STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Franceschini, Andrea; Szklarczyk, Damian; Frankild, Sune; Kuhn, Michael; Simonovic, Milan; Röth, Alexander; Lin, Jianyi; Mínguez, Pablo; Bork, Peer; Mering, Christian von; Jensen, Lars Juhl

doi:10.1093/nar/gks1094

Cited by 3,923 publications

(3,608 citation statements)

References 60 publications

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“…Functional protein association networks of genes identified from the genomewide RNAi screen (Lee et al ., 2010) were analyzed using STRING (http://string-db.org/) (Franceschini et al ., 2013). Networks were modified and revisualized using Cytoscape (http://www.cytoscape.org/) (Smoot et al ., 2011).…”

Section: Methodsmentioning

confidence: 99%

Inhibition of elongin C promotes longevity and protein homeostasis via HIF‐1 in C. elegans

et al. 2015

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SummaryThe transcription factor hypoxia‐inducible factor 1 (HIF‐1) is crucial for responses to low oxygen and promotes longevity in Caenorhabditis elegans. We previously performed a genomewide RNA interference screen and identified many genes that act as potential negative regulators of HIF‐1. Here, we functionally characterized these genes and found several novel genes that affected lifespan. The worm ortholog of elongin C, elc‐1, encodes a subunit of E3 ligase and transcription elongation factor. We found that knockdown of elc‐1 prolonged lifespan and delayed paralysis caused by impaired protein homeostasis. We further showed that elc‐1 RNA interference increased lifespan and protein homeostasis by upregulating HIF‐1. The roles of elongin C and HIF‐1 are well conserved in eukaryotes. Thus, our study may provide insights into the aging regulatory pathway consisting of elongin C and HIF‐1 in complex metazoans.

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Section: Methodsmentioning

confidence: 99%

Inhibition of elongin C promotes longevity and protein homeostasis via HIF‐1 in C. elegans

et al. 2015

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“…Known and predicted associations among the genes within each functional category/pathway were retrieved from the STRING database (http://string-db.org; Franceschini et al , 2013) using default parameters. (A) Lipid metabolism.…”

Section: Pathophysiological Insightsmentioning

confidence: 99%

The impact of genome‐wide association studies on the pathophysiology and therapy of cardiovascular disease

2016

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Cardiovascular diseases are leading causes for death worldwide. Genetic disposition jointly with traditional risk factors precipitates their manifestation. Whereas the implications of a positive family history for individual risk have been known for a long time, only in the past few years have genome‐wide association studies (GWAS) shed light on the underlying genetic variations. Here, we review these studies designed to increase our understanding of the pathophysiology of cardiovascular diseases, particularly coronary artery disease and myocardial infarction. We focus on the newly established pathways to exemplify the translation from the identification of risk‐related genetic variants to new preventive and therapeutic strategies for cardiovascular disease.

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“…Next, we performed a STRING analysis 23 of the proteins enriched in BMDMs and RAW 264.7 cells (Fig. 2B).…”

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confidence: 99%

High‐resolution quantitative proteome analysis reveals substantial differences between phagosomes of RAW 264.7 and bone marrow derived macrophages

et al. 2015

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Macrophages are important immune cells operating at the forefront of innate immunity by taking up foreign particles and microbes through phagocytosis. The RAW 264.7 cell line is commonly used for experiments in the macrophage and phagocytosis field. However, little is known how its functions compare to primary macrophages. Here, we have performed an in‐depth proteomics characterization of phagosomes from RAW 264.7 and bone marrow derived macrophages by quantifying more than 2500 phagosomal proteins. Our data indicate that there are significant differences for a large number of proteins including important receptors such as mannose receptor 1 and Siglec‐1. Moreover, bone marrow derived macrophages phagosomes mature considerably faster by fusion with endosomes and the lysosome which we validated using fluorogenic phagocytic assays. We provide a valuable resource for researcher in the field and recommend careful use of the RAW 264.7 cell line when studying phagosome functions. All MS data have been deposited in the ProteomeXchange with identifier PXD001293 (http://proteomecentral.proteomexchange.org/dataset/PXD001293).

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STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Cited by 3,923 publications

References 60 publications

Inhibition of elongin C promotes longevity and protein homeostasis via HIF‐1 in C. elegans

Inhibition of elongin C promotes longevity and protein homeostasis via HIF‐1 in C. elegans

The impact of genome‐wide association studies on the pathophysiology and therapy of cardiovascular disease

High‐resolution quantitative proteome analysis reveals substantial differences between phagosomes of RAW 264.7 and bone marrow derived macrophages

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