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Protocols

OriDB specifications

Information


Unique identifier OMICS_03108
Name OriDB
Alternative name DNA replication Origin DataBase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae

Maintainer


  • person_outline Conrad Nieduszynski

Publications for DNA replication Origin DataBase

OriDB citations

 (9)
library_books

The effects of transcription and recombination on mutational dynamics of short tandem repeats

2017
Nucleic Acids Res
PMCID: 5814968
PMID: 29300948
DOI: 10.1093/nar/gkx1253

[…] lite was then calculated using Bam-readcount (https://github.com/genome/bam-readcount).The locations of replication origins (autonomously replicating sequences) were downloaded from the Saccharomyces DNA Replication Origin Database (http://cerevisiae.oridb.org) and we restricted our analyses to the 352 ‘confirmed’ origins of replication. […]

library_books

Reduced cohesin destabilizes high level gene amplification by disrupting pre replication complex bindings in human cancers with chromosomal instability

2015
Nucleic Acids Res
PMCID: 4737181
PMID: 26420833
DOI: 10.1093/nar/gkv933

[…] red the binding of pre-RC to the APIP/PDHX/CD44 locus in CIN+ SNU16 cells with a highly amplified APIP/PDHX/CD44 locus on HSRs and DMs and HCT116 cells having two copies of APIP/PDHX/CD44. Based on a DNA replication origin database (DeOri; http://tubic.tju.edu.cn/deori/), we identified four DNA replication origins near the APIP/PDHX/CD44 locus (Figure ). pre-RC is composed of several proteins, suc […]

call_split

Replication Coupled PCNA Unloading by the Elg1 Complex Occurs Genome wide and Requires Okazaki Fragment Ligation

2015
Cell Rep
PMCID: 4534484
PMID: 26212319
DOI: 10.1016/j.celrep.2015.06.066
call_split See protocol

[…] on inhibitor hydroxyurea [HU], and late origins as those that do not fire in wild-type but fire in the checkpoint-deficient mutant rad53-11 in HU). Only “confirmed” origins referenced in the database OriDB () were included (i.e., “dubious” and “likely” origins were removed). ChIP-seq data were aligned to origins, and the median enrichment in PCNA signals was plotted. […]

library_books

Mechanism of Gene Amplification via Yeast Autonomously Replicating Sequences

2015
Sci World J
PMCID: 4320851
PMID: 25685838
DOI: 10.1155/2015/387367

[…] model.it, bend.it, SDSC, TwistFlex, EMBOSS, and RNAfold). This analysis was essentially carried out to investigate the role of sequential behaviour of the APS in promoting gene amplification. SGD and oriDB databases were used for collation of information. Also, an effort was made to identify the presence and location of known replication enhancer (RE) sequences and matrix attachment regions (MAR) […]

library_books

The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G quadruplex motifs to prevent DNA damage

2014
BMC Biol
PMCID: 4275981
PMID: 25471935
DOI: 10.1186/s12915-014-0101-5

[…] ibution in S. pombe with known functional genomic regions. We considered the following genome annotations: ORFs, dubious genes, essential genes, highly expressed genes [], origins of replication from OriDB [], telomeres (Webb and VAZ, submitted), LTRs, 5S rRNA, tRNAs, centromeres, NDRs [see Additional file ] [] called using Podbat [], rDNA repeats and meiotic DSB hot spots []. Unless otherwise not […]

library_books

Rif1 Regulates Initiation Timing of Late Replication Origins throughout the S. cerevisiae Genome

2014
PLoS One
PMCID: 4039536
PMID: 24879017
DOI: 10.1371/journal.pone.0098501

[…] lized between replicates. Two experimental replicates were averaged and smoothed again. BrdU peaks were called using MACS (p<0.01) . Called peaks were then cross-referenced against origins defined in OriDB as “confirmed” or “likely” to eliminate any peaks not aligning with an origin. Origin peaks were subjected to DiffBind analysis (FDR <0.05) for calling of differential peak sizes . A final.txt […]

Citations

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OriDB institution(s)
Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, UK
OriDB funding source(s)
Supported by the Royal Society, The University of Nottingham and the Biotechnology and Biological Sciences Research Council (grant numbers BB/E023754/1, BB/G001596/1); David Phillips Fellowship.

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