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Pathway topology
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CTCF binding to DNA helps partition the mammalian genome into discrete structural and regulatory domains. Complete removal of CTCF from mammalian cells causes catastrophic genome dysregulation, likely due to widespread collapse of 3D chromatin looping and alterations to inter- and intra-TAD interactions within the nucleus.
17p
vigalileogalilei
27-02-2022
13
1
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Pathway analysis is widely applied in transcriptome analysis. Given certain transcriptomic changes, current pathway analysis tools tend to search for the most impacted pathways, which provides insight into underlying biological mechanisms.
12p
vijeeni2711
30-06-2021
7
1
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A flood-based information flow analysis and network minimization method for gene regulatory networks
Biological networks tend to have high interconnectivity, complex topologies and multiple types of interactions. This renders difficult the identification of sub-networks that are involved in condition- specific responses. In addition, we generally lack scalable methods that can reveal the information flow in gene regulatory and biochemical pathways.
12p
viwyoming2711
16-12-2020
9
1
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Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn.
10p
vikentucky2711
26-11-2020
13
3
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Adjusting the capacity of metabolic pathways in response to rapidly changing environmental conditions is an important component of microbial adaptation strategies to stochastic environments.
13p
vikentucky2711
24-11-2020
10
2
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Discovering robust markers for cancer prognosis based on gene expression data is an important yet challenging problem in translational bioinformatics. By integrating additional information in biological pathways or a protein-protein interaction (PPI) network, we can find better biomarkers that lead to more accurate and reproducible prognostic predictions.
10p
vioklahoma2711
19-11-2020
11
0
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Pathway analysis methods, in which differentially expressed genes are mapped to databases of reference pathways and relative enrichment is assessed, help investigators to propose biologically relevant hypotheses.
8p
vioklahoma2711
19-11-2020
9
1
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Autophagy is a conserved molecular pathway involved in the degradation and recycling of cellular components. It is active either as response to starvation or molecular damage. Evidence is emerging that autophagy plays a key role in the degradation of damaged cellular components and thereby affects aging and lifespan control.
15p
vioklahoma2711
19-11-2020
13
1
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Pathway enrichment analysis is extensively used in the analysis of Omics data for gaining biological insights into the functional roles of pre-defined subsets of genes, proteins and metabolites. A large number of methods have been proposed in the literature for this task.
14p
vicolorado2711
23-10-2020
10
1
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To identify and prioritize the influential hub genes in a gene-set or biological pathway, most analyses rely on calculation of marginal effects or tests of statistical significance. These procedures may be inappropriate since hub nodes are common connection points and therefore may interact with other nodes more often than non-hub nodes do. Such dependence among gene nodes can be conjectured based on the topology of the pathway network or the correlation between them.
11p
vicolorado2711
22-10-2020
8
0
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Homology modeling in combination with transmembrane topology predictions are used to build the atomic model of Neurospora crassaplasmamembrane H + -ATPase, using as template the 2.6 A ˚ crystal structure of rabbit sarcoplasmic reticulum Ca 2+ -ATPase [Toyoshima, C., Nakasako, M., Nomura, H. & Ogawa, H. (2000)Nature405, 647–655].
13p
tumor12
22-04-2013
33
2
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Each router has a full picture of the network topology, including bandwidth information for links to remote networks. Therefore, each router is able to independently select a loop-free and efficient pathway, based on cost, to reach every network in the area.
31p
danhson1409
02-12-2010
65
6
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