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iRefIndex specifications


Unique identifier OMICS_02921
Name iRefIndex
Restrictions to use None
Maintained Yes

Publication for iRefIndex

iRefIndex citations


Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease

Nat Commun
PMCID: 5954157
PMID: 29765022
DOI: 10.1038/s41467-018-04269-7

[…] ositive prize values. The cost of edges c(e) were assigned based our confidence in physical protein–protein interactions (PPI), as defined in prior human interaction databases. In particular, we used iRefIndex verion 13, which scores a protein interaction based on publications about that interaction, the experimental method used to detect the interaction, and the type of interaction.We first ran a […]


Determining the minimum number of protein protein interactions required to support known protein complexes

PLoS One
PMCID: 5919440
PMID: 29698482
DOI: 10.1371/journal.pone.0195545

[…] s set [, ] without any known PPIs, to estimate the minimum number of PPIs, and to pairs of CYC2008 and eight PPI datasets (STRING [], MINT [], BioGRID [], DIP [], BIND [], WI-PHI [], IntAct [, ], and iRefIndex []) to estimate the minimum number of additional PPIs.However, as mentioned above, known PPI data suffers from a significant amount of noise. In particular, there are a large amount of missi […]


Global Transcriptome Sequencing Reveals Molecular Profiles of Summer Diapause Induction Stage of Onion Maggot, Delia antiqua (Diptera: Anthomyiidae)

PMCID: 5765349
PMID: 29158334
DOI: 10.1534/g3.117.300393

[…] PPI network analysis was constructed using the iRefIndex database with default parameters to identify coexpressed gene networks, gene modules, and the hub genes (top connectivity with other genes) in each module ( (). […]


Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases

PLoS Comput Biol
PMCID: 5638204
PMID: 29023450
DOI: 10.1371/journal.pcbi.1005580

[…] on SKAT-O detected 39% of the genes. It is interesting to point out that one of the true genes uniquely found by Conflux, KCNMA1, is actually not in the neighbourhood of the other causal genes in the iRefIndex network. This shows that since Conflux is only using the network as a prior, it can still identify genes even if they are not necessarily connected to others in the considered network. Hotne […]


Genome wide association analysis of insomnia complaints identifies risk genes and genetic overlap with psychiatric and metabolic traits

Nat Genet
PMCID: 5600256
PMID: 28604731
DOI: 10.1038/ng.3888

[…] 5, 2101, and 2077 genes for full, female, and male analyses respectively). The -log10(P value) was defined as input gene score. HotNet2 was performed based on protein-protein interactions reported by iRefIndex. For four delta thresholds (minimum edge weight) that were automatically chosen by HotNet2, the significance of N subnetworks at k (the minimum number of proteins in a subnetwork) were repor […]


A novel network regularized matrix decomposition method to detect mutated cancer genes in tumour samples with inter patient heterogeneity

Sci Rep
PMCID: 5460199
PMID: 28588243
DOI: 10.1038/s41598-017-03141-w

[…] ne interaction network as an additional source to identify cancer genes mutated in perturbed pathways–. Considering both mutation frequencies of genes and information from interaction network such as iRefIndex, HPRD, STRING and others–, these approaches detect mutated cancer genes by determining whether the investigated genes are recurrently mutated in their network context. For example, HotNet, […]


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iRefIndex institution(s)
The Biotechnology Centre of Oslo, University of Oslo, Blindern, Oslo, Norway

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