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InnateDB specifications

Information


Unique identifier OMICS_26579
Name InnateDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained No

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Publications for InnateDB

InnateDB citations

 (67)
library_books

Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma

2018
PMCID: 5875410
PMID: 29618931
DOI: 10.2147/OTT.S150565

[…] (DC), and closeness centrality (CC) of the nodes in PPI network were analyzed to further identify hub nodes. In addition, the information of human protein subcellular localization were obtained from InnateDB database (http://www.innatedb.com/), including extracellular space, cell surface, cytoplasm, plasma membrane, and nucleus. Afterward, protein subcellular localizations of the nodes in the PPI […]

library_books

Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis

2018
Front Genet
PMCID: 5820528
PMID: 29503661
DOI: 10.3389/fgene.2018.00042

[…] nt PPI databases. These databases like IntAct (Orchard et al., ), MINT (Licata et al., ), DIP (Salwinski et al., ), BIND (Isserlin et al., ), and BioGRID (Chatr-Aryamontri et al., ) are integrated in InnateDB (Breuer et al., ). Topological properties (such as betweenness centrality and degree distribution) of the constructed PPI network were calculated by NetworkAnalyzer in Cytoscape (Shannon et a […]

library_books

Cholangiocarcinoma associated genes identified by integrative analysis of gene expression data

2018
PMCID: 5866017
PMID: 29436659
DOI: 10.3892/mmr.2018.8594

[…] Network analyst uses a comprehensive, high-quality PPI database downloaded from InnateDB (), which is part of the International Molecular Exchange (IMEx) consortium (). It additionally contains manually curated protein interaction data from published literature and experimental d […]

library_books

System analysis of the regulation of the immune response by CD147 and FOXC1 in cancer cell lines

2018
Oncotarget
PMCID: 5849184
PMID: 29560120
DOI: 10.18632/oncotarget.24161

[…] We compared the expression profile of CD147 with that of 662 immune-related genes (Immu_Genes) derived from the intersection of genes from InnateDB database (http://www.innatedb.com) [] and Immunogenetic Related Information Source database (IRIS) (http://jtpc4.path.cam.ac.uk/immunedb/IRIS/home.htm) []. Next, we intersected the 662 genes […]

library_books

Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex

2017
Sci Rep
PMCID: 5738336
PMID: 29263411
DOI: 10.1038/s41598-017-18205-0

[…] by the DE genes. The gene ontology and KEGG pathway analyses of DE genes were performed using DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov). Innate immune genes of cattle curated at InnateDB (http://www.innatedb.com) were used to identify immune function genes found to be DE in the RNA-Seq data. Pathway painting was performed using KEGG mapper (http://www.genome.jp/kegg/mapper.ht […]

library_books

Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis

2017
Sci Rep
PMCID: 5719083
PMID: 29213115
DOI: 10.1038/s41598-017-17000-1

[…] nt of Gene Ontology Mouse specific Biological Processes terms using the BINGO app in Cytoscape. Groupings were further analyzed using the ReactomeFIViz in Cytoscape. A list of IRGs was generated from innateDB and a list of metabolic genes was generated from KEGG. These genes were independently clustered based on FPKM values using GENE-E [http://www.broadinstitute.org/cancer/software/GENE-E/index.h […]

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InnateDB institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Animal & Bioscience Research Department, AGRIC, Teagasc, Grange, Dunsany, County Meath, Ireland; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
InnateDB funding source(s)
Supported by Genome BC through the Pathogenomics of Innate Immunity (PI2) project and by the Foundation for the National Institutes of Health and the Canadian Institutes of Health Research under the Grand Challenges in Global Health Research Initiative [Grand Challenges ID: 419]; by AllerGen grants 12ASI1 and 12B&B2; by a postdoctoral trainee award from the Michael Smith Foundation for Health Research (MSFHR) and by a MSFHR Senior Scholar and a Canada Research Chair (CRC).

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