The Consensus CDS
Names
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The Consensus CDS
metasource: Fairsharing.org
version: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
CCDS
metasource: Fairsharing.org
version: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
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The Consensus CDS
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
CCDS
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
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The Consensus CDS
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
CCDS
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations.
Description
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The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations.
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
The Consensus CoDing Sequence (CCDS) project identifies the position of protein-coding regions of human and mouse genes that are annotated consistently by the collaborators and are supported by transcript evidence, use of canonical splice sites, and other quality assurance measures. The CCDS set is calculated after a coordinated whole-genome annotation update by the collaborating annotation groups: NCBI, EBI, and WTSI. The CCDS set includes only those protein coding annotations that precisely agree in every exon placement across the entire coding region. UCSC provides independent and intensive quality control procedures augmented by work from the other groups. Once a coding gene structure is agreed, it will be maintained for future releases unless there is good evidence to modify or remove it. The collaboration has improved independent annotation methods (both computational analysis and manual annotation) and we expect continued growth in the CCDS set as more gene structures and more organisms are included in the collection. The long-term goal of the CCDS project is to converge toward a full set of standard gene annotations for finished high-quality genomes. We anticipate that through continued manual review, experimental validation of weakly supported genes, and as automatic annotation methods continue to improve, the CCDS set will become more complete. The CCDS web site (http://www.ncbi.nlm.nih.gov/CCDS/) provides information about CCDS and sequence identifiers, the CDS data as both coordinates and sequence, and links to genome browsers. WTSI, UCSC, EBI and NCBI web sites indicate genome annotation data that have a CCDS status.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://www.ncbi.nlm.nih.gov/CCDS/Webpage
More detailed information about this field from each metasource.
http://www.ncbi.nlm.nih.gov/CCDS/
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: CCDS Attribution requiredLicence name
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CCDS Attribution required
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
Licence URL
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https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
Publications:
Publications
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The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
PMID: 19498102
metasource: Fairsharing.org
version: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://dx.doi.org/10.1093/nar/gkt1059
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
PMID: 19498102
metasource: Fairsharing.org
version: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://dx.doi.org/10.1093/nar/gkt1059
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
PubMed citations: 315.
315 articles citing: The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins. PMID:35891797
Association between germline variants and somatic mutations in colorectal cancer. PMID:35715570
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. PMID:35148171
Mouse genomic and cellular annotations. PMID:35124726
Meta-imputation of transcriptome from genotypes across multiple datasets by leveraging publicly available summary-level data. PMID:35100255
Efficient gene editing through an intronic selection marker in cells. PMID:35098362
ROSIE: RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data. PMID:35072570
Genomic studies controvert the existence of the CUX1 p75 isoform. PMID:34997000
The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer. PMID:34987166
Optimizing the evaluation of gene-targeted panels for tumor mutational burden estimation. PMID:34702927
Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist. PMID:34686207
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration. PMID:34172972
MTR3D: identifying regions within protein tertiary structures under purifying selection. PMID:34050760
WEScover: selection between clinical whole exome sequencing and gene panel testing. PMID:34016036
Sub-genic intolerance, ClinVar, and the epilepsies: A whole-exome sequencing study of 29,165 individuals. PMID:33932343
A catalog of associations between rare coding variants and COVID-19 outcomes. PMID:33655273
Systems biology analysis identifies TNFRSF9 as a functional marker of tumor-infiltrating regulatory T-cell enabling clinical outcome prediction in lung cancer. PMID:33598101
Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures. PMID:33575596
RNAsamba: neural network-based assessment of the protein-coding potential of RNA sequences. PMID:33575571
Failure to replicate the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19. PMID:33398295
Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations. PMID:33345188
The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits. PMID:33137877
Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer. PMID:32879421
Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors. PMID:32755029
The multicomparative 2-n-way genome suite. PMID:32727870
Mutational bias and the protein code shape the evolution of splicing enhancers. PMID:32504065
Progress, Challenges, and Surprises in Annotating the Human Genome. PMID:32421357
Design and analysis of CRISPR-Cas experiments. PMID:32284587
Comparison of commonly used solid tumor targeted gene sequencing panels for estimating tumor mutation burden shows analytical and prognostic concordance within the cancer genome atlas cohort. PMID:32217764
Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. PMID:32039202
Quality of whole genome sequencing from blood versus saliva derived DNA in cardiac patients. PMID:31996208
Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics. PMID:31947757
About three-fourths of mouse proteins unexpectedly appear at a low position of SDS-PAGE, often as additional isoforms, questioning whether all protein isoforms have been eliminated in gene-knockout cells or organisms. PMID:31930537
Identification of pathogenic variant enriched regions across genes and gene families. PMID:31871067
Human gene expression variability and its dependence on methylation and aging. PMID:31810449
Accurate detection of short and long active ORFs using Ribo-seq data. PMID:31750902
MiPepid: MicroPeptide identification tool using machine learning. PMID:31703551
The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. PMID:31691385
De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. PMID:31586052
RNA Transcription and Splicing Errors as a Source of Cancer Frameshift Neoantigens for Vaccines. PMID:31578439
Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression. PMID:31556460
Beyond sequencing: re-visiting annotations for PJL as a test case. PMID:31366397
Pathogenic WDFY3 variants cause neurodevelopmental disorders and opposing effects on brain size. PMID:31327001
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease. PMID:31249063
A new mouse model to study the role of ectopic Nanos3 expression in cancer. PMID:31208373
Phosphorylation mapping of Laminin β1-chain: Kinases in association with active sites. PMID:31180068
Codon selection reduces GC content bias in nucleic acids encoding for intrinsically disordered proteins. PMID:31175370
Codon usage optimization in pluripotent embryonic stem cells. PMID:31174582
Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes. PMID:31160636
Novel likely pathogenic variants in TMEM126A identified in non-syndromic autosomal recessive optic atrophy: two case reports. PMID:30961538
CD91 on dendritic cells governs immunosurveillance of nascent, emerging tumors. PMID:30944251
A farnesyltransferase inhibitor activates lysosomes and reduces tau pathology in mice with tauopathy. PMID:30918111
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. PMID:30902113
Untouchable genes in the human genome: Identifying ideal targets for cancer treatment. PMID:30803560
The circular RNome of primary breast cancer. PMID:30692147
Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance. PMID:30686509
Mutations in an Innate Immunity Pathway Are Associated with Poor Overall Survival Outcomes and Hypoxic Signaling in Cancer. PMID:30590044
Discovery of common and rare genetic risk variants for colorectal cancer. PMID:30510241
Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples. PMID:30453881
TFmapper: A Tool for Searching Putative Factors Regulating Gene Expression Using ChIP-seq Data. PMID:30416387
ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching. PMID:30295032
Overexpressed TTC3 Protein Tends to be Cleaved into Fragments and Form Aggregates in the Nucleus. PMID:30203323
A machine learning approach for somatic mutation discovery. PMID:30185652
In Vitro Multiexon Skipping by Antisense PMOs in Dystrophic Dog and Exon 7-Deleted DMD Patient. PMID:30171540
A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes. PMID:30108239
Curating Clinically Relevant Transcripts for the Interpretation of Sequence Variants. PMID:30096381
Blood lipid-related low-frequency variants in LDLR and PCSK9 are associated with onset age and risk of myocardial infarction in Japanese. PMID:29802317
OMGene: mutual improvement of gene models through optimisation of evolutionary conservation. PMID:29703150
Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. PMID:29626081
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease. PMID:29590295
Does adaptation to vertebrate codon usage relate to flavivirus emergence potential? PMID:29385205
Ubiquitin Specific Peptidase 22 Regulates Histone H2B Mono-Ubiquitination and Exhibits Both Oncogenic and Tumor Suppressor Roles in Cancer. PMID:29210986
A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations. PMID:29186148
Rare copy number variants identified in prune belly syndrome. PMID:29174092
Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data. PMID:29161273
Ensembl 2018. PMID:29155950
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. PMID:29126148
APPRIS 2017: principal isoforms for multiple gene sets. PMID:29069475
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics. PMID:28797091
A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major. PMID:28638238
Genome annotation for clinical genomic diagnostics: strengths and weaknesses. PMID:28558813
Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients. PMID:28505210
Revealing phenotype-associated functional differences by genome-wide scan of ancient haplotype blocks. PMID:28445522
Aligning coding sequences with frameshift extension penalties. PMID:28373895
Editing the genome of hiPSC with CRISPR/Cas9: disease models. PMID:28303292
IFT56 regulates vertebrate developmental patterning by maintaining IFTB complex integrity and ciliary microtubule architecture. PMID:28264835
Genes encoding intrinsic disorder in Eukaryota have high GC content. PMID:28232902
Multiregion ultra-deep sequencing reveals early intermixing and variable levels of intratumoral heterogeneity in colorectal cancer. PMID:28145097
INDELseek: detection of complex insertions and deletions from next-generation sequencing data. PMID:28056804
Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer. PMID:28050010
Linking the Epigenome with Exposure Effects and Susceptibility: The Epigenetic Seed and Soil Model. PMID:28049737
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. PMID:28038678
An atlas of human kinase regulation. PMID:27909043
COSMIC: somatic cancer genetics at high-resolution. PMID:27899578
Genenames.org: the HGNC and VGNC resources in 2017. PMID:27799471
Signatures of Archaic Adaptive Introgression in Present-Day Human Populations. PMID:27756828
Preferential use of minor codons in the translation initiation region of human genes. PMID:27726012
Explorations to improve the completeness of exome sequencing. PMID:27568008
The miR-644a/CTBP1/p53 axis suppresses drug resistance by simultaneous inhibition of cell survival and epithelial-mesenchymal transition in breast cancer. PMID:27409664
The Ensembl gene annotation system. PMID:27337980
Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses. PMID:27270402
Purifying selection shapes the coincident SNP distribution of primate coding sequences. PMID:27255481
MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments. PMID:27154272
Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls. PMID:27152526
CoReCG: a comprehensive database of genes associated with colon-rectal cancer. PMID:27114494
RNA-binding protein IGF2BP3 targeting of oncogenic transcripts promotes hematopoietic progenitor proliferation. PMID:26974154
Identification of a G-Protein Subunit-α11 Gain-of-Function Mutation, Val340Met, in a Family With Autosomal Dominant Hypocalcemia Type 2 (ADH2). PMID:26818911
The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. PMID:26781712
Ensembl 2016. PMID:26687719
Rare copy number variants implicated in posterior urethral valves. PMID:26663319
The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome. PMID:26642228
Improved Classification of Lung Cancer Using Radial Basis Function Neural Network with Affine Transforms of Voss Representation. PMID:26625358
The UCSC Genome Browser database: 2016 update. PMID:26590259
Novel myristoylation of the sperm-specific hexokinase 1 isoform regulates its atypical localization. PMID:26581589
dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs. PMID:26555599
Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer. PMID:26546047
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. PMID:26527726
Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. PMID:26449678
Ptpn22 and Cd2 Variations Are Associated with Altered Protein Expression and Susceptibility to Type 1 Diabetes in Nonobese Diabetic Mice. PMID:26438525
Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling. PMID:26394049
The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity. PMID:26332131
Nucleosome Organization in Human Embryonic Stem Cells. PMID:26305225
Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. PMID:26300000
Comparison of predicted and actual consequences of missense mutations. PMID:26269570
Lineage-Specific Changes in Biomarkers in Great Apes and Humans. PMID:26247603
MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR. PMID:26109350
Analysis of Low Frequency Protein Truncating Stop-Codon Variants and Fasting Concentration of Growth Hormone. PMID:26086970
Genetics and genotype-phenotype correlations in Finnish patients with dilated cardiomyopathy. PMID:26084686
Identification of genomic features in the classification of loss- and gain-of-function mutation. PMID:26043747
Rapid Detection of Rare Deleterious Variants by Next Generation Sequencing with Optional Microarray SNP Genotype Data. PMID:26037133
GC3-biased gene domains in mammalian genomes. PMID:26019240
Roles of solvent accessibility and gene expression in modeling protein sequence evolution. PMID:25987828
The evolutionary fate of alternatively spliced homologous exons after gene duplication. PMID:25931610
High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer. PMID:25808843
Lung cancer prediction using neural network ensemble with histogram of oriented gradient genomic features. PMID:25802891
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. PMID:25735770
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. PMID:25711833
Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. PMID:25668385
Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. PMID:25597990
High throughput exome coverage of clinically relevant cardiac genes. PMID:25496018
Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism. PMID:25495354
Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells. PMID:25418962
Conservation of trans-acting circuitry during mammalian regulatory evolution. PMID:25409825
Regulation of translation by upstream translation initiation codons of surfactant protein A1 splice variants. PMID:25326576
Epigenome variation in severe asthma. PMID:25288825
Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives. PMID:25268389
Novel copy-number variants in a population-based investigation of classic heterotaxy. PMID:25232849
The landscape of kinase fusions in cancer. PMID:25204415
Phen-Gen: combining phenotype and genotype to analyze rare disorders. PMID:25086502
Analysis of stop-gain and frameshift variants in human innate immunity genes. PMID:25058640
GrabBlur--a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files. PMID:25055742
Rare-variant association analysis: study designs and statistical tests. PMID:24995866
Choice of transcripts and software has a large effect on variant annotation. PMID:24944579
In silico identification of plant miRNAs in mammalian breast milk exosomes--a small step forward? PMID:24933019
Evolutionary origin and methylation status of human intronic CpG islands that are not present in mouse. PMID:24923327
Performance comparison of four exome capture systems for deep sequencing. PMID:24912484
OTX2 duplication is implicated in hemifacial microsomia. PMID:24816892
Patterns of coding variation in the complete exomes of three Neandertals. PMID:24753607
BARP suppresses voltage-gated calcium channel activity and Ca2+-evoked exocytosis. PMID:24751537
Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays. PMID:24705123
Exonic splicing signals impose constraints upon the evolution of enzymatic activity. PMID:24692663
Should pharmacologists care about alternative splicing? IUPHAR Review 4. PMID:24670145
Nuclear ARVCF protein binds splicing factors and contributes to the regulation of alternative splicing. PMID:24644279
N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. PMID:24623590
Molecular evolution and functional divergence of the metallothionein gene family in vertebrates. PMID:24557429
Polygenic inheritance of paclitaxel-induced sensory peripheral neuropathy driven by axon outgrowth gene sets in CALGB 40101 (Alliance). PMID:24513692
Genome-scale sequencing to identify genes involved in Mendelian disorders. PMID:24510651
Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline. PMID:24478219
The genomic landscape of Neanderthal ancestry in present-day humans. PMID:24476815
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. PMID:24467687
Single molecule fluorescence approaches shed light on intracellular RNAs. PMID:24417544
CpG distribution and methylation pattern in porcine parvovirus. PMID:24392033
Regularized rare variant enrichment analysis for case-control exome sequencing data. PMID:24382715
A tale of two drug targets: the evolutionary history of BACE1 and BACE2. PMID:24381583
Identification of expressed and conserved human noncoding RNAs. PMID:24344320
Transparency tools in gene patenting for informing policy and practice. PMID:24316644
The Vertebrate Genome Annotation browser 10 years on. PMID:24316575
Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. PMID:24285302
Exome sequencing finds a novel PCSK1 mutation in a child with generalized malabsorptive diarrhea and diabetes insipidus. PMID:24280991
ExoLocator--an online view into genetic makeup of vertebrate proteins. PMID:24271393
The UCSC Genome Browser database: 2014 update. PMID:24270787
RefSeq: an update on mammalian reference sequences. PMID:24259432
Current status and new features of the Consensus Coding Sequence database. PMID:24217909
Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length. PMID:24161523
A horizontal alignment tool for numerical trend discovery in sequence data: application to protein hydropathy. PMID:24130469
Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. PMID:24086152
Forward genetics identifies Kdf1/1810019J16Rik as an essential regulator of the proliferation-differentiation decision in epidermal progenitor cells. PMID:24075906
Comparison of RefSeq protein-coding regions in human and vertebrate genomes. PMID:24063302
Epigenetic and genetic features of 24 colon cancer cell lines. PMID:24042735
M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci. PMID:24002112
Genic intolerance to functional variation and the interpretation of personal genomes. PMID:23990802
Molecular characterization of mutant mouse strains generated from the EUCOMM/KOMP-CSD ES cell resource. PMID:23912999
Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. PMID:23906727
Estimating exome genotyping accuracy by comparing to data from large scale sequencing projects. PMID:23902830
Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. PMID:23865674
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. PMID:23843252
Sequencing studies in human genetics: design and interpretation. PMID:23752795
Long runs of homozygosity are enriched for deleterious variation. PMID:23746547
Paleoproteomic study of the Iceman's brain tissue. PMID:23739949
A comprehensive strategy to identify stoichiometric membrane protein interactomes. PMID:23676845
Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. PMID:23636849
Distinct types of disorder in the human proteome: functional implications for alternative splicing. PMID:23633940
Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays. PMID:23594746
Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting. PMID:23586822
Pervasive sequence patents cover the entire human genome. PMID:23522065
Finding protein-coding genes through human polymorphisms. PMID:23349826
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. PMID:23340843
The genetic landscape of high-risk neuroblastoma. PMID:23334666
CRAVAT: cancer-related analysis of variants toolkit. PMID:23325621
Alternative splicing in the aldo-keto reductase superfamily: implications for protein nomenclature. PMID:23298867
Identification of TP53 as an acute lymphocytic leukemia susceptibility gene through exome sequencing. PMID:23255406
Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing. PMID:23231371
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. PMID:23197657
Database resources of the National Center for Biotechnology Information. PMID:23193264
Genenames.org: the HGNC resources in 2013. PMID:23161694
APPRIS: annotation of principal and alternative splice isoforms. PMID:23161672
The UCSC Genome Browser database: extensions and updates 2013. PMID:23155063
The genetic landscape of mutations in Burkitt lymphoma. PMID:23143597
Exome sequencing of only seven Qataris identifies potentially deleterious variants in the Qatari population. PMID:23139751
An integrated genome-wide approach to discover tumor-specific antigens as potential immunologic and clinical targets in cancer. PMID:23135912
Modeling read counts for CNV detection in exome sequencing data. PMID:23089826
High throughput sequencing approaches to mutation discovery in the mouse. PMID:22991087
GENCODE: the reference human genome annotation for The ENCODE Project. PMID:22955987
Systematic localization of common disease-associated variation in regulatory DNA. PMID:22955828
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PMID:22952639
DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. PMID:22893128
SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. PMID:22870267
Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. PMID:22853326
De novo mutations in ATP1A3 cause alternating hemiplegia of childhood. PMID:22842232
Limitations of the human reference genome for personalized genomics. PMID:22811759
Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models. PMID:22724066
Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling. PMID:22698544
Early Diagnosis of Werner's Syndrome Using Exome-Wide Sequencing in a Single, Atypical Patient. PMID:22654791
Linear motifs confer functional diversity onto splice variants. PMID:22638587
Transcriptional enhancers in protein-coding exons of vertebrate developmental genes. PMID:22567096
Comparing the similarity of different groups of bacteria to the human proteome. PMID:22558081
SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update). PMID:22544707
De novo gene disruptions in children on the autistic spectrum. PMID:22542183
Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. PMID:22537301
Identification and characterization of lineage-specific highly conserved noncoding sequences in Mammalian genomes. PMID:22505575
The importance of identifying alternative splicing in vertebrate genome annotation. PMID:22434846
Tracking and coordinating an international curation effort for the CCDS Project. PMID:22434842
DNA sequencing: clinical applications of new DNA sequencing technologies. PMID:22354974
An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia. PMID:22311686
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program. PMID:22199257
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
Targeted sequencing library preparation by genomic DNA circularization. PMID:22168766
Human genetics and genomics a decade after the release of the draft sequence of the human genome. PMID:22155605
Database resources of the National Center for Biotechnology Information. PMID:22140104
neXtProt: a knowledge platform for human proteins. PMID:22139911
The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process. PMID:22127862
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. PMID:22121212
The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. PMID:22102592
Ensembl 2012. PMID:22086963
The UCSC Genome Browser database: extensions and updates 2011. PMID:22086951
An evaluation of different target enrichment methods in pooled sequencing designs for complex disease association studies. PMID:22069447
Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing. PMID:22020387
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. PMID:21994248
A high-resolution map of human evolutionary constraint using 29 mammals. PMID:21993624
The UCSC Genome Browser. PMID:21975940
A comparative analysis of exome capture. PMID:21958622
Comparison of solution-based exome capture methods for next generation sequencing. PMID:21955854
Exome sequencing as a tool for Mendelian disease gene discovery. PMID:21946919
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets. PMID:21932440
Three periods of regulatory innovation during vertebrate evolution. PMID:21852499
A copy number variation morbidity map of developmental delay. PMID:21841781
Whole-exome sequencing identifies compound heterozygous mutations in WDR62 in siblings with recurrent polymicrogyria. PMID:21834044
Thrombospondin-1 and angiotensin II inhibit soluble guanylyl cyclase through an increase in intracellular calcium concentration. PMID:21823650
Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. PMID:21795384
Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. PMID:21787409
Challenges and recommendations for conducting epidemiological studies in the field of epilepsy pharmacogenetics. PMID:21747586
A flexible approach for highly multiplexed candidate gene targeted resequencing. PMID:21738606
Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. PMID:21731509
Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. PMID:21685096
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. PMID:21685081
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. PMID:21685053
Identification of methylated genes associated with aggressive clinicopathological features in mantle cell lymphoma. PMID:21603610
A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. PMID:21602305
Saturation of the human phenome. PMID:21532833
dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. PMID:21520341
MAISTAS: a tool for automatic structural evaluation of alternative splicing products. PMID:21498402
Disease and phenotype data at Ensembl. PMID:21400687
The GENCODE exome: sequencing the complete human exome. PMID:21364695
Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders. PMID:21278187
The Genomic HyperBrowser: inferential genomics at the sequence level. PMID:21182759
Noisy splicing drives mRNA isoform diversity in human cells. PMID:21151575
Enrichment of ultraconserved elements among genomic imbalances causing mental delay and congenital anomalies. PMID:21092253
Ensembl 2011. PMID:21045057
The UCSC Genome Browser database: update 2011. PMID:20959295
T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. PMID:20937630
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. PMID:20929875
genenames.org: the HGNC resources in 2011. PMID:20929869
AnnoTrack--a tracking system for genome annotation. PMID:20923551
Massively parallel sequencing and rare disease. PMID:20846941
Antisense PMO found in dystrophic dog model was effective in cells from exon 7-deleted DMD patient. PMID:20805873
Loss-of-function variants in the genomes of healthy humans. PMID:20805107
Exome sequencing: the sweet spot before whole genomes. PMID:20705737
Comparative Membranome expression analysis in primary tumors and derived cell lines. PMID:20668533
Novel multi-nucleotide polymorphisms in the human genome characterized by whole genome and exome sequencing. PMID:20488869
Consistent annotation of gene expression arrays. PMID:20459806
Between a chicken and a grape: estimating the number of human genes. PMID:20441615
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
International network of cancer genome projects. PMID:20393554
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Mutation patterns in cancer genomes. PMID:19995982
The UCSC Genome Browser. PMID:19957273
The European Bioinformatics Institute's data resources. PMID:19934258
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. PMID:19933760
Exome sequencing identifies the cause of a mendelian disorder. PMID:19915526
DBTSS provides a tissue specific dynamic view of Transcription Start Sites. PMID:19910371
The UCSC Genome Browser database: update 2010. PMID:19906737
Ensembl's 10th year. PMID:19906699
The Universal Protein Resource (UniProt) in 2010. PMID:19843607
The completion of the Mammalian Gene Collection (MGC). PMID:19767417 - http://dx.doi.org/10.1093/nar/gkt1059
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More detailed information about this field from each metasource.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: CCDS; The Consensus CDS; DOI: https://doi.org/10.25504/FAIRsharing.46s4nt; Last edited: April 26, 2021, 11:49 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
gene protein human and other vertebrate genomes model organisms
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