iNetModels


33849075	iNetModels 2.0: an interactive visualization and database of multi-omics data. [PMID: 33849075] Arif M, Zhang C, Li X, Güngör C, Çakmak B, Arslantürk M, Tebani A, Özcan B, Subaş O, Zhou W, Piening B, Turkez H, Fagerberg L, Price N, Hood L, Snyder M, Nielsen J, Uhlen M, Mardinoglu A. Abstract It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation. Nucleic Acids Res. 2021:49(W1) \| 22 Citations (from Europe PMC, 2025-03-22)
29069445	TCSBN: a database of tissue and cancer specific biological networks. [PMID: 29069445] Lee S, Zhang C, Arif M, Liu Z, Benfeitas R, Bidkhori G, Deshmukh S, Al Shobky M, Lovric A, Boren J, Nielsen J, Uhlen M, Mardinoglu A. Abstract Biological networks provide new opportunities for understanding the cellular biology in both health and disease states. We generated tissue specific integrated networks (INs) for liver, muscle and adipose tissues by integrating metabolic, regulatory and protein-protein interaction networks. We also generated human co-expression networks (CNs) for 46 normal tissues and 17 cancers to explore the functional relationships between genes as well as their relationships with biological functions, and investigate the overlap between functional and physical interactions provided by CNs and INs, respectively. These networks can be employed in the analysis of omics data, provide detailed insight into disease mechanisms by identifying the key biological components and eventually can be used in the development of efficient treatment strategies. Moreover, comparative analysis of the networks may allow for the identification of tissue-specific targets that can be used in the development of drugs with the minimum toxic effect to other human tissues. These context-specific INs and CNs are presented in an interactive website http://inetmodels.com without any limitation. Nucleic Acids Res. 2018:46(D1) \| 35 Citations (from Europe PMC, 2025-03-22)

iNetModels 2.0: an interactive visualization and database of multi-omics data. [PMID: 33849075]

Arif M, Zhang C, Li X, Güngör C, Çakmak B, Arslantürk M, Tebani A, Özcan B, Subaş O, Zhou W, Piening B, Turkez H, Fagerberg L, Price N, Hood L, Snyder M, Nielsen J, Uhlen M, Mardinoglu A.

Abstract

It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.

Nucleic Acids Res. 2021:49(W1) | 22 Citations (from Europe PMC, 2025-03-22)

TCSBN: a database of tissue and cancer specific biological networks. [PMID: 29069445]

Lee S, Zhang C, Arif M, Liu Z, Benfeitas R, Bidkhori G, Deshmukh S, Al Shobky M, Lovric A, Boren J, Nielsen J, Uhlen M, Mardinoglu A.

Abstract

Biological networks provide new opportunities for understanding the cellular biology in both health and disease states. We generated tissue specific integrated networks (INs) for liver, muscle and adipose tissues by integrating metabolic, regulatory and protein-protein interaction networks. We also generated human co-expression networks (CNs) for 46 normal tissues and 17 cancers to explore the functional relationships between genes as well as their relationships with biological functions, and investigate the overlap between functional and physical interactions provided by CNs and INs, respectively. These networks can be employed in the analysis of omics data, provide detailed insight into disease mechanisms by identifying the key biological components and eventually can be used in the development of efficient treatment strategies. Moreover, comparative analysis of the networks may allow for the identification of tissue-specific targets that can be used in the development of drugs with the minimum toxic effect to other human tissues. These context-specific INs and CNs are presented in an interactive website http://inetmodels.com without any limitation.

Nucleic Acids Res. 2018:46(D1) | 35 Citations (from Europe PMC, 2025-03-22)

URL:	https://inetmodels.com
Full name:	an interactive visualization and database of multi-omics data
Description:	Biological networks provide new opportunities for understanding the cellular biology in both health and disease states. We generated tissue specific integrated networks (INs) for liver, muscle and adipose tissues by integrating metabolic, regulatory and protein-protein interaction networks.
Year founded:	2018
Last update:	2021
Version:	2.0
Accessibility:	Accessible
Country/Region:	Sweden

Data type:	Protein
Data object:	Animal
Database category:	Expression Interaction
Major species:	Homo sapiens
Keywords:	co-expression networks integrated networks

University/Institution:	Chalmers University of Technology
Address:	Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
City:
Province/State:
Country/Region:	Sweden
Contact name (PI/Team):	Adil Mardinoglu
Contact email (PI/Helpdesk):	es.balefilics@mlida

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Database Commons a catalog of worldwide biological databases