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Cyclebase specifications

Information


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

Taxon


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

Maintainer


  • person_outline Lars Juhl Jensen

Publications for Cyclebase

Cyclebase citations

 (8)
call_split

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

2017
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 cyclebase.org []. T. cruzi orthologues for […]

call_split

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

2017
Oncotarget
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 […]

library_books

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

2015
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 […]

library_books

Identification of yeast cell cycle regulated genes based on genomic features

2013
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 […]

library_books

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

2013
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 […]

library_books

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

2013
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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