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Gene regulatory network databases | Pathway analysis

HRGRN
Dataset

HRGRN

Offers a way to search and discover the relationships among genes, proteins,…

Offers a way to search and discover the relationships among genes, proteins, compounds and small RNAs in plant signal transduction, metabolism and gene regulatory networks. HRGRN models the…

Regulatory…
Dataset

Regulatory circuits

A comprehensive resource of 394 cell type- and tissue-specific gene regulatory…

A comprehensive resource of 394 cell type- and tissue-specific gene regulatory networks for human, each specifying the genome-wide connectivity among transcription factors, enhancers, promoters and…

KEGG PATHWAY
Dataset

KEGG PATHWAY

Consists in a collection of manually drawn pathway maps. KEGG PATHWAY concerns…

Consists in a collection of manually drawn pathway maps. KEGG PATHWAY concerns mainly molecular interaction, reaction and relation networks for: (1) drug development; (2) human diseases; (3)…

RegTransBase
Dataset

RegTransBase

Consists of two modules - a database of regulatory interactions based on…

Consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites. This literature based information in…

EGRIN
Dataset

EGRIN Environment and Gene Regulatory Influence Network

Provides a gene-gene association network. EGRIN models the condition specific…

Provides a gene-gene association network. EGRIN models the condition specific global transcriptional state of the cell as a function of combinations of transient transcription factor (TF)-based…

SporeWeb
Dataset

SporeWeb

Serves as an interactive knowledge platform about the sporulation cycle of…

Serves as an interactive knowledge platform about the sporulation cycle of Bacillus subtilis.

ccNET
Dataset

ccNET

Facilitates network analysis and gene annotation by (i) presenting…

Facilitates network analysis and gene annotation by (i) presenting co-expression networks with gene expression views in multiple dimensions (tissue-preferential and stress-differential expression…

SCoPNet
Web

SCoPNet Seed Co-Prediction Network

Provides the result of coprediction network using BioHEL with the Arabidopsis…

Provides the result of coprediction network using BioHEL with the Arabidopsis seed gene expression training set. SCoPNet is a computational methodology provides more of 13,500 nodes and 146,500…

MMP
Dataset

MMP Methanococcus maripaludis S2

Provides models of dynamic regulation of all genes in Methanococcus…

Provides models of dynamic regulation of all genes in Methanococcus maripaludis. MMP was created by generating a comprehensive list of coding and noncoding RNAs through comparative analysis of the…

Network portal
Dataset
EndoNet
Web

EndoNet Endosperm Network

Provides coexpression networks for the endosperm. EndoNet is a method developed…

Provides coexpression networks for the endosperm. EndoNet is a method developed for data visualization and mining. It provides a powerful resource to gain further understanding of the roles of…

GSKB
Dataset

GSKB Gene Set Knowledgebase

A comprehensive knowledgebase for pathway analysis in mouse. Interpretation of…

A comprehensive knowledgebase for pathway analysis in mouse. Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack…

ARN
Dataset

ARN Adipogenic Regulation Network

Contains several information and literature about Adipogenesis Regulation…

Contains several information and literature about Adipogenesis Regulation Network. ARN is a database of molecule-molecule regulatory interactions identified via the manual curation of PubMed…

SeedNet
Web

SeedNet Seed Network

Defines accurately seed germination regulators. SeedNet is a network model…

Defines accurately seed germination regulators. SeedNet is a network model describing global transcriptional interactions mediating the maintenance, and transition between, the two discrete…

MTB Network Portal
Dataset

MTB Network Portal Mycobacterium tuberculosis Network Portal

Provides Mycobacterium tuberculosis (MTB) regulatory network data. MTB Network…

Provides Mycobacterium tuberculosis (MTB) regulatory network data. MTB Network Portal was constructed on the basis of large-scale ChIP-seq and expression analyses. It offers detailed definitions of…

miRDR
Dataset

miRDR microRNA Dynamic Regulation Database

Provides data about dynamic miRNA-gene interactions, particularly focusing on…

Provides data about dynamic miRNA-gene interactions, particularly focusing on the conditional interactions that are associated with tumor progression in multiple human cancers. miRDR concerns cancers…

RegCyanoDB
Dataset

RegCyanoDB

Provides regulatory interactions in cyanobacteria. RegCyanoDB contains 20,280…

Provides regulatory interactions in cyanobacteria. RegCyanoDB contains 20,280 interactions with confidence levels for 30 cyanobacterial strains. It provides the computationally predicted regulatory…

ESCAPE
Dataset

ESCAPE Embryonic Stem Cell Atlas from Pluripotency Evidence

A mouse and human embryonic stem cells (m/hESC)-centered database integrating…

A mouse and human embryonic stem cells (m/hESC)-centered database integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep…

CMRegNet
Dataset

CMRegNet

Provides easy access to a total of 3,103 known regulations in C. glutamicum…

Provides easy access to a total of 3,103 known regulations in C. glutamicum ATCC 13032 and M. tuberculosis H37Rv and to 38,940 evolutionary conserved interactions for 18 non-model species of the CMNR…

TRED
Dataset

TRED Transcriptional Regulatory Element Database

A mammalian Transcriptional Regulatory Element Database with associated data…

A mammalian Transcriptional Regulatory Element Database with associated data analysis functions. TRED collects cis- and trans-regulatory elements and is dedicated to easy data access and analysis for…

RegNetwork
Dataset

RegNetwork

A knowledge-based database of gene regulatory networks for human and mouse by…

A knowledge-based database of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among transcription factors (TFs), microRNAs (miRNAs)…

TRRUST
Dataset
SoyFN
Dataset

SoyFN Soybean (Glycine max) Functional Network

A comprehensive web tool about soybean functional gene network (SoyFGN) and…

A comprehensive web tool about soybean functional gene network (SoyFGN) and microRNA functional network (SoymiRFN). SoyFN contains all 37827 genes of the release of UniprotKB version 111 and all 555…

TSmiR
Dataset

TSmiR Tissue Specific miRNA database

A web-searchable database which provides information on interaction maps of…

A web-searchable database which provides information on interaction maps of transcription factor (TF) and tissue-specific (TS) miRNAs from experimentally validated and predicted data. TSmiR covers…

RnR
Dataset

RnR Regulatory-network Research

Provides access to over-expression experiments in Arabidopsis T87 cultured…

Provides access to over-expression experiments in Arabidopsis T87 cultured cells. RnR is a database allowing users to submit a gene or metabolite to study regulatory relationship between gene and…

BacillOndex
Desktop

BacillOndex

A semantically annotated, integrated knowledge database for the model…

A semantically annotated, integrated knowledge database for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of Bacillus subtilis data sources,…

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SYSTOMONAS
Dataset

SYSTOMONAS

Compiles data about the pseudomonas. SYSTOMONAS registers information on eight…

Compiles data about the pseudomonas. SYSTOMONAS registers information on eight different Pseudomonas species and strains, which genomes have been completely sequenced and functionally annotated. The…

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The aMAZE…
Dataset

The aMAZE LightBench

A web interface to the aMAZE relational database, which contains information on…

A web interface to the aMAZE relational database, which contains information on gene expression, catalysed chemical reactions, regulatory interactions, protein assembly, as well as metabolic and…

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