Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

Wang, Zichen; Monteiro, Caroline D.; Jagodnik, Kathleen M.; Fernandez, Nicolas; Gundersen, Gregory W.; Rouillard, Andrew D.; Jenkins, Sherry L.; Feldmann, Axel S.; Hu, Kevin; McDermott, Michael G.; Duan, Qiaonan; Clark, Neil R.; Jones, Matthew R.; Kou, Yan; Goff, Troy; Woodland, Holly; Amaral, Fabio; Szeto, Gregory L.; Fuchs, Oliver; Rose, Sophia Miryam Schüssler‐Fiorenza; Sharma, Shvetank; Schwartz, Uwe; Bausela, Xabier Bengoetxea; Szymkiewicz, Maciej; Maroulis, Vasileios; Salykin, Anton; Barra, Carolina; Kruth, Candice D.; Bongio, Nicholas J.; Mathur, Vaibhav; Todoric, Radmila D.; Rubin, Udi; Malatras, Apostolos; Fulp, Carl T.; Galindo, John A.; Motiejunaite, Ruta; Jüschke, Christoph; Dishuck, Philip C.; Lahl, Katharina; Jafari, Mohieddin; Aibar, Sara; Zaravinos, Apostolos; Steenhuizen, Linda H.; Allison, Lindsey R.; Gamallo, Pablo; Segura, Fernando de Andres; Devlin, Tyler Dae; Pérez-García, Vicente; Ma’ayan, Avi

doi:10.1038/ncomms12846

Cited by 237 publications

(254 citation statements)

References 73 publications

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“…A recent trend in clinical trials is the “crowdsourcing” different aspects of clinical studies, such as mining and analyzing clinical trial data and informing the design of a clinical trial . The hope is that crowdsourcing, by harnessing the wisdom of the researcher, clinician, patient, and advocate community, will lead to accelerated research and development.…”

Section: Discussionmentioning

confidence: 99%

Crowdsourced Asparagus Urinary Odor Population Kinetics

Ramamoorthy

Sadler²,

Hasselt

et al. 2017

CPT Pharmacom & Syst Pharma

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The consumption of asparagus is associated with the production of malodorous urine with considerable interindividual variability (IIV). To characterize the urinary odor kinetics after consumption of asparagus spears, we conducted a study with consenting attendees from two American Society for Clinical Pharmacology and Therapeutics (ASCPT) meetings. Subjects were randomized to eat a specific number of asparagus spears, and then asked to report their urinary odor perception. Eighty‐seven subjects were included in the final analysis. A mixed effect proportional odds model was developed that adequately characterized the dose‐response relationship. We estimated the half‐life of the asparagus effect on malodorous urine to be 4.7 hours (relative standard error (RSE) = 13.2%), and identified a dose‐response slope term with good precision (24.3%). Age was found as the predictor of IIV in slope estimates. This study design and tools can be used as a demonstration “crowdsourcing” project for studying population kinetics in organizational and educational settings.

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Section: Discussionmentioning

confidence: 99%

Crowdsourced Asparagus Urinary Odor Population Kinetics

Ramamoorthy

Sadler²,

Hasselt

et al. 2017

CPT Pharmacom & Syst Pharma

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“…53 We thus compared the HDM transcriptome to psoriasis lesions, 38 44,54,55 We also evaluated how the HDM profile enriched with available signatures of other inflammatory diseases. 56 The HDM transcriptome showed similarity to the signature of psoriasis vulgaris, other Th17-polarized diseases (allergic contact dermatitis, acne, Crohn's disease), 37,57,58 as well as Th2-centered conditions (eczema, ulcerative colitis, asthma) 59 ( Figure 6F; Table S9).…”

Section: Hdm Shows Strongest Th17-skewed Inflammation But Capturesmentioning

confidence: 92%

Dust mite induces multiple polar T cell axes in human skin

Malik

Ungar

Garcet

et al. 2017

Clin Experimental Allergy

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“…KIT/PDGFRA mutations serve as characteristic oncogenic mutations, present iñ 98% of GISTs. 23 The genes downregulated in active KIT/PDGFRA mutations from GISTs, curated from the CREED database (initial source data: GSE17743), 24 are significantly enriched with the stromal score correlated gene signature (Fig. 3c).…”

Section: Gc Epithelium Interacts With Stromal Cells Via An Actinbindimentioning

confidence: 99%

Multiscale network analysis reveals molecular mechanisms and key regulators of the tumor microenvironment in gastric cancer

Song

Lin

Liao

et al. 2019

Intl Journal of Cancer

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Gastric cancer (GC) is the third leading cause of cancer deaths and the fourth most prevalent malignancy worldwide. The high incidence and mortality rates of gastric cancer result from multiple factors such as ineffective screening, diagnosis, and limited treatment options. In our study, we sought to systematically identify predictive molecular networks and key regulators to elucidate complex interacting signaling pathways in GC. We performed an integrative network analysis of the transcriptomic data in The Cancer Genome Atlas (TCGA) gastric cancer cohort and then comprehensively characterized the predictive subnetworks and key regulators by the matched genetic and epigenetic data. We identified 221 gene subnetworks (modules) in GC. The most prognostic subnetworks captured multiple aspects of the tumor microenvironment in GC involving interactions among stromal, epithelial and immune cells. We revealed the genetic and epigenetic underpinnings of those subnetworks and their key transcriptional regulators. We computationally predicted and experimentally validated specific mechanisms of anticancer effects of GKN2 in gastric cancer proliferation and invasion in vitro. The network models and the key regulators of the tumor microenvironment in GC identified here pave a way for developing novel therapeutic strategies for GC.

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Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

Cited by 237 publications

References 73 publications

Crowdsourced Asparagus Urinary Odor Population Kinetics

Crowdsourced Asparagus Urinary Odor Population Kinetics

Dust mite induces multiple polar T cell axes in human skin

Multiscale network analysis reveals molecular mechanisms and key regulators of the tumor microenvironment in gastric cancer

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