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Gene co-expression databases | Gene expression data analysis

Coexpression analysis is a powerful, widely used methodology for the investigation of underlying patterns in gene expression data. This "guilt-by-association" approach aims to find groups of genes with closely correlated expression profiles.…
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ATTED-II
Dataset

ATTED-II

A coexpression database for plant species, which provides a parallel view of…

A coexpression database for plant species, which provides a parallel view of multiple coexpression data sets with network analysis tools. The user can effectively find functional gene relationships…

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COXPRESdb
Dataset

COXPRESdb COeXPRESsion database

Provides coexpression relationships for multiple animal species, as comparisons…

Provides coexpression relationships for multiple animal species, as comparisons of coexpressed gene lists can enhance the reliability of gene coexpression determinations. New developments greatly…

SoyNet
Dataset

SoyNet

A database of soybean co-functional networks and a companion web tool for…

A database of soybean co-functional networks and a companion web tool for network-based functional predictions. SoyNet maps 1 940 284 co-functional links between 40 812 soybean genes (covering 72.8%…

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COEXPEDIA
Dataset

COEXPEDIA

Contains information about co-expressions. COEXPEDIA gathers co-expressions…

Contains information about co-expressions. COEXPEDIA gathers co-expressions from individual studies associated with medical subject headings (MeSH) and calculated from a statistical test for…

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RiceFREND
Dataset

RiceFREND

A rice gene coexpression database to identify gene modules with similar…

A rice gene coexpression database to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions.

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Retina
Dataset

Retina

An accurate and high-resolution atlas of gene expression and gene co-regulation…

An accurate and high-resolution atlas of gene expression and gene co-regulation in human retina. We collected 50 high-quality post-mortem human retinas from donors and performed high-coverage…

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CoxPathDB
Dataset

CoxPathDB CO-eXpressed PATHways DataBase for tomato

Provides a ranked list of pathways in which higher-ranked pathways are more…

Provides a ranked list of pathways in which higher-ranked pathways are more likely related to each tomato gene. CoxPathDB can be used to predict the function of tomato genes from the results of…

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GeneFriends
Dataset

GeneFriends

Employs a RNAseq based gene co-expression network for candidate gene…

Employs a RNAseq based gene co-expression network for candidate gene prioritization, based on a seed list of genes, and for functional annotation of unknown genes in humans. GeneFriends is freely…

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FamNet
Dataset

FamNet

Allows the user to retrieve conserved and multiplied modules across and within…

Allows the user to retrieve conserved and multiplied modules across and within eight plant species. FamNet detects conserved association between Pfam and PLAZA labels in the co-expression networks.…

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AraNet
Web

AraNet

A probabilistic functional gene network for Arabidopsis thaliana, which is a…

A probabilistic functional gene network for Arabidopsis thaliana, which is a model plant organism that has been studied intensively for several decades. AraNet v2 is an improved version of AraNet by…

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ImmuCo
Dataset

ImmuCo

A cell-specific database that contains information about gene co-expression in…

A cell-specific database that contains information about gene co-expression in immune cells, identifying co-expression and correlation between any two genes. The strength of co-expression of queried…

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ALCOdb
Dataset

ALCOdb Algae Gene Coexpression database

Provides microalgal gene coexpression information with a user-friendly…

Provides microalgal gene coexpression information with a user-friendly interface. ALCOdb currently supports two model algae: the green alga Chlamydomonas reinhardtii and the red alga Cyanidioschyzon…

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TENOR
Dataset

TENOR Transcriptome ENcyclopedia Of Rice

A database that encompasses large-scale mRNA sequencing (mRNA-seq) data…

A database that encompasses large-scale mRNA sequencing (mRNA-seq) data obtained from rice under a wide variety of conditions. We used mRNA-seq and performed a time-course transcriptome analysis of…

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coexpressMAP
Dataset

coexpressMAP

Allows to search differences in co-expression between human and mouse.…

Allows to search differences in co-expression between human and mouse. coexpressMAP facilitates inquiry into the differences and similarities of general co-expression relationships between the human…

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PODC
Dataset

PODC Plant Omics Data Center

A web repository for NGS transcriptomes and gene expression networks (GENs)…

A web repository for NGS transcriptomes and gene expression networks (GENs) with an interactive network viewer. Compared with existing GEN databases, the content depth of NGS mRNA-Seq data in our…

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KAGIANA
Dataset

KAGIANA Kazusa Arabidopsis Gene Information And Network Analysis

Allows retrieval of summary information about Arabidopsis genes. KAGIANA…

Allows retrieval of summary information about Arabidopsis genes. KAGIANA summarizes various Arabidopsis omics analyses from databases and tools and provides links to pages for genes of interest in…

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EXPath
Dataset

EXPath

A database resource that collects and utilizes gene expression profiles derived…

A database resource that collects and utilizes gene expression profiles derived from microarray platforms under various conditions to infer metabolic pathways for plants. EXPath was developed to not…

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PAN
Dataset

PAN PlantArrayNet

Provides co-expression information between genes in terms of correlation…

Provides co-expression information between genes in terms of correlation coefficients from accumulated microarray data. Given the correlation of a gene pair, the degrees of closeness between gene…

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ViBrism
Dataset

ViBrism Virtual Brain with 3D-ISM

Offers a comprehensive spatial overview of gene expression patterns of the…

Offers a comprehensive spatial overview of gene expression patterns of the mouse brain. ViBrism provides more than 36,000 expression maps of the adult mouse brain and 45,000 expression maps of each…

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CSB.DB
Dataset

CSB.DB Comprehensive Systems-Biology DataBase

Presents the results of bio-statistical analyses on gene expression data in…

Presents the results of bio-statistical analyses on gene expression data in association with additional biochemical and physiological knowledge. The main aim of CSB.DB is to provide tools that…

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CoP
Dataset

CoP Co-expressed biological Processes

A database for associating co-expressed gene modules with biological…

A database for associating co-expressed gene modules with biological information such as gene ontology terms and, if available, metabolic pathway names. The database includes the gene modules for…

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CGCDB
Dataset

CGCDB CHO Gene Coexpression Database

Aims to provide access to gene coexpression patterns derived from the…

Aims to provide access to gene coexpression patterns derived from the microarray analysis of transcript expression during industrial cell culture of CHO. Users can access correlations between pairs…

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VTCdb
Dataset

VTCdb ViTis Co-expression DataBase

Offers an online platform for transcriptional regulatory inference in the…

Offers an online platform for transcriptional regulatory inference in the cultivated grapevine. VTCdb provides users to query gene(s), modules or biological processes of interests in several ways.…

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PLANEX
Dataset

PLANEX PLAnt co-EXpression database

An internet-based database for plant gene analysis. PLANEX contains publicly…

An internet-based database for plant gene analysis. PLANEX contains publicly available GeneChip data obtained from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology…

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COXSIMdb
Dataset

COXSIMdb COeXpression SIMilarity database

Provides a list of genes, with a view of the results of the coexpression…

Provides a list of genes, with a view of the results of the coexpression conservation of a gene.

RiceNet
Dataset

RiceNet

A genome-scale functional network server constructed by integrating diverse…

A genome-scale functional network server constructed by integrating diverse genomics data and demonstrated the use of the network in genetic dissection of rice biotic stress responses and its…

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