COXPRESdb statistics

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Protocols

COXPRESdb specifications

Information


Unique identifier OMICS_02876
Name COXPRESdb
Alternative name CO-eXPRESsed gene database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 7.1
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

Documentation


Maintainer


  • person_outline Kengo Kinoshita

Additional information


http://coxpresdb.jp/top_help.shtml http://coxpresdb.jp/overview.shtml

Publications for CO-eXPRESsed gene database

COXPRESdb citations

 (13)
call_split

Bioinformatic Analysis of Circadian Expression of Oncogenes and Tumor Suppressor Genes

2017
Bioinform Biol Insights
PMCID: 5734456
PMID: 29276378
DOI: 10.1177/1177932217746991
call_split See protocol

[…] COXPRESdb database (http://coxpresdb.jp) was used to analyze the coexpression between Notable Oncogenes/TSGs, selected by cluster analysis, and their corresponding circadian genes/CCGs. The COXPRESdb […]

library_books

Dissecting nutrient related co expression networks in phosphate starved poplars

2017
PLoS One
PMCID: 5319788
PMID: 28222153
DOI: 10.1371/journal.pone.0171958

[…] sts were tested with p ≤ 0.01 against a “population” data set consisting of all genes present on the array as described above. Enriched GO terms were displayed using GOPathDrawer (version 6.0, http://coxpresdb.jp/top_draw.shtml). For an overview, significant GO terms were uploaded into REVIGO (http://revigo.irb.hr/, accessed October 2016; []), which used the GO term version Jul 2015 monthly releas […]

call_split

Investigation of the effects of estrogen on skeletal gene expression during zebrafish larval head development

2016
PeerJ
PMCID: 4824909
PMID: 27069811
DOI: 10.7717/peerj.1878
call_split See protocol

[…] facial skeletal formation/morphogenesis ( and ). Finally, we extended our list of candidates by adding more genes showing co-expression with the estrogen receptor esr1 based on the zebrafish database COXPRESdb (http://coxpresdb.jp/) version 6.0 (). To obtain the maximum number of coexpressed genes with a high degree of reliability, we filtered the genes by setting the mutual rank (MR) to the top-r […]

library_books

MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation

2015
J Immunol Res
PMCID: 4735977
PMID: 26881263
DOI: 10.1155/2015/140819

[…] coexpression databases peculiarly for mammals recently have been established and widely used by researchers and have thus accelerated the coexpression analysis process in the field of bioinformatics. COXPRESdb [] was constructed with gene expression data from 63 human tissues and it utilizes the correlation rank to compare the coexpression strengths among multiple species. The database GeneFriends […]

library_books

G Links: a gene centric link acquisition service

2015
F1000Res
PMCID: 4670005
PMID: 26673001
DOI: 10.5256/f1000research.6153.r6750

[…] ted Values (TSV) text format for programmatic access. The HTML format displays a gallery of image resources on the top, such as the pathway maps from KEGG database ( ), co-expressed gene network from COXPRESdb ( ), and protein 3D structure from Protein Data Bank ( ), followed by a long table of text annotations and cross-references including database name, ID, and resource URL. shows an overview […]

library_books

The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA seq in Humans Improve Normalization of Neonatal Equine Ovary RT qPCR Data

2015
PLoS One
PMCID: 4633174
PMID: 26536597
DOI: 10.1371/journal.pone.0142122

[…] it was ranked ahead of all single genes.In order to exclude the association of highly coexpressed genes which could affect the stability of the normalization factor, coexpression was identified with COXPRESdb [] software, which calculates Pearson’s correlation coefficient for each gene pair, and then transfers these values to the mutual rank value, which is the geometric average of asymmetric ran […]

Citations

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COXPRESdb institution(s)
Graduate School of Information Sciences, Tohoku University, Sendai, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
COXPRESdb funding source(s)
Supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED [JP187am0101067].

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