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GeneFriends: a human RNA-seq-based gene and transcript co-expression database.

van Dam S, Craig T, de Magalhães JP - Nucleic Acids Res. (2014)

Bottom Line: Co-expression networks have proven effective at assigning putative functions to genes based on the functional annotation of their co-expressed partners, in candidate gene prioritization studies and in improving our understanding of regulatory networks.The results users obtain from GeneFriends include a co-expression network as well as a summary of the functional enrichment among the co-expressed genes.Furthermore, our updated tool allows candidate transcripts to be linked to diseases and processes using a guilt-by-association approach.

View Article: PubMed Central - PubMed

Affiliation: Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

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Related in: MedlinePlus

A graphical overview of the steps involved in retrieving results from GeneFriends: (1) Insert genes (2) Validate input (3) Retrieve co-expressed genes (4) Investigate functional enrichment (5) Visualize network of co-expressed genes using Bioloayout (6) Use Biololayout to select the network of interest selecting different thresholds.
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Figure 2: A graphical overview of the steps involved in retrieving results from GeneFriends: (1) Insert genes (2) Validate input (3) Retrieve co-expressed genes (4) Investigate functional enrichment (5) Visualize network of co-expressed genes using Bioloayout (6) Use Biololayout to select the network of interest selecting different thresholds.

Mentions: To employ GeneFriends the user can submit one or multiple gene/transcript IDs. The results then contain the following sections: (i) a list of the 50 strongest co-expressed genes and the corresponding HGNC annotation for each gene; (ii) a list of the 25 strongest co-expressed transcription factors; (iii) top 20 functional enrichment categories of the co-expressed list of genes, including GO (42), KEGG (43) and OMIM (44). To assess functional enrichment among the co-expressed genes, DAVID web services (45) are used, which is a commonly used tool to assess overrepresentation of functional categories among a list of genes. To obtain the DAVID web results the top 1500 co-expressed genes/transcripts are used (or fewer if there are fewer genes significantly co-expressed (cutoff P-value < 10−6; since correction for multiple testing using the Bonferroni correction: 0.05/44248 = 1.12*10−6 (13)). Additionally, full lists can be downloaded, as well as a network file that can be imported into Biolayout (46) or Cytoscape (47) for visualization and further analyses. Lastly, there is an option to download the functional enrichment of those genes that have an expression pattern which negatively correlates with the expression of the gene(s) of interest, thus those genes with an opposing expression pattern. This is especially interesting for genes/RNAs that downregulate expression of others. Further details can be found on http://www.GeneFriends.org/RNAseq/about/. A graphical overview of the steps involved in retrieving results from GeneFriends is depicted in Figure 2.


GeneFriends: a human RNA-seq-based gene and transcript co-expression database.

van Dam S, Craig T, de Magalhães JP - Nucleic Acids Res. (2014)

A graphical overview of the steps involved in retrieving results from GeneFriends: (1) Insert genes (2) Validate input (3) Retrieve co-expressed genes (4) Investigate functional enrichment (5) Visualize network of co-expressed genes using Bioloayout (6) Use Biololayout to select the network of interest selecting different thresholds.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383890&req=5

Figure 2: A graphical overview of the steps involved in retrieving results from GeneFriends: (1) Insert genes (2) Validate input (3) Retrieve co-expressed genes (4) Investigate functional enrichment (5) Visualize network of co-expressed genes using Bioloayout (6) Use Biololayout to select the network of interest selecting different thresholds.
Mentions: To employ GeneFriends the user can submit one or multiple gene/transcript IDs. The results then contain the following sections: (i) a list of the 50 strongest co-expressed genes and the corresponding HGNC annotation for each gene; (ii) a list of the 25 strongest co-expressed transcription factors; (iii) top 20 functional enrichment categories of the co-expressed list of genes, including GO (42), KEGG (43) and OMIM (44). To assess functional enrichment among the co-expressed genes, DAVID web services (45) are used, which is a commonly used tool to assess overrepresentation of functional categories among a list of genes. To obtain the DAVID web results the top 1500 co-expressed genes/transcripts are used (or fewer if there are fewer genes significantly co-expressed (cutoff P-value < 10−6; since correction for multiple testing using the Bonferroni correction: 0.05/44248 = 1.12*10−6 (13)). Additionally, full lists can be downloaded, as well as a network file that can be imported into Biolayout (46) or Cytoscape (47) for visualization and further analyses. Lastly, there is an option to download the functional enrichment of those genes that have an expression pattern which negatively correlates with the expression of the gene(s) of interest, thus those genes with an opposing expression pattern. This is especially interesting for genes/RNAs that downregulate expression of others. Further details can be found on http://www.GeneFriends.org/RNAseq/about/. A graphical overview of the steps involved in retrieving results from GeneFriends is depicted in Figure 2.

Bottom Line: Co-expression networks have proven effective at assigning putative functions to genes based on the functional annotation of their co-expressed partners, in candidate gene prioritization studies and in improving our understanding of regulatory networks.The results users obtain from GeneFriends include a co-expression network as well as a summary of the functional enrichment among the co-expressed genes.Furthermore, our updated tool allows candidate transcripts to be linked to diseases and processes using a guilt-by-association approach.

View Article: PubMed Central - PubMed

Affiliation: Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

Show MeSH
Related in: MedlinePlus