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Differential expression of nodes at 12 h is highlighted.
The expression of initial cell type node decreases rapidly in the first several cell cycles; the expression of ESC node increases rapidly from 11th cell cycle on; the expression of upper level neighbor and sibling node first increases and then decreases; the expression of nodes in lineages other than that of the initial cell type remain near zero.
For example, x B (t + 1) for the node B in Figure 1 is defined in Equation (6), where f B, f A and f O are defined in Equations (1), (4) and (3) respectively, and x C t and x E t represent the expression of nodes C and E at the time instant t. (6) A snapshot of the activity level of all the genes in the network at time t is called the state of the network.
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However, the different expression levels of nodes in different tissue types might suggest otherwise.
Visual linking is superior to traditional gene expression augmentation of nodes because it is not limited to the small area on top of the nodes.
The connection weights between any pair of two nodes i and j were computed by where corr i, j) is the correlation between the expression levels of nodes i and j across all stages.
It should be noted that an edge between two nodes does not necessarily indicate a causal interaction between these nodes as it could equally be interpreted as co-regulated expression of both nodes by a common regulator.
We compared this transportation network with two transcriptional regulatory networks, which relate the expression of genes (nodes) that interact by producing proteins, termed transcription factors, that may alter the expression level of other genes.
Where k = 3, p1 and p2 are the p-values of differential expression of two nodes, p3 is the p-value of their co-expression.
Aberrant expression of central nodes of such ceRNA networks may cause a disturbance that could contribute to disease pathogenesis [ref-2].
Differential expression of metabolite nodes are superimposed onto network graphs to help with the interpretation of their involvement in metabolic networks and facilitate biological interpretation.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com