Table 2 - uploaded by Christopher Deboever
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Background
Human disease often arises as a consequence of alterations in a set of associated genes rather than alterations to a set of unassociated individual genes. Most previous microarray-based meta-analyses identified disease-associated genes or biomarkers independent of genetic interactions. Therefore, in this study, we present the first meta-...
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Context 1
... sequence similarity between any two probes (Affymetrix probe set-matched target sequences or Agilent spotted sequences) is defined by subtracting an evolutionary distance value from 1.0, where the evolutionary distance whose domain is [0.0, 1.0] between the two sequences was taken as the branch length of the maximum likelihood tree containing only the two sequences, under a set model of substitution [30]. Table 2 shows a toy example of probe sequence similarity matrix of 3 platforms: PF 1 , PF 2 and PF 3 . We define an identifier PF-P-G which is composed of a plat- form ID, probe ID and gene ID. ...
Context 2
... we extend the toy example stated in the above paragraph to describe this algorithm. Let DS = {DS 1 , DS 2 , DS 3 } be three microarray datasets and M be the probe sequence similarity matrix in Table 2. Assuming EI = {PF 1 -P 1 -G 1 , PF 3 -P 2 -G 3 }, a c-LM will be introduced to the algorithm c-LM identification (Figure 2). ...
Context 3
... et al. reported that protein CXCL14 (top-2) is a member of 8 markers complemen- tary to a currently used marker, alpha-fetoprotein (AFP) [41]. Interestingly, the CXCL14 gene also co-occurred with PPIA in three of our improved c-LMs (#11, #14 and #22 in Additional file 1: Table S2). We postulated that this gene might be the best proxy for the AFP. ...
Citations
... Development of tools for predicting the putative protein sequences, structure, and function of proteins/genes based on DNA sequences [48][49][50][51][52][53][54][55][56][57][58], completing full genome sequences, and building web-based genome databases for many prokaryotic and eukaryotic organisms [58] has provided a great advance in the bioinformatics field. In addition, rapid genome-wide gene expression profiling and analysis opportunities [59][60][61][62], biological pathway assignment and identification, data storing, and mining and querying for large volume of biological datasets [63][64][65][66][67][68][69][70][71][72][73] have further provided unprecedented popularity of bioinformatics in the scene of world science, which has been briefly reviewed below. ...
Bioinformatics is an interdisciplinary scientific field of life sciences. Bioinformatics research and application include the analysis of molecular sequence and genomics data; genome annotation, gene/protein prediction, and expression profiling; molecular folding, modeling, and design; building biological networks; development of databases and data management systems; development of software and analysis tools; bioinformatics services and workflow; mining of biomedical literature and text; and bioinformatics education and training. Astronomical accumulation of genomics, proteomics, and metabolomics data as well as a need for their storage, analysis, annotation, organization, systematization, and integration into biological networks and database systems were the main driving forces for the emergence and development of bioinformatics. Current critical needs for bioinformatics among others highlighted in this chapter, however, are to understand basics and specifics of bioinformatics as well as to prepare new generation scientists and specialists with integrated, interdisciplinary, and multilingual knowledge who can use modern bioinformatics resources powered with sophisticated operating systems, software, and database/networking technologies. In this introductory chapter, I aim to give an overall picture on basics and developments of the bioinformatics field for readers with some future perspectives, highlighting chapters published in this book.
Available for free download at: http://www.intechopen.com/books/bioinformatics-updated-features-and-applications/bioinformatics-basics-development-and-future
