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ChaperoneNet overview
ChaperoneNet presents co-expression relationships between chaperones per tissue (1). It takes as input a query chaperone and a tissue, and outputs a graphical network view of the query chaperone and its co-expressed chaperones. The user can also define a co-expression threshold, otherwise a default value is used.
The graphical view presents chaperones whose absolute co-expression correlations with the query chaperones exceed a user-defined (or a default) threshold. The threshold, as well as the selected tissue, can be altered dynamically by the user. For the sake of visibility and upload time, the graphical view is limited to at most 100 chaperones.
ChaperoneNet input
Users select a query chaperone and a tissue. They can also define a co-expression threshold, otherwise a default value is used.
The list of chaperones supported by the web-server includes human proteins that were denoted as chaperones in (1), as well as additional genes annotated as chaperones by other studies (2). The list of chaperones is available for download at the website input page.
The tissue menu includes 29 main tissues for which expression data were gathered by the GTEx project. The tissue can be altered dynamically by the user.
The co-expression threshold is absolute, and ranges between zero and one. Co-expression relationships were computed for each pair of chaperones per tissue, by calculating the Spearman correlation between the expression levels of the two chaperones across all samples of that tissue. The co-expression correlation threshold can be altered dynamically by the user.
ChaperoneNet output
The output includes a graphical network view of the query chaperone, which is connected to other chaperones. The absolute expression correlation between the query chaperones and each of the other chaperones exceeds the user-defined (or default) threshold in the selected tissue.
The tissue and the threshold can be changed dynamically by the user.
The graphical view is accompanied by a tabular view. Once the user selects a chaperone from the network view, the tabular view shows the following:
- A property tab that includes chaperone identifiers, chaperone family, differential expression in the selected tissue, core/variable annotation, impact of its mutation on growth, and OMIM accession if one exists.
- A gene ontology (GO) tab that includes its GO annotations and gene description (3).
- A correlation tab. Once an interaction is selected, the tab shows its Spearman correlation across tissues.
- An expression tab, showing the expression level and differential expression of the selected chaperone in each of the 29 human tissues.
Once the user selects an interaction, its Spearman co-expression correlation value appears in the Properties tab.
An additional ‘Graph Options’ tab allows the user to edit the network.
More information about the data sources appears in (1).
References
- Shemesh N+, Jubran J+, Dror S, Simonovsky E, Basha O, Argov CM#, Hekselman I#, Abu-Qarn M, Vinogradov E, Mauer O, Carra S, Ben-Zvi A* and Yeger-Lotem E*. The landscape of molecular chaperones across human tissues reveals a layered architecture of core-variable chaperones. Submitted.
- Brehme M, Voisine C, Rolland T, Wachi S, Soper JH, Zhu Y, Orton K, Villella A, Garza D, Vidal M, Ge H, Morimoto RI. A chaperone subnetwork safeguards proteostasis in aging and neurodegenerative disease. Cell Rep. 2014 9(3):1135-50. doi: 10.1016/j.celrep.2014.09.042.
- Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C High-performance web services for querying gene and variant annotation. Genome Biology 2016 17(1):1-7.
+,# These authors contributed equally to this study.* Correspondence to Prof. Esti Yeger-Lotem, Email: estiyl@bgu.ac.il Prof. Anat Ben-Zvi, Email: anatbz@bgu.ac.il