Cyclebase

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More detailed information about this field from each metasource. ×

Cyclebase

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:33.112423

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CycleBase

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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cyclebase

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:33.112423

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Other names: CycleBase, cyclebase

Cyclebase is a database to visualize and download results from genome-wide cell-cycle-related experiments. In addition to genome annotation, Cyclebase also provides mRNA data, protein expression data, and integrated cell-cycle phenotype information from high-content screens and model organism databases.

Webpage:

Licence:

Publications:

Publications

More detailed information about this field from each metasource. ×

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes
PMID: 25378319

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
PMID: 19934261

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:33.112423

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http://dx.doi.org/10.1093/nar/gku1092

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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• Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes PubMed citations: 84.

  84 articles citing: Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

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  GRP75-driven, cell-cycle-dependent macropinocytosis of Tat/pDNA-Ca2+ nanoparticles underlies distinct gene therapy effect in ovarian cancer. PMID:35858873

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  G1/S restriction point coordinates phasic gene expression and cell differentiation. PMID:35760790

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  Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown. PMID:35640599

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  Whi5 is diluted and protein synthesis does not dramatically increase in pre-Start G1. PMID:35482510

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  TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation. PMID:35350773

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  Time-resolved single-cell sequencing identifies multiple waves of mRNA decay during the mitosis-to-G1 phase transition. PMID:35103592

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  CCPE: cell cycle pseudotime estimation for single cell RNA-seq data. PMID:34931240

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  Functional organization of the maternal and paternal human 4D Nucleome. PMID:34877507

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  Endogenous protein tagging in medaka using a simplified CRISPR/Cas9 knock-in approach. PMID:34870593

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  Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles. PMID:34850215

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  Therapeutic Targeting of Cancer: Epigenetic Homeostasis. PMID:34765551

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  Identification of neural progenitor cells and their progeny reveals long distance migration in the developing octopus brain. PMID:34425939

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  Selective therapeutic strategy for p53-deficient cancer by targeting dysregulation in DNA repair. PMID:34253820

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  Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast. PMID:34239087

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  Neural G0: a quiescent-like state found in neuroepithelial-derived cells and glioma. PMID:34101353

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  CENP-A overexpression promotes distinct fates in human cells, depending on p53 status. PMID:33772115

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  Melanoma subpopulations that rapidly escape MAPK pathway inhibition incur DNA damage and rely on stress signalling. PMID:33741929

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  Tos4 mediates gene expression homeostasis through interaction with HDAC complexes independently of H3K56 acetylation. PMID:33713703

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  Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. PMID:33627808

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  Accumulation of cis- and trans-regulatory variations is associated with phenotypic divergence of a complex trait between yeast species. PMID:33609368

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  Pan-Cancer Drivers Are Recurrent Transcriptional Regulatory Heterogeneities in Early-Stage Luminal Breast Cancer. PMID:33531373

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  The transcriptome dynamics of single cells during the cell cycle. PMID:33205894

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  Loss of FZO1 gene results in changes of cell dynamics in fission yeast. PMID:33125111

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  Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells. PMID:33116115

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  Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory. PMID:33046889

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  p50 mono-ubiquitination and interaction with BARD1 regulates cell cycle progression and maintains genome stability. PMID:33024116

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  The Contribution of lincRNAs at the Interface between Cell Cycle Regulation and Cell State Maintenance. PMID:32619701

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  A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels. PMID:32581248

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  Differential Impacts on Host Transcription by ROP and GRA Effectors from the Intracellular Parasite Toxoplasma gondii. PMID:32518180

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  Single-cell transcriptomics of alloreactive CD4+ T cells over time reveals divergent fates during gut graft-versus-host disease. PMID:32484791

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  Targeted Perturb-seq enables genome-scale genetic screens in single cells. PMID:32483332

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  Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes. PMID:32295847

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  Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery. PMID:32176685

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  Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveal coordinate control of lipid metabolism. PMID:32129706

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  Using Transcriptomic Analysis to Assess Double-Strand Break Repair Activity: Towards Precise in vivo Genome Editing. PMID:32085662

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  Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data. PMID:32054475

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  BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. PMID:32042152

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  Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication. PMID:32042151

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  Co-regulation of the antagonistic RepoMan:Aurora-B pair in proliferating cells. PMID:31967936

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  The Tumor Suppressor Role of Zinc Finger Protein 671 (ZNF671) in Multiple Tumors Based on Cancer Single-Cell Sequencing. PMID:31781507

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  Boolean gene regulatory network model of centromere function in Saccharomyces cerevisiae. PMID:31175490

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  Two Distinct E2F Transcriptional Modules Drive Cell Cycles and Differentiation. PMID:31130414

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  Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. PMID:31091168

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  The telomeric Cdc13-Stn1-Ten1 complex regulates RNA polymerase II transcription. PMID:31006804

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  Understanding Human-Virus Protein-Protein Interactions Using a Human Protein Complex-Based Analysis Framework. PMID:30984872

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  A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle. PMID:30833602

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  Single-cell RNA-seq of cultured human adipose-derived mesenchymal stem cells. PMID:30806636

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  Unbiased data mining identifies cell cycle transcripts that predict non-indolent Gleason score 7 prostate cancer. PMID:30616540

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  Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts. PMID:30510006

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  Centromere DNA Destabilizes H3 Nucleosomes to Promote CENP-A Deposition during the Cell Cycle. PMID:30503616

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  Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation. PMID:30355343

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  CancerSEA: a cancer single-cell state atlas. PMID:30329142

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  A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers. PMID:30232014

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  Cycling to Meet Fate: Connecting Pluripotency to the Cell Cycle. PMID:29974052

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  DNA methylation loss in late-replicating domains is linked to mitotic cell division. PMID:29610480

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  Population snapshots predict early haematopoietic and erythroid hierarchies. PMID:29466336

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  Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity. PMID:29294086

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  Transcriptome-wide analysis of the Trypanosoma cruzi proliferative cycle identifies the periodically expressed mRNAs and their multiple levels of control. PMID:29182646

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  Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates. PMID:29069283

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  Gene Expression Signatures and Immunohistochemical Subtypes Add Prognostic Value to Each Other in Breast Cancer Cohorts. PMID:28972043

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  Mitochondria chaperone GRP75 moonlighting as a cell cycle controller to derail endocytosis provides an opportunity for nanomicrosphere intracellular delivery. PMID:28938577

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  Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. PMID:28630425

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  Quantitative Cell Cycle Analysis Based on an Endogenous All-in-One Reporter for Cell Tracking and Classification. PMID:28564611

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  SCnorm: robust normalization of single-cell RNA-seq data. PMID:28418000

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  Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria. PMID:28345074

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  The ribosome-engaged landscape of alternative splicing. PMID:27820807

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  CSL protein regulates transcription of genes required to prevent catastrophic mitosis in fission yeast. PMID:27687771

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  Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. PMID:27670849

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  In silico analysis of the transportome in human pancreatic ductal adenocarcinoma. PMID:27652669

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  Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PMID:27632082

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  Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity. PMID:27611590

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  Principal component analysis based unsupervised feature extraction applied to budding yeast temporally periodic gene expression. PMID:27366210

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  Pseudotime estimation: deconfounding single cell time series. PMID:27318198

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  Evidence for cohesin sliding along budding yeast chromosomes. PMID:27278645

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  Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics. PMID:27134283

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  Cdk1 activity acts as a quantitative platform for coordinating cell cycle progression with periodic transcription. PMID:27045731

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  Circular piecewise regression with applications to cell-cycle data. PMID:26991351

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  Mechanisms of nuclear lamina growth in interphase. PMID:26883443

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  Feedback regulation between atypical E2Fs and APC/CCdh1 coordinates cell cycle progression. PMID:26882548

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  Sense-antisense gene-pairs in breast cancer and associated pathological pathways. PMID:26517092

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  Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development. PMID:26474389

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  Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells. PMID:26387834

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  Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. PMID:26301841

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  Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex. PMID:26217014
• Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results PubMed citations: 34.

  34 articles citing: Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results

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  The evolution and functional divergence of the histone H2B family in plants. PMID:32716939

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  dBMHCC: A comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers. PMID:32497121

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  Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation. PMID:32395662

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  Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. PMID:31091168

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  Phosphoregulation of the oncogenic protein regulator of cytokinesis 1 (PRC1) by the atypical CDK16/CCNY complex. PMID:30992425

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  Lack of a peroxiredoxin suppresses the lethality of cells devoid of electron donors by channelling electrons to oxidized ribonucleotide reductase. PMID:28640807

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  One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin. PMID:28235832

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  Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development. PMID:26474389

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  A new transcription factor for mitosis: in Schizosaccharomyces pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression. PMID:25908789

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  Modeling bi-modality improves characterization of cell cycle on gene expression in single cells. PMID:25032992

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  Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. PMID:24837679

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  Fuzziness and noise in nucleosomal architecture. PMID:24586063

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  Predicting the dynamics of protein abundance. PMID:24532840

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  Cell-cycle regulated transcription associates with DNA replication timing in yeast and human. PMID:24098959

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  Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. PMID:24026178

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  Measurement and modeling of transcriptional noise in the cell cycle regulatory network. PMID:24013422

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  PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes. PMID:23951317

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  Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PMID:23874175

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  Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes. PMID:23793816

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  VAMP4 is required to maintain the ribbon structure of the Golgi apparatus. PMID:23677696

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  Cell cycle-regulated protein abundance changes in synchronously proliferating HeLa cells include regulation of pre-mRNA splicing proteins. PMID:23520512

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  Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer. PMID:23372565

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  Subcellular redistribution and mitotic inheritance of transition metals in proliferating mouse fibroblast cells. PMID:23212029

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  Dynamic hubs show competitive and static hubs non-competitive regulation of their interaction partners. PMID:23118954

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  Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network. PMID:23093924

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  Dynamic deposition of histone variant H3.3 accompanies developmental remodeling of the Arabidopsis transcriptome. PMID:22570629

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  Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. PMID:22373820

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  Transcriptional regulation is a major controller of cell cycle transition dynamics. PMID:22238641

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  A higher-order generalized singular value decomposition for comparison of global mRNA expression from multiple organisms. PMID:22216090

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  Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry. PMID:22046265

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  A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover. PMID:21998594

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  Integrating multiple types of data to predict novel cell cycle-related genes. PMID:21689484

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  Converging evidence of mitochondrial dysfunction in a yeast model of homocysteine metabolism imbalance. PMID:21504896

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  A genetic engineering solution to the "arginine conversion problem" in stable isotope labeling by amino acids in cell culture (SILAC). PMID:20460254
• http://dx.doi.org/10.1093/nar/gku1092

Tags:

Tags

More detailed information about this field from each metasource. ×

cell cycle

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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genome

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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messenger rna

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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model organism

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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phenotype

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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post-translational protein modification

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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protein expression

metasource: Fairsharing.org
version: FAIRsharing.org: Cyclebase; Cyclebase; DOI: https://doi.org/10.25504/FAIRsharing.dOFQ7p; Last edited: Jan. 29, 2020, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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microarray data and other gene expression databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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genotype and phenotype

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:33.112423

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gene transcripts

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:33.112423

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gene expression

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:33.112423

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model organisms

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:33.112423

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cell cycle genome messenger rna model organism phenotype post-translational protein modification protein expression microarray data and other gene expression genotype and phenotype gene transcripts gene expression model organisms