Networks of functional couplings, or functional associations, inferred from high-throughput data and gold standards derived from protein complexes, physical interactions, metabolic pathways and signaling pathways.
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Networks of functional couplings/associations - FunCoup | funcoup.sbc.su.se Reviews
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Networks of functional couplings, or functional associations, inferred from high-throughput data and gold standards derived from protein complexes, physical interactions, metabolic pathways and signaling pathways.
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Data sources and statistics of the latest release - FunCoup
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Sizes of the summary networks with the strongest links from each class for different ranges of final Bayesian scores (FBS). The fist interval corresponds roughly to an confidence score interval of 0.1 to 0.25 the second interval to 0.25 to 0.75 and the last interval to 0.75 to 1. Number of genes (nodes) in the summary networks of the different species. Phylogenetic profile similarity (PHP). Shared transcription factor binding (TFB). Co-miRNA regulation by shared miRNA targeting (MIR). Li and White (2003).
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The name FunCoup [fən kəp] stands for fun. Ling FunCoup is a framework to infer genome-wide functional couplings in 11 model organisms. Functional coupling, or functional association, is an unspecific form of association that encompasses direct physical interaction but also more general types of direct or indirect interaction like regulatory interaction or participation the same process or pathway. Evidence is transfered across species using orthology assignments from InParanoid. Are combined, where inte...
MaxLink search - FunCoup
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Maxlink search for top interactors. Rendering time: 5 ms. Stockholm Bioinformatics Centre 2013. Please enable JavaScript, then refresh this page.
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FC30 A.thaliana full.gz. FC30 C.elegans full.gz. FC30 C.familiaris full.gz. FC30 C.intestinalis full.gz. FC30 D.melanogaster full.gz. FC30 D.rerio full.gz. FC30 G.gallus full.gz. FC30 H.sapiens full.gz. FC30 M.musculus full.gz. FC30 R.norvegicus full.gz. FC30 S.cerevisiae full.gz. The full format is a tab-separated value (TSV) format with the following columns:. The final Bayesian score (FBS) of the strongest coupling class. The Ensembl gene identifier of the gene pair. FC30 A.thaliana compact.gz.
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Comparative Genomics, KB8007, 7.5 ECTS. Applied Bioinformatics, DD2397, 7.5 ECTS at KTH. Introduces elementary programming techniques for Bioinformatics, including script programming, some UNIX basics, and relational databases. Please contact Lars Arvestad. For additional information. The course is offered by CSC. And is held in English in period 2 (Nov/Dec). Omic Data and Systems Biology, DD2399, 7.5 ECTS. Please contact Jens Lagergren. For additional information. The course is offered by CSC.
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Services that are marked with * are not hosted at SBC but were developed fully or partly by people at SBC. Calculate trees from multiple alignments. Consensus fold recognition and meta server with homology modelling. A threading method for membrane proteins. A fold recognition server. A protein model quality predictor. A combined transmembrane topology and signal peptide predictor. Predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Prediction of signal peptides.
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Schibich, D., Gloge, F., Pohner, I., Bjorkholm, P., Wade, R.C., von Heijne, G., Bukau, B. and Kramer, G. (2016) Global profiling of SRP interaction with nascent polypeptides. Nature. Rodriguez, D., Chakraborty, S., Warnick, E., Crane, S., Gao, Z.G., O'Connor, R., Jacobson, K.A. and Carlsson, J. (Epub 2016) Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists. ACS Chem Biol (Epub ahead of print). Heusser, S.A., Yoluk, O., Klement, G., Riederer, E&#...Soderstrom, B...
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FAQ – GeneMANIA documentation
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What biological questions can GeneMANIA answer? How do I interpret GeneMANIA’s results? What makes GeneMANIA unique? How does the GeneMANIA algorithm work? How do I interpret the network weights? What gene identifiers does GeneMANIA recognize? How are networks computed? Where can I download GeneMANIA data? How do I cite GeneMANIA? How do I link to GeneMANIA? What happened to the old, blue version of GeneMANIA? What biological questions can GeneMANIA answer? Find more genes like these. If you enter a gene...
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JSquid is a Java-Applet used for displaying FunCoup. Result graphs. It is based on Medusa. But offers several new features to explore and manipulate the graph. The program is published under the GPLv3. Therefore it is free of charge and can be used and modified by anyone according to the license's policy. JSquid has been published in Bioinformatics. The tutorial for creating XML input files has been added. 2007 · Klammer and Roopra ·.
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Networks of functional couplings/associations - FunCoup
Search for functional couplings. Functional coupling, or functional association, is an unspecific form of association that encompasses direct physical interaction but also more general types of direct or indirect interaction like regulatory interaction or participation the same process or pathway. To search for genes coupled to your genes of interest or for couplings between them enter your genes in the text box and hit the search button. Supported identifier types for the search are:. A set of genes.
FunCoup
Members of the same complex. Which gene/protein IDs to use? Glycolysis / Gluconeogenesis, KEGG00010. Citrate cycle (TCA cycle), KEGG00020. Pentose phosphate pathway, KEGG00030. Pentose and glucuronate interconversions, KEGG00040. Fructose and mannose metabolism, KEGG00051. Galactose metabolism, KEGG00052. Ascorbate and aldarate metabolism, KEGG00053. Starch and sucrose metabolism, KEGG00500. Amino sugar and nucleotide sugar metabolism, KEGG00520. Pyruvate metabolism, KEGG00620. ATP synthesis, KEGG00193.
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