dbOrtho statistics

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Citations per year

Number of citations per year for the bioinformatics software tool dbOrtho
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Tool usage distribution map

This map represents all the scientific publications referring to dbOrtho per scientific context
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Associated diseases

This word cloud represents dbOrtho usage per disease context
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Popular tool citations

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Protocols

dbOrtho specifications

Information


Unique identifier OMICS_31299
Name dbOrtho
Interface Web user interface
Restrictions to use None
Input data An ID list and a organism of interest.
Output data A two-columns table including the inputs and the wanted ID and organisms.
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
    • Plasmodium falciparum
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Arabidopsis thaliana
    • Oryza sativa
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

Maintainer


  • person_outline Robert Stephens

Additional information


https://biodbnet-abcc.ncifcrf.gov/dbInfo/faq.php

Publication for dbOrtho

dbOrtho citations

 (4)
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The RBM14/CoAA interacting, long intergenic non coding RNA Paral1 regulates adipogenesis and coactivates the nuclear receptor PPARγ

2017
Sci Rep
PMCID: 5658386
PMID: 29075020
DOI: 10.1038/s41598-017-14570-y
call_split See protocol

[…] GEO dataset GSE21069 . Human WAT RNAs were analysed as described.Human gene symbols were attributed to each murine gene using the Orthologue Conversion software (https://biodbnet-abcc.ncifcrf.gov/db/dbOrtho.php) and resulting files were analysed with the GSEA software [Broad Institute, v2.2.2]. Pathway-enrichment scores were calculated with the GSEA pre-ranking tool and the KEGG Pathway gene set. […]

library_books

Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis

2016
Oncotarget
PMCID: 4914272
PMID: 26933814
DOI: 10.18632/oncotarget.7728

[…] sly, 7704 genes were identified as HIF binding targets [, ]. After conversion of zebrafish genes to their corresponding human orthologs using the conversion tools (http://biodbnet.abcc.ncifcrf.gov/db/dbOrtho.php, http://david.abcc.ncifcrf.gov) we identified a total of 76 genes induced during regeneration that were previously reported to be HIF-associated gene targets in human cells, suggesting tha […]

call_split

Evolutionary Footprints of Short Tandem Repeats in Avian Promoters

2016
Sci Rep
PMCID: 4725869
PMID: 26766026
DOI: 10.1038/srep19421
call_split See protocol

[…] The gene ID converter (dbOrtho) implemented in the biological database network or BioDBnet was used to search for orthologous genes between chicken and other birds. Next, we investigated the ratio of STR motifs identified i […]

library_books

Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population specific expression analysis

2015
Front Neurosci
PMCID: 4288238
PMID: 25620908
DOI: 10.3389/fnins.2014.00441

[…] 2.0 microarray platform. To compare our PSEA-based expression predictions from human tissues to the mouse data, murine probesets were annotated with current corresponding HGNC gene assignments using dbOrtho tool in bioDBnet (Mudunuri et al., ) and the list of probesets for which PSEA achieved suitable expression models (Tables , ) were reduced to unique HGNC ids. Then for each assignment of expre […]


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dbOrtho institution(s)
Advanced Biomedical Computing Center, Advanced Technology Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD, USA
dbOrtho funding source(s)
Supported by National Cancer Institute; National Institutes of Health (contract N01-CO-12400).

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