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Cyclebase specifications


Unique identifier OMICS_03307
Name Cyclebase
Restrictions to use None
Version 3.0
Maintained Yes


  • Plants and Fungi
    • Arabidopsis thaliana
  • Primates
    • Homo sapiens


  • person_outline Lars Juhl Jensen

Publications for Cyclebase

Cyclebase citations


Transcriptome wide analysis of the Trypanosoma cruzi proliferative cycle identifies the periodically expressed mRNAs and their multiple levels of control

PLoS One
PMCID: 5705152
PMID: 29182646
DOI: 10.1371/journal.pone.0188441
call_split See protocol

[…] comparison with the human and yeast cell-cycle studies, the putative orthologue genes were determined by one-way blast (tBLASTx), filtering the results with cutoffs of 1E-4 E-value and 50 bit-Score. Cyclebase was taken as the reference database for cell-cycle gene expression, then the lists of periodically regulated genes were retrieved from the website []. T. cruzi orthologues for […]


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

PMCID: 5601673
PMID: 28938577
DOI: 10.18632/oncotarget.17234
call_split See protocol

[…] n predicting N-terminal mTP and calculating the probability of proteins imported into the mitochondria, were used to predict the subcellular localization of EGFP-fused GRP75 proteins. Online database Cyclebase 3.0 [], a multi-organism database on cell-cycle regulation and phenotypes, inside which mRNA and protein expression information based on high-content screens and model organism data integrat […]


Single cell transcriptomic reconstruction reveals cell cycle and multi lineage differentiation defects in Bcl11a deficient hematopoietic stem cells

Genome Biol
PMCID: 4576406
PMID: 26387834
DOI: 10.1186/s13059-015-0739-5

[…] cycle-associated genes in the merged Bcl11a+/+ HSC dataset (Bcl11a+/+ and sBcl11a+/+). We compiled a list of 2212 cell cycle-associated genes based on the annotations in the GO term “cell cycle”, the Cyclebase database and a recent study on G0/G1 transition by Oki et al. [] (Additional file ). PCA was performed to transform the high dimensional expression data into individual linearly uncorrelated […]


Identification of yeast cell cycle regulated genes based on genomic features

BMC Syst Biol
PMCID: 3734186
PMID: 23895232
DOI: 10.1186/1752-0509-7-70

[…] apply the penalized logistic regression (PLR) method to classify yeast genes into cell cycle and non-cell cycle ones. To train the model, a positive and a negative gene set are prepared based on the Cyclebase as described above. From the TF binding and motif features, we pre-select those that are significantly different between the cell cycle and the non-cell cycle gene set (p-value <0.001, the s […]


Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein coding Genes and Non coding RNAs

PLoS Comput Biol
PMCID: 3708869
PMID: 23874175
DOI: 10.1371/journal.pcbi.1003132

[…] d in many studies .We prepared a dataset of cell cycle genes and non-cell cycle genes in HeLa cells that have been experimentally verified with high confidence based on the meta-analysis described in Cyclebase . In the 424 ENCODE ChIP-seq TF binding profiles, 46 were performed in HeLa cells, for which we calculated the regulatory scores using TIP and the average binding signals in a 2 kb DNA regio […]


Genome Wide Assessment of the Association of Rare and Common Copy Number Variations to Testicular Germ Cell Cancer

PMCID: 3557397
PMID: 23372565
DOI: 10.3389/fendo.2013.00002

[…] , ), BioCarta, NCI-Nature curated pathways (Pathway Interaction Database; Schaefer et al., ), GO (Gene Ontology; Ashburner et al., ), COSMIC (Catalog of Somatic Mutations In Cancer; Forbes et al., ), Cyclebase (Gauthier et al., ), protein–protein interaction complexes (Lage et al., ), OMIM (Online Mendelian Inheritance in Man), MGI (Mouse Genome Informatics) and a set of candidate infertility gene […]


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Cyclebase institution(s)
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark

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