Computational Systems Biology Methods and Protocols.7z
Yan Z, Shah PK, Amin SB, Samur MK, Huang N, Wang X, Misra V, Ji H, Gabuzda D, Li C (2012) Integrative analysis of gene and miRN ...
Zhu R, Zhao Q, Zhao H, Ma S (2016) Inte- grating multidimensional omics data for can- cer outcome. Biostatistics 17(4):605–618. ...
Chapter 8 The Reconstruction and Analysis of Gene Regulatory Networks Guangyong Zheng and Tao Huang Abstract In post-genomic era ...
gxa), an integrative expression database providing differential and baseline expression information [6]. On the other hand, the ...
are standard deviations of genes X and Y, andσRxandσRyare standard deviations of rank variablesXandY. In the recent years, the G ...
CMI measurement between genes X and Y given the gene Z as a condition is defined as follows. CMI XðÞ¼;YjZ X x∈X,y∈Y,z∈Z pxðÞ;y;z ...
maximizing the probability of P(G|D), which means Bayesian model identifies the optimal network topology that best explains the ...
consensus gene connections from different networks are identified based onp-value calculated by the Fisher’s inverse^2 test. Pe ...
x∗iðÞ¼t xiðÞþt uiðÞt, i¼1,2,...m, t¼1, 2,...k xiðÞ¼tþ 1 Xm j¼ 1 bi,jfxjðÞt þviðÞt,fxjðÞt ¼ 1 1 þexj ð 9 Þ wherebi,jpresen ...
network. The incoming degree gives the number of links pointed to the target node. The outgoing degree presents the number of co ...
approaches, such as MCL [33], NEMO [34], and MINE [35], have been proposed to identify highly interconnected gene sets. After ob ...
4 Identification of Disease Gene One of the key applications of network analysis is to identify novel disease genes based on kno ...
This process is repeated until the difference between two states is small enough to stop. At last, each gene on the network will ...
can find the optimal path fromstot[64]. Therefore, ifbhvðÞis set to be the cost of an optimal path fromvtot, which can be found ...
5.3 bnlearn Both the ARACNE and WGCNA software can only build up net- works without directions. Such networks can be fast built ...
6.1 STRING STRING (Search Tool for the Retrieval of Interacting Genes/ Proteins) [70] is technically a protein functional associ ...
References Strogatz SH (2001) Exploring complex net- works. Nature 410(6825):268–276.https:// doi.org/10.1038/35065725 Bray D ( ...
networks. Nat Biotechnol 24(1):51–53. https://doi.org/10.1038/nbt0106-51 Cooper GF (1990) The computational com- plexity of pro ...
Comput Biol 4(7):e1000112. https://doi. org/10.1371/journal.pcbi.1000112 Movahedi S, Van de Peer Y, Vandepoele K Comparative ne ...
cost paths. IEEE Transactions on Systems Sci- ence and Cybernetics 4:100–107 EW D (1959) A note on two problems in connection w ...
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