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TOWARD DISCOVERING DISEASE-SPECIFIC GENE NETWORKS FROM ONLINE LITERATURE
2005
Proceedings of the 3rd Asia-Pacific Bioinformatics Conference
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We compared the gene networks of two complex human CNS diseases extracted by DiseasePathweaver to the corresponding networks from the human-curated KEGG database and found that our system can accurately ...
Using DiseasePathweaver, a biologist can obtain a global overview of the gene interaction network related to a specific human disease, together with well-documented evidences linking to each gene and its ...
We have applied DPW to discover a disease-specific interaction network for ALS. The resulting network is shown in Figure 3 . ...
doi:10.1142/9781860947322_0016
fatcat:4256eoaygvc4rc6cet4vqes5ci
Systems Biology Approaches for Discovering Biomarkers for Traumatic Brain Injury
2013
Journal of Neurotrauma
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As an exemplar, we apply network and pathway analysis to a manually compiled list of 32 protein biomarker candidates from the literature, recover known TBI-related mechanisms, and generate hypothetical ...
One possibility is to apply emerging systems biology strategies to holistically probe and analyze the complex interweaving molecular pathways and networks that mediate the secondary cellular response through ...
Pathways are often manually curated from the literature into large online compendia (see Table 3 for a list), which can be exploited to link disease-or injury-specific differentially expressed genes ...
doi:10.1089/neu.2012.2631
pmid:23510232
pmcid:PMC3700463
fatcat:esd3io3qpjh27ghjpuja5nzyzu
Enriching Human Interactome with Functional Mutations to Detect High-Impact Network Modules Underlying Complex Diseases
2019
Genes
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However, carving a disease network module from the whole interactome is a difficult task. ...
Specifically, our approach incorporates and propagates the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on PPIs to implicate the genes that are most likely influenced by ...
Specifically, we derived the seed genes for network propagation from the GWAS dataset (see Section 2.2 in Methods). ...
doi:10.3390/genes10110933
pmid:31731769
pmcid:PMC6895925
fatcat:hlfpixohdvcwxdmm3fvgwgmbfa
Treating Different Diseases With the Same Method—A Traditional Chinese Medicine Concept Analyzed for Its Biological Basis
2020
Frontiers in Pharmacology
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establish a digital dictionary of gene specifically related to individual diseases. ...
We aim to use big data technology and complex network theory to mine the genes specifically relevant to these TCM syndromes. ...
A total of 21 sub networks (right of Figure 6 ) were discovered from the gene division of Qi deficiency and blood stasis syndromes of stroke. ...
doi:10.3389/fphar.2020.00946
pmid:32670064
pmcid:PMC7332878
fatcat:bep3hmltprbaflv54b7kwbbmj4
Integrative networks illuminate biological factors underlying gene-disease associations
[article]
2016
bioRxiv
pre-print
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Once constructed, these networks provide the means to identify broad biological patterns underlying genes associated with complex traits and diseases. ...
Such networks become more valuable as they become more context specific, for example, by capturing how genes work together in a certain tissue or cell type. ...
identified in sequencing studies or weak associations mined from literature. ...
doi:10.1101/062695
fatcat:pqccv76v4zgwlfstlpwcuqqjlu
Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations
2016
Current Genetic Medicine Reports
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Such networks become more valuable as they become more context specific, for example, by capturing how genes work together in a certain tissue or cell type. ...
Once constructed, these networks provide the means to identify broad biological patterns underlying genes associated with complex traits and diseases. ...
identified in sequencing studies or weak associations mined from literature. ...
doi:10.1007/s40142-016-0102-5
fatcat:kidqk7ei7bfzxfszk7nmdpo4xi
Chapter 2: Data-Driven View of Disease Biology
2012
PLoS Computational Biology
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Here we discuss approaches that effectively weight and integrate hundreds of heterogeneous datasets to genegene networks that focus on a specific process or disease. ...
Investigators often use these datasets individually to help elucidate molecular mechanisms of human diseases. ...
These experiments range from those targeted towards tissue specificity [9] to those targeted towards specific diseases such as cancer [10] . ...
doi:10.1371/journal.pcbi.1002816
pmid:23300408
pmcid:PMC3531282
fatcat:mst53agedra3jhlubdoy4otavi
Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
[article]
2014
bioRxiv
pre-print
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From this network composed of 40,343 nodes and 1,608,168 edges, we extracted features that describe the topology between specific genes and diseases. ...
First we constructed a network with 18 node types—genes, diseases, tissues, pathophysiologies, and 14 MSigDB (molecular signatures database)collections—and 19 edge types from high-throughput publicly-available ...
Disease-specific performance tends towards the mean, as disease-specific information has been altered by permutation. ...
doi:10.1101/011569
fatcat:uwxh3nidtfh37afyj7s2ipn46m
The Alzheimer's comorbidity phenome: mining from a large patient database and phenome-driven genetics prediction
2018
JAMIA Open
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We aim to construct a heterogeneous network that integrates disease comorbidity network (DCN) from FAERS with protein-protein interaction (PPI) to prioritize the AD risk genes using network-based ranking ...
We built a DCN based on indication data from FAERS using association rule mining. DCN was further integrated with PPI network. ...
To test the performance of our network, we compared comorbidities of AD from DCN with known comorbidities of AD from literature. ...
doi:10.1093/jamiaopen/ooy050
pmid:30944912
pmcid:PMC6434979
fatcat:hcgswvfhzfchze2b7p3tyqlkhi
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation
2011
Genome Biology
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We show that BioGraph can retrospectively confirm recently discovered disease genes and identify potential susceptibility genes, outperforming existing technologies, without requiring prior domain knowledge ...
The platform offers prioritizations of putative disease genes, supported by functional hypotheses. ...
Acknowledgements This work was supported by the GOA project 'BioGraph: Text mining on heterogeneous databases: An application to optimized discovery of disease relevant genetic variants' of the University ...
doi:10.1186/gb-2011-12-6-r57
pmid:21696594
pmcid:PMC3218845
fatcat:zrc6r2d6djep3bmuu7ghq5swlu
BioMap
2004
Proceedings of the 2004 ACM symposium on Applied computing - SAC '04
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Knowledge, in this case, is defined as one-to-many and many-to-many relationships among biological entities such as gene, protein, drug, disease, etc. ...
As data and information space continue to grow exponentially, the need for rapidly surveying the published literature, synthesizing, and discovering the embedded "knowledge" is becoming critical to allow ...
The relationships thus discovered from the MEDLINE collection will be maintained in a relational database along with the specific links to literature sources, genes and protein sequence databases, popular ...
doi:10.1145/967900.967927
dblp:conf/sac/KumarPMSL04
fatcat:2usbpchpzbfadlrhki5ionnqqu
Understanding human metabolic physiology: a genome-to-systems approach
2009
Trends in Biotechnology
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Efforts have been initiated towards developing context-specific metabolic networks from high-throughput data [51, 53] , providing the basis for constructing specific, segmented networks from a global ...
Literature documents specific biochemical details from experiments on the gene product functions, such as reaction mechanism and substrate specificity.
Figure 3 . 3 Figure 3. ...
doi:10.1016/j.tibtech.2008.09.007
pmid:19010556
fatcat:2dasytln5nagjn72cbuxvdlxxe
Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks
2021
Genes
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Here we present a meta-analysis of the reasons why different genes have been studied and to what extent, with a focus on the gene-specific biological features. ...
The reasons for selecting a gene for further study might vary from historical momentum to funding availability, thus leading to unequal attention distribution among all genes. ...
It is possible that most genes were first discovered in isolation and only then added to regulatory networks. ...
doi:10.3390/genes12020319
pmid:33672419
fatcat:unnlnjicrvaldl2iswz4qchf7a
Target discovery from data mining approaches
2009
Drug Discovery Today
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network, as long as it is relevant to a specific disease and its progression [4] . ...
The list of seed genes was then used to construct a disease-specific gene-interaction network mined from the full text articles stored in PubMed Central (PMC), based on the dependency parsing and support ...
doi:10.1016/j.drudis.2008.12.005
pmid:19135549
fatcat:plsts2psuvclneuhgd5tlianwi
Target discovery from data mining approaches
2012
Drug Discovery Today
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network, as long as it is relevant to a specific disease and its progression [4] . ...
The list of seed genes was then used to construct a disease-specific gene-interaction network mined from the full text articles stored in PubMed Central (PMC), based on the dependency parsing and support ...
doi:10.1016/j.drudis.2011.12.006
pmid:22178890
fatcat:c7k3puzntbhcrmzjlw6uvgxhny
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