE JOURNAL.pdf

description: This study explores the development of a company profile website for small businesses using the Waterfall method. Each phase of the methodology—from requirements analysis to maintenance—is meticulously executed, ensuring a clear development path. The website is built using <b>Next.js</b> for optimized performance and <b>Tailwind CSS</b> for responsive and efficient UI design. Key features include an interactive homepage, a product showcase, and integrated contact functionality. Despite challenges like limited resources and maintaining responsive design, the outcome is a user-friendly, professional website tailored to business needs. The deployment strategy and SEO optimization are also discussed to enhance visibility and user engagement.
DOI: 10.6084/m9.figshare.28031957.v2
title: COMPANY PROFILE JOURNAL.pdf

description: This study explores the development of a company profile website for small businesses using the Waterfall method. Each phase of the methodology—from requirements analysis to maintenance—is meticulously executed, ensuring a clear development path. The website is built using <b>Next.js</b> for optimized performance and <b>Tailwind CSS</b> for responsive and efficient UI design. Key features include an interactive homepage, a product showcase, and integrated contact functionality. Despite challenges like limited resources and maintaining responsive design, the outcome is a user-friendly, professional website tailored to business needs. The deployment strategy and SEO optimization are also discussed to enhance visibility and user engagement.
DOI: 10.57841/casdc.0004242
title: 测试1
DOI: 10.15468/dl.n8mgby
title: Occurrence Download

description: A dataset containing 236 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paraplagusia japonica (Temminck & Schlegel, 1846)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 236 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035797-241126133413365/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.3819253_d2.v1
title: Additional file 2: of Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model

description: Table S1â  S4. DEGs from the four stages. Table S5. Genes in the WGCNA modules. Table S6. RNA expression and protein staining scores from The Human Protein Atlas. (XLSX 181 kb)
DOI: 10.6084/m9.figshare.c.3819253_d2
title: Additional file 2: of Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model

description: Table S1â  S4. DEGs from the four stages. Table S5. Genes in the WGCNA modules. Table S6. RNA expression and protein staining scores from The Human Protein Atlas. (XLSX 181 kb)
DOI: 10.6084/m9.figshare.c.3819169_d5
title: Additional file 5: Table S1. of Characterization of Schistosoma japonicum CP1412 protein as a novel member of the ribonuclease T2 molecule family with immune regulatory function

description: Data of single egg granuloma area of infection mice and infection after immunization. (XLS 19 kb)
DOI: 10.15468/dl.62536n
title: Occurrence Download

description: A dataset containing 84711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Alsophila R.Br."
 ]
}

 The dataset includes 84711 records from 393 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035794-241126133413365/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.3818083_d1
title: Additional file 1: Table S1. of Microarray study of gene expression profile to identify new candidate genes involved in the molecular mechanism of leptin-induced knee joint osteoarthritis in rat

description: Complete list of DEGs between control and leptin-induced groups. (XLSX 568Â kb)
DOI: 10.6084/m9.figshare.c.3817747_d2
title: Additional file 2: of Gene expression variations in high-altitude adaptation: a case study of the Asiatic toad (Bufo gargarizans)

description: List of differentially expressed genes (DEGs) between toads from high- and low-altitude sites in three tissues (brain, heart, and liver) and the Gene Ontology (GO) categories over-represented by these genes. DEGs include both fixed and plastic, which were determined by a reciprocal transplant experiment. (XLSX 152Â kb)
DOI: 10.6084/m9.figshare.c.3817747_d2.v1
title: Additional file 2: of Gene expression variations in high-altitude adaptation: a case study of the Asiatic toad (Bufo gargarizans)

description: List of differentially expressed genes (DEGs) between toads from high- and low-altitude sites in three tissues (brain, heart, and liver) and the Gene Ontology (GO) categories over-represented by these genes. DEGs include both fixed and plastic, which were determined by a reciprocal transplant experiment. (XLSX 152Â kb)
DOI: 10.6084/m9.figshare.c.3817735_d5
title: Additional file 5 of Comparative analysis of lincRNA in insect species

description: Annotations of N.vitripennis lincRNAs. (GFF 179 kb)
DOI: 10.6084/m9.figshare.c.3817735_d5.v1
title: Additional file 5 of Comparative analysis of lincRNA in insect species

description: Annotations of N.vitripennis lincRNAs. (GFF 179 kb)
DOI: 10.6084/m9.figshare.c.3817735_d4.v1
title: Additional file 4 of Comparative analysis of lincRNA in insect species

description: Annotations of T.castaneum lincRNAs. (GFF 190 kb)
DOI: 10.6084/m9.figshare.c.3817735_d3.v1
title: Additional file 3 of Comparative analysis of lincRNA in insect species

description: Table S6. (ODS 26 kb)
DOI: 10.6084/m9.figshare.c.3817735_d4
title: Additional file 4 of Comparative analysis of lincRNA in insect species

description: Annotations of T.castaneum lincRNAs. (GFF 190 kb)
DOI: 10.6084/m9.figshare.c.3817735_d3
title: Additional file 3 of Comparative analysis of lincRNA in insect species

description: Table S6. (ODS 26 kb)
DOI: 10.6084/m9.figshare.c.3817735_d2.v1
title: Additional file 2 of Comparative analysis of lincRNA in insect species

description: Table S5. (ODS 28 kb)
DOI: 10.6084/m9.figshare.c.3817735_d2
title: Additional file 2 of Comparative analysis of lincRNA in insect species

description: Table S5. (ODS 28 kb)
DOI: 10.15468/dl.wszqk5
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plagusia japonica Temminck & Schlegel, 1846",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035799-241126133413365/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.3817693_d3
title: Additional file 3: of Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)

description: The differential alternative splicing events between three genotypes (XLSX 740 kb)
DOI: 10.6084/m9.figshare.c.3817618_d4
title: Additional file 4: Table S3. of Identity-by-descent refines mapping of candidate regions for preaxial polydactyly II /III in a large Chinese pedigree

description: Mutations in intron 5 of LMBR1.
DOI: 10.6084/m9.figshare.c.3817618_d3.v1
title: Additional file 3: Table S2. of Identity-by-descent refines mapping of candidate regions for preaxial polydactyly II /III in a large Chinese pedigree

description: IBD segments of LMBR1 and SHH.
DOI: 10.6084/m9.figshare.c.3817618_d4.v1
title: Additional file 4: Table S3. of Identity-by-descent refines mapping of candidate regions for preaxial polydactyly II /III in a large Chinese pedigree

description: Mutations in intron 5 of LMBR1.
DOI: 10.6084/m9.figshare.c.3817618_d3
title: Additional file 3: Table S2. of Identity-by-descent refines mapping of candidate regions for preaxial polydactyly II /III in a large Chinese pedigree

description: IBD segments of LMBR1 and SHH.
DOI: 10.6084/m9.figshare.c.3817618_d2.v1
title: Additional file 2: Table S1. of Identity-by-descent refines mapping of candidate regions for preaxial polydactyly II /III in a large Chinese pedigree

description: Top 0.01% peak signals.
DOI: 10.6084/m9.figshare.c.3817618_d2
title: Additional file 2: Table S1. of Identity-by-descent refines mapping of candidate regions for preaxial polydactyly II /III in a large Chinese pedigree

description: Top 0.01% peak signals.
DOI: 10.23728/b2share.baad40f40fa049408e38a4d729e8e72d
title: Potential candidate genes of filter feeding species as a toolkit for monitoring microplastics impact

description: Supplementary Table 1 of the paper "Potential candidate genes of filter feeding species as a toolkit for monitoring microplastics impact"