Reconstruction of a KEGG pathway

Reconstruction of a KEGG pathway. In this figure we present the KEGG pathway (A) and the reconstructed analogue of our ENFRN-based method. A grey shaded rectangle represents genes that compose a complex. The edges inside these circles are considered as correct edges since genes inside the same circle will co-express with some delay. In blue colour we have correct determined interactions, in dotted blue we have interactions that are true via an intermediate gene and false interactions are indicated in red colour. 71.4% of the interactions extracted were in absolute accordance with biological knowledge, and this percentage rose to 85.7% when considering the interactions that were correct via an intermediate gene.
Reconstruction of a KEGG pathway
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Publication

Gene regulatory networks modelling using a dynamic evolutionary hybrid. (2010) Ioannis A Maraziotis, et al. BMC Bioinformatics. 2010;11:140-140. Figure: F2.

Gene mentions


Organism Group Word Match Source NCBI Symbol NCBI ID
Homo sapiens Primates CLN2 CLN2 ncbigene_synonym TPP1 1200
Homo sapiens Primates CLN3 CLN3 ncbigene_symbol CLN3 1201
Homo sapiens Primates CDC20 CDC20 ncbigene_symbol CDC20 991
Homo sapiens Primates CDC6 CDC6 ncbigene_symbol CDC6 990
Saccharomyces cerevisiae S288C Plants and Fungi FUS3 FUS3 ncbigene_symbol FUS3 852265
Saccharomyces cerevisiae S288C Plants and Fungi CLN2 CLN2 ncbigene_symbol CLN2 855819
Saccharomyces cerevisiae S288C Plants and Fungi CDC28 CDC28 ncbigene_symbol CDC28 852457
Saccharomyces cerevisiae S288C Plants and Fungi SWI4 SWI4 ncbigene_symbol SWI4 856847
Saccharomyces cerevisiae S288C Plants and Fungi CLN3 CLN3 ncbigene_symbol CLN3 851191
Saccharomyces cerevisiae S288C Plants and Fungi CLB6 CLB6 ncbigene_symbol CLB6 853003
Saccharomyces cerevisiae S288C Plants and Fungi CDC20 CDC20 ncbigene_symbol CDC20 852762
Saccharomyces cerevisiae S288C Plants and Fungi CDC6 CDC6 ncbigene_symbol CDC6 853244

Chemical mentions

Word Match MeSH Name ChEBI

Disease mentions

Word Match MeSH Name DOID