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Educational and Software Resources for Data Clustering
Published in Charu C. Aggarwal, Chandan K. Reddy, Data Clustering, 2018
Charu C. Aggarwal, Chandan K. Reddy
To evaluate the biological data clustering, there is a plethora of websites that host gene expression datasets which can be used to evaluate the clustering algorithms. Gene Expression Omnibus (GEO) repository [68] contains a comprehensive collection of gene expression datasets along with raw source files used to generate this data. Gene Expression Model Selector provides a simple repository of the most widely studied gene expression datasets [69] and several other cancer-specific gene expression datasets are available at [70]. Similarly, to test the performance of biological network clustering algorithms, there are a plenty of databases that contain protein-protein interactions. The most popular ones are DIP (Database of Interacting Proteins) [66], BioGRID [67], STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) [65] and MIPS (Mammalian Protein-Protein Interaction Database) [64]. The last resource contains links to several other interaction network databases.
Supportness of the protein complex standards in PPI networks
Published in Journal of Information and Telecommunication, 2022
Milana Grbić, Vukašin Crnogorac, Milan Predojević, Aleksandar Kartelj, Dragan Matić
The rest of 7/16 PPIs, which are newly added to WI-PHI network, now connects the protein YMR116C to the proteins: YER102W, YGR027C, YGR118W, YIL069C, YLR287C-A, YML024W, YNL302C. These proteins had not any interaction inside the considered complex in the started network. Contrary, the situation is pretty different in BioGRID network, since these proteins already have many interactions with other proteins. For example, protein YIL069C has 24 interactions with other proteins in Biogrid network inside the considered complex (Figure 14).