As previously stated, the effects of this constant are not considered by the present approach

, 2015 10 / 19 Sub-SPIA Materials and Methods Dataset The first is the CRC dataset, which compares 12 CRC samples with 10 normal samples [71] by using the Affymetrix HG-U133 Plus 2.0 microarray platform (ID = GSE4107). The second dataset, which was initially analyzed by Landi et al. [72], is a lung cancer dataset and is publicly available at the GEO database (accession number GSE10072).This dataset contains 58 tumor samples and 49 normal samples and uses the Affymetrix Human Genome U133A Array. Minimal-Spanning Tree A spanning tree is a subgraph that is PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19666694 a tree and connects all the vertices of the parent graph. Minimal-spanning trees (MSTs) have many applications in telecommunication and transportation-route design. As GS 4059 19667093?dopt=Abstract” title=View Abstract(s)”>PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19667093 mentioned in the introduction, genes in a pathway are generally sparsely connected and the DEGs mapped in it may not be connected directly, so we search for a minimal-spanning tree that includes both the maximum number of signature nodes and the minimum number of non-signature nodes. This concept is more flexible than the k-clique concept for representing a subpathway. After trimming these non-signature nodes in the leaves, we obtain the MST that includes the maximum number of signature nodes and the minimum number of non-signature nodes. Flexibility can be introduced to this subpathway strategy by varying the parameter ns. A smaller value of ns means that only those nodes meeting stricter distance similarities will be added to the corresponding subpathway, and the subpathways thus identified become smaller compared with what happens with larger values of ns. A smaller number of permitted non-signature nodes helps to increase the ratio of signature nodes in the located subpathway regions. In this paper, we

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