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Network enrichment analysis
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Biological interpretation of genomic summary data such as those resulting from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies is one of the major bottlenecks in medical genomics research, calling for efficient and integrative tools to resolve this problem.
20p
vioraclene
31-03-2024
7
1
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Basal cell carcinoma (BCC) of the skin is the most common form of human cancer, with more than 90% of tumours presenting with clear genetic activation of the Hedgehog pathway. However, polygenic risk factors affecting mechanisms such as DNA repair and cell cycle checkpoints or which modulate the tumour microenvironment or host immune system play significant roles in determining whether genetic mutations culminate in BCC development.
12p
vibransone
28-03-2024
3
2
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Pathway enrichment analysis (PEA) is a common method for exploring functions of hundreds of genes and identifying disease-risk pathways. Moreover, diferent pathways exert their functions through crosstalk.
20p
viellison
28-03-2024
2
1
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Ebook "Transformation and sustainability in agriculture: Connecting practice with social theory" shows that for upscaling novel practices and organizational models it is important to include meso-level regime aspects in analysis and practice. The argument presented is that our understanding of the human and social dimensions of transformation processes can be enriched by anchoring practice and policy in social theory. A focus on transitions offers a clear view on the direction and velocity of change.
158p
tachieuhoa
28-01-2024
5
2
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Continued part 1, part 2 of ebook "Event management guide" provide readers with content about: configuring event enrichment; configuring event gateway plug-ins; configuring root-cause analysis; configuration of the probe for tivoli Netcool/OMNIbus;... Please refer to the part 2 of ebook for details!
106p
langmongnhu
14-12-2022
10
7
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A bottleneck in high-throughput functional genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Gene Ontology (GO) enrichment methods provide insight at the gene set level.
35p
viarchimedes
26-01-2022
6
0
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Despite the introduction of targeted therapies, most patients with myeloid malignancies will not be cured and progress. Genomics is useful to elucidate the mutational landscape but remains limited in the prediction of therapeutic outcome and identification of targets for resistance.
15p
vimahuateng
26-11-2021
13
1
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A promising approach for solving this problem is to compare gene networks built using experimental gene sets with random networks. One of the resources that make such an analysis possible is CrossTalkZ, which uses the FunCoup database. However, existing methods, including CrossTalkZ, do not take into account individual types of interactions, such as protein/protein interactions, expression regulation, transport regulation, catalytic reactions, etc., but rather work with generalized types characterizing the existence of any connection between network members.
14p
vibeauty
23-10-2021
9
0
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Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer’s payment.
13p
vigiselle2711
30-08-2021
8
1
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Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated the genetic mechanisms underlying the variation of Braford resistance to tick infestation.
20p
viansan2711
30-07-2021
10
1
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Marine endophytic fungi (MEF) are good sources of structurally unique and biologically active secondary metabolites. Due to the increase in antimicrobial resistance, the secondary metabolites from MEF ought to be fully explored to identify candidates which could serve as lead compounds for novel drug development.
17p
vijeeni2711
24-07-2021
7
0
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Rosaceae species are economically highly relevant crops. Their cultivation systems are constrained by phytopathogens causing severe losses. Plants respond to invading pathogens through signaling mechanisms, a component of which are of them being plant elicitor peptides (Peps).
18p
vilichoo2711
23-06-2021
8
1
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Due to the fact that pulmonary tuberculosis (PTB) is a highly infectious respiratory disease characterized by high herd susceptibility and hard to be treated, this study aimed to search novel effective biomarkers to improve the prognosis and treatment of PTB patients.
7p
vimichigan2711
26-03-2021
16
2
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Biological networks have a growing importance for the interpretation of high-throughput “omics” data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and performs enrichment analysis to annotate the modules with ontology terms or other available knowledge.
14p
vikentucky2711
26-11-2020
13
1
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Enrichment analysis of gene expression data is essential to find functional groups of genes whose interplay can explain experimental observations. Numerous methods have been published that either ignore (set-based) or incorporate (network-based) known interactions between genes.
11p
vioklahoma2711
19-11-2020
5
2
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The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular level, the adaptations of the immune system in host defense and its dysregulation in pathological conditions.
14p
vioklahoma2711
19-11-2020
14
1
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Under both physiological and pathological conditions gene expression programs are shaped through the interplay of regulatory proteins and their gene targets, interactions between which form intricate gene regulatory networks (GRN).
14p
vioklahoma2711
19-11-2020
6
1
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Accurate identification of differentially expressed (DE) genes in time course RNA-Seq data is crucial for understanding the dynamics of transcriptional regulatory network. However, most of the available methods treat gene expressions at different time points as replicates and test the significance of the mean expression difference between treatments or conditions irrespective of time.
13p
vioklahoma2711
19-11-2020
21
2
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Inference of active regulatory cascades under specific molecular and environmental perturbations is a recurring task in transcriptional data analysis. Commercial tools based on large, manually curated networks of causal relationships offering such functionality have been used in thousands of articles in the biomedical literature.
15p
vioklahoma2711
19-11-2020
12
1
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More than fifty percent of neuroblastoma (NB) patients with adverse prognosis do not benefit from treatment making the identification of new potential targets mandatory. Hypoxia is a condition of low oxygen tension, occurring in poorly vascularized tissues, which activates specific genes and contributes to the acquisition of the tumor aggressive phenotype.
11p
vioklahoma2711
19-11-2020
12
2
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