Mining frequent biological sequences based on bitmap without candidate sequence generation

MpBsmi: A new algorithm for the recognition of continuous biological sequence pattern based on index structure

A significant approach for the discovery of biological regulatory rules of genes, protein and their inheritance relationships is the extraction of meaningful patterns from biological sequence data. The existing algorithms of sequence pattern discovery, like MSPM and FBSB, suffice their low efficiency and accuracy. In order to deal with this issue, this paper presents a new algorithm for biological sequence pattern mining abbreviated MpBsmi based on the data index structure. The MpBsmi algorithm employs a sequence position table abbreviated ST and a sequence database index structure named DB-Index for data storing, mining and pattern expansion. The ST and DB-Index of single items are firstly obtained through scanning sequence database once. Then a new algorithm for fast support counting is developed to mine the table ST to identify the frequent single items. Based on a connection strategy, the frequent patterns are expanded and the expanded table ST is updated by scanning the DB-Index. The fast support counting algorithm is used for obtaining the frequent expansion patterns. Finally, a new pruning technique is developed for extended pattern to avoid the generation of unnecessarily large number of candidate patterns. The experiments results on multiple classical protein sequences from the Pfam database validate the performance of the proposed algorithm including the accuracy, stability and scalability. It is showed that the proposed algorithm has achieved the better space efficiency, stability and scalability comparing with MSPM, FBSB which are the two main algorithms for biological sequence mining.

A global view of regulatory networks in lung cancer: An approach to understand homogeneity and heterogeneity

A number of new biotechnologies are used to identify potential biomarkers for the early detection of lung cancer, enabling a personalized therapy to be developed in response. The combinatorial cross-regulation of hundreds of biological function-specific transcription factors (TFs) is defined as the understanding of regulatory networks of molecules within the cell. Here we integrated global databases with 537 patients with lung adenocarcinoma (ADC), 140 with lung squamous carcinoma (SCC), 9 with lung large-cell carcinoma (LCC), 56 with small-cell lung cancer (SCLC), and 590 without cancer with the understanding of TF functions. The present review aims at the homogeneity or heterogeneity of gene expression profiles among subtypes of lung cancer. About 5, 136, 52, or 16 up-regulated or 19, 24, 122, or 97down-regulated type-special TF genes were identified in ADC, SCC, LCC or SCLC, respectively. DNA-binding and transcription regulator activity associated genes play a dominant role in the differentiation of subtypes in lung cancer. Subtype-specific TF gene regulatory networks with elements should be an alternative for diagnostic and therapeutic targets for early identification of lung cancer and can provide insightful clues to etiology and pathogenesis.