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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
Publications for CO-eXPRESsed gene database
COXPRESdb: a database of comparative gene coexpression networks of elevenspecies for mammals
COXPRESdb citations
(13)Bioinformatic Analysis of Circadian Expression of Oncogenes and Tumor Suppressor Genes
[…] 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 […]
Dissecting nutrient related co expression networks in phosphate starved poplars
[…] 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 […]
Investigation of the effects of estrogen on skeletal gene expression during zebrafish larval head development
[…] 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 […]
MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation
[…] 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 […]
G Links: a gene centric link acquisition service
[…] 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 […]
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
[…] 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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