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CellBase specifications


Unique identifier OMICS_14259
Name CellBase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Version 4.0.0
Stability Stable
Perl, Ensembl API, MongoDB, Tomcat
Maintained Yes




No version available



  • person_outline Ignacio Medina

Publication for CellBase

CellBase citations


Recent advances in predicting gene–disease associations

PMCID: 5414807
PMID: 28529714
DOI: 10.12688/f1000research.10788.1

[…] nt data sources are constantly updated. One would need to determine whether the different components are using the same database version. A solution would be to use third-party data providers such as CellBase , which provides web services for retrieving biological information from heterogeneous sources to handle data harmonisation across different tools.Unconventional approaches such as crowdsourc […]


The pan cancer pathological regulatory landscape

Sci Rep
PMCID: 5175166
PMID: 28000771
DOI: 10.1038/srep39709

[…] utative TFBSs within the ChIP-seq peaks (details can be found in specific Ensembl web pages). This information is accessible in a more efficient way in different publicly available resources, such as CellBase, whose web services were used here. shows the list of target genes for each TF. […]


Identification of epistatic interactions through genome wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas

BMC Med Genomics
PMCID: 4685628
PMID: 26690675
DOI: 10.1186/s12920-015-0160-7

[…] ion localization was taken from the Human Protein Atlas [] and the GEO repository []. Finally, information about non-coding RNAs was obtained from neXtProt [], NONCODE v4.0 [] and Ensembl through the CellBase application []. […]


Long Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array

PLoS One
PMCID: 3977849
PMID: 24710337
DOI: 10.1371/journal.pone.0093466

[…] tion or tracking. Cells are introduced by simple flow loading, devices are readily available from microfluidic foundries (Caltech, Stanford), and device schematics and software tools are available at cellbase.epfl.ch. […]


VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next Generation Sequencing

Nucleic Acids Res
PMCID: 3394276
PMID: 22693211
DOI: 10.1093/nar/gks572

[…] Tful Web Service API to calculate consequence types has been implemented in Java to make accessible the information contained in the database with simple calls. For example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/genomic/variant/13:32906982:T/consequence_type returns the consequence type of a substitution of the reference base by a T in the position 32906982 of the chromosome 13.http:/ […]


Whole genome bisulfite DNA sequencing of a DNMT3B mutant patient

PMCID: 3398983
PMID: 22595875
DOI: 10.4161/epi.20523

[…] We perform the sequences alignment and methylation calling with version 2.43 of BSMAP software. All genomic information, unless otherwise expressly stated, was obtained using CellBase. SAM/BAM and BED files handling was done using SAMtools and bedtools. Statistical analysis and graphic representation was performed with R (http://www.R-project.org) and libraries multicore a […]


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CellBase institution(s)
Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain; CIBER de Enfermedades Raras, Valencia, Spain; Functional Genomics Node (INB) at CIPF, Valencia, Spain; Research Center on Software Production Methods (ProS). DSIC Universitat Politècnica de València (UPV), Valencia, Spain
CellBase funding source(s)
The Spanish Ministry of Science and Innovation (MICINN) [BIO2011-27069]; the Conselleria de Educacio of the Valencian Community [PROMETEO/2010/001]; National Institute of Bioinformatics (www.inab.org); CIBER de Enfermedades Raras (CIBERER), ISCIII and MICINN; Red Tematica de Investigacion Cooperativa en Cancer (RTICC) [RD06/0020/1019] ISCIII, MICINN and INNPACTO [IPT-010000-2010-43], MICINN.

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