| title | description | published | date | tags | editor |
|---|---|---|---|---|---|
FANTOM |
Designed with the idea that network predictions should be made available in an easily queriable format that will allow end user biologists to extract from the high level fuzzball of an entire network, intuitive views of the genes. |
true |
2020-08-27 17:08:05 UTC |
genes, proteins, database, data visualization, gene expression, model organism, eukaryota, interaction, networks, organism-specific |
markdown |
FANTOM4-EEDB (Edge Express DB) was designed with the idea that network predictions should be made available in an easily queriable format that will allow end user biologists to extract from the high level fuzzball of an entire network, intuitive views of the genes that they are currently studying.
For FANTOM4 the temporal expression patterns of mRNAs, microRNAs, and promoters, were measured in a human myeloid leukemia cell line undergoing differentiation. Using the expression profiles, and promoter regions identified by deep sequencing of Cap Analysis of gene expression (deepCAGE), expression weighted transcription factor binding sites were predicted. Thereby allowing us to predict regulatory EDGES between a transcription factor and a target promoter (of a gene/miRNA), and place a weight on the likelihood that the transcription factor truly regulates the expression of the promoter.
In addition to predicted TF-> target gene edges we also assembled a combination of siRNA perturbation edges, chromatin immunoprecipitation edges, protein-protein interaction edges and miRNA target gene edges.
For users interested in what the FANTOM4 data can tell you about gene regulation, please try a search for your favourite gene using the gene centric view. Alternatively if you are interested in the way a set of genes may interact try the subnet view. For an example demonstrating these views please click here and for an explanation of edge types and nodes click here.
EdgeExpressDB (EEDB) is a novel database which is designed for integrating and interpreting large high-throughput expression datasets in the context of biological networks. For those interested in installing your own instances of EEDB the source code is available via CPAN and is being further developed within the Omics Science Center by Jessica Severin. Please feel free to contact us at this address . {.is-info}
- FANTOM EEDB About
- Edge Express Main Center View
- Edge Express Networks Subnet View
- FANTOM Genome Browser THP-1 Genome Browser {.links-list}
- Best for comparative work on proteins/genes conserved in bacteria and proteins (database is human/mouse specific)
- Limited in scope, but useful for comparisons due to tools available; allows for gene-focused view of expression and visualization of interaction networks
- Easy to use; easy to navigate
- Users may benefit from prior knowledge of gene/protein names, etc.
- J. Severin et al., FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions Genome Biology volume 10, Article number: R39 (2009)
- H. Kawaji et al., The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation Genome Biology volume 10, Article number: R40 (2009) {.grid-list}