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KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data

Nicolas Alcaraz, Hande Kücük, Jochen Weile, Anil Wipat, Jan Baumbach
2011 Internet Mathematics  
Specifically, given network and gene expression data, KeyPathwayMiner identifies those maximal subgraphs where all but k nodes of the subnetwork are expressed similarly in all but l cases in the gene expression  ...  Recent advances in systems biology have provided us with massive amounts of pathway data that describe the interplay of genes and their products.  ...  Furthermore, we wish to thank Igor Ulitsky (Whitehead Institute) for providing us with the data sets used in this study.  ... 
doi:10.1080/15427951.2011.604548 fatcat:pw2q32pcxffyplfovnwagt5ek4

KeyPathwayMineR: De Novo Pathway Enrichment in the R Ecosystem

Konstantinos Mechteridis, Michael Lauber, Jan Baumbach, Markus List
2022 Frontiers in Genetics  
De novo pathway enrichment is a systems biology approach in which OMICS data are projected onto a molecular interaction network to identify subnetworks representing condition-specific functional modules  ...  To close this gap, we have implemented an R package KeyPathwayMineR (KPM-R).  ...  Specifically, the plots compare all parameter configurations by plotting the average active cases per node (e.g., the sum of differentially expressed cases for a certain gene) against the number of nodes  ... 
doi:10.3389/fgene.2021.812853 pmid:35173764 pmcid:PMC8842393 fatcat:3rylry2ypfbnvilnrrpbnx4c7a

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape

Nicolas Alcaraz, Josch Pauling, Richa Batra, Eudes Barbosa, Alexander Junge, Anne GL Christensen, Vasco Azevedo, Henrik J Ditzel, Jan Baumbach
2014 BMC Systems Biology  
Results: We present a new release of KeyPathwayMiner (version 4.0) that is not limited to analyses of single omics data sets, e.g. gene expression, but is able to directly combine several different omics  ...  Traditionally, these approaches focus on combining gene expression data with protein-protein interaction (PPI) networks.  ...  However, for unconnected datasets, where the number of cases doesn't match (e.g. different sample sets used for expression data and methylation data), KeyPathwayMiner was extended to accept multiple matrices  ... 
doi:10.1186/s12918-014-0099-x pmid:25134827 pmcid:PMC4236746 fatcat:yvm544tkpvh7jdoqccrf4ipcg4

KeyPathwayMinerWeb: online multi-omics network enrichment

Markus List, Nicolas Alcaraz, Martin Dissing-Hansen, Henrik J. Ditzel, Jan Mollenhauer, Jan Baumbach
2016 Nucleic Acids Research  
Given a biological interaction network (e.g. protein-protein interactions) and a series of molecular profiles derived from one or multiple OMICS studies (gene expression, for instance), KeyPathwayMiner  ...  The web interface at (http: //keypathwayminer.compbio.sdu.dk) implements all core functionalities of the KeyPathwayMiner tool set such as data integration, input of background knowledge, batch runs for  ...  BIOLOGICAL USE CASE We demonstrate the usability of KeyPathwayMinerWeb by analyzing a whole-genome gene expression dataset on HD (18) together with the human interactome (19) .  ... 
doi:10.1093/nar/gkw373 pmid:27150809 pmcid:PMC4987922 fatcat:u2i5z4b3mrhxvpw5pukukierdu

ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks

Sebastian Vlaic, Theresia Conrad, Christian Tokarski-Schnelle, Mika Gustafsson, Uta Dahmen, Reinhard Guthke, Stefan Schuster
2018 Scientific Reports  
The module is validated using single-nucleotide polymorphism (SNP) data from independent genome-wide association studies and gene enrichment tests.  ...  We present ModuleDiscoverer, a novel approach for the identification of regulatory modules from PPINs and gene expression data.  ...  The algorithm was run using expression data of all six samples (three control, three case) for the full set of genes available on the microarray.  ... 
doi:10.1038/s41598-017-18370-2 pmid:29323246 pmcid:PMC5764996 fatcat:qv3mgp7w2femnhzsjpubfcdx6y

A Genome-Wide Integrative Association Study of DNA Methylation and Gene Expression Data and Later Life Cognitive Functioning in Monozygotic Twins

Mette Soerensen, Dominika Marzena Hozakowska-Roszkowska, Marianne Nygaard, Martin J. Larsen, Veit Schwämmle, Kaare Christensen, Lene Christiansen, Qihua Tan
2020 Frontiers in Neuroscience  
The strength of the unsupervised method is that it can reveal previously uncharacterized sub-pathways and detect interplay between biological processes, which remain undetected by the current supervised  ...  Integrated analyses were performed with an unsupervised approach using KeyPathwayMiner, and a supervised approach using the KEGG and Reactome databases.  ...  Also, KeyPathwayMiner can detect interplay between biological processes, which remain undetected by the current GSEA methods that are based on Frontiers in Neuroscience | www.frontiersin.org 2 April 2020  ... 
doi:10.3389/fnins.2020.00233 pmid:32327964 pmcid:PMC7160301 fatcat:5pexzsww6jgjzei4ot2hset2cm

CellFateScout – a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction

Marcin Siatkowski, Volkmar Liebscher, Georg Fuellen
2013 Cell Communication and Signaling  
Results: We developed CellFateScout that uses the method of Latent Variables to turn differential high-throughput expression data and a functional network into a list of active signaling pathways.  ...  We validated our approach systematically, using expression data of small molecule perturbations, yielding better predictions than popular bioinformatics tools.  ...  Second best tool is ExprEssence, which is better than KeyPathwayMiner and jActiveModules by one or two cases.  ... 
doi:10.1186/1478-811x-11-85 pmid:24206562 pmcid:PMC3833265 fatcat:auh3b35elfbspkdzjyu6tuypme

Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin

T. Conrad, O. Kniemeyer, S. G. Henkel, T. Krüger, D. J. Mattern, V. Valiante, R. Guthke, I. D. Jacobsen, A. A. Brakhage, S. Vlaic, J. Linde
2018 BMC Systems Biology  
We analyzed the omics data using two different approaches: First, we applied a simple, classical approach by comparing lists of differentially expressed genes (DEGs), differentially synthesized proteins  ...  Omics data provide deep insights into overall biological processes of organisms.  ...  The RNA-Seq data that support the findings of this study are available as mentioned in Altwasser et al. [26] .  ... 
doi:10.1186/s12918-018-0620-8 fatcat:zqibuyczkjf6vh7glolqeoiwxe

Systems Level Analysis and Identification of Pathways and Networks Associated with Liver Fibrosis

Mohamed Diwan M. AbdulHameed, Gregory J. Tawa, Kamal Kumar, Danielle L. Ippolito, John A. Lewis, Jonathan D. Stallings, Anders Wallqvist, Christina Chan
2014 PLoS ONE  
We identified genes relevant to liver fibrosis using standard differential expression and co-expression analyses, and then used these genes in pathway enrichment and protein-protein interaction (PPI) network  ...  Towards this end, we analyzed rat gene expression data from a range of chemical exposures that produced observable periportal liver fibrosis as documented in DrugMatrix, a publicly available toxicogenomics  ...  We used KeyPathwayMiner with ant-colony optimization algorithm, node exceptions (K) set to 100, and case exceptions (L) set to 0.  ... 
doi:10.1371/journal.pone.0112193 pmid:25380136 pmcid:PMC4224449 fatcat:6cjwbxo7ijev5hoekujssywty4

Network-based analysis of omics data: The LEAN method

Frederik Gwinner, Gwénola Boulday, Claire Vandiedonck, Minh Arnould, Cécile Cardoso, Iryna Nikolayeva, Oriol Guitart-Pla, Cécile V. Denis, Olivier D. Christophe, Johann Beghain, Elisabeth Tournier-Lasserve, Benno Schwikowski
2016 Bioinformatics  
Evaluation on simulated and biological data suggests that LEAN generally detects dysregulated subnetworks better, and reflects biological similarity between experiments more clearly than standard approaches  ...  LEAN can be used to pinpoint statistically significant local subnetworks in any genomescale dataset.  ...  Using a classical gene-by-gene analysis of our transcriptomic data, ablation of neither one of the three CCM genes lead to VWF mRNA differential expression.  ... 
doi:10.1093/bioinformatics/btw676 pmid:27797778 pmcid:PMC5408824 fatcat:zhcgvoukqraa3k75stomfpjfiq

De novo pathway-based biomarker identification

Nicolas Alcaraz, Markus List, Richa Batra, Fabio Vandin, Henrik J. Ditzel, Jan Baumbach
2017 Nucleic Acids Research  
We propose and discuss a novel MG approach based on de novo pathways, which for the first time have been used as features in a multi-class setting to predict cancer subtypes.  ...  Attempts to mitigate these drawbacks have led to the development of network-based approaches that integrate pathway information to produce meta-gene (MG) features.  ...  In case of de novo pathway extraction, we use KPM, which efficiently extracts all pathways, irrespective of size, containing a high number of subtype-specific expressed genes.  ... 
doi:10.1093/nar/gkx642 pmid:28934488 pmcid:PMC5766193 fatcat:w5hnrsw5mbfc7pv3hwb6545ljq

Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method [article]

Marta Lucchetta, Marco Pellegrini
2020 bioRxiv   pre-print
Next, we use four specific disease test cases (colorectal cancer, prostate cancer, asthma and rheumatoid arthritis), four state-of-the-art algorithms (ModuleDiscoverer, Degas, KeyPathwayMiner and ClustEx  ...  Moreover for the two cancer data sets, Core&Peel detects further nine relevant pathways enriched in the predicted disease module, not discovered by the other methods used in the comparative analysis.  ...  Limitations In our active sub-network detection approach we have as input both a biological gene interaction network (called the "bio-network" data) and a list of gene expression data on cohorts of cases  ... 
doi:10.1101/2020.05.27.118414 fatcat:appd5rsgorcihhh3ghat6waq7u

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

Sepideh Sadegh, Julian Matschinske, David B. Blumenthal, Gihanna Galindez, Tim Kacprowski, Markus List, Reza Nasirigerdeh, Mhaned Oubounyt, Andreas Pichlmair, Tim Daniel Rose, Marisol Salgado-Albarrán, Julian Späth (+5 others)
2020 Nature Communications  
Scenario a: Starting from a selection of viral proteins, we use the PPI network to identify the biological mechanism or pathway utilized by the virus.  ...  We select the interactors of these viral proteins reported for SARS-CoV-2 and use the multi-Steiner tree algorithm to uncover the biological pathway involved.  ...  Tissue-specific gene expression levels were obtained from the GTEx data portal (https:// www.gtexportal.org/home/, dbGaP Accession phs000424.v8.p2).  ... 
doi:10.1038/s41467-020-17189-2 pmid:32665542 fatcat:di7tqljxanfuld5gw7orjxtfjy

Comprehensive analysis of high-throughput screens with HiTSeekR

Markus List, Steffen Schmidt, Helle Christiansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Jan Baumbach
2016 Nucleic Acids Research  
We chose three use cases that demonstrate the potential of HiTSeekR to fully exploit HTS screening data in quite heterogeneous contexts to generate novel hypotheses for follow-up experiments: (i) a genome-wide  ...  It is the first approach to close the gap between raw data processing, network enrichment and wet lab target generation for various HTS screen types.  ...  The result of these effects is a signal bias that is in most cases row and column specific.  ... 
doi:10.1093/nar/gkw554 pmid:27330136 pmcid:PMC5001608 fatcat:5exuui7rinaqlob7yd3ppdcqv4

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing [article]

Sepideh Sadegh, Julian Matschinske, David B. Blumenthal, Gihanna Galindez, Tim Kacprowski, Markus List, Reza Nasirigerdeh, Mhaned Oubounyt, Andreas Pichlmair, Tim Daniel Rose, Marisol Salgado-Albarrán, Julian Späth (+5 others)
2020 arXiv   pre-print
KeyPathwayMiner is a network enrichment tool that identifies condition-specific subnetworks (key pathways) 27 .  ...  We then use the multi-Steiner Tree algorithm with the parameters shown in Table S1 to uncover the biological pathway involved.  ... 
arXiv:2004.12420v1 fatcat:jwqfg5tderhpdloudccdzcc3fm
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