Supplementary file 1: Search Terms Version 1
A list of the search terms used for identifying SARS-CoV2 studies involving enrichment analysis. A random sample of 100 papers were used as input to the experiment.
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supplementary file 1.txt
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(("2019-nCoV"[All Fields] OR "2019nCoV"[All Fields] OR "COVID-19"[All Fields] OR "SARS-CoV-2"[All Fields] OR ("wuhan"[All Fields] AND "coronavirus"[All Fields]) OR "Coronavirus"[All Fields] OR "Corona virus"[All Fields] OR "corona-virus"[All Fields] OR "corona viruses"[All Fields] OR "coronaviruses"[All Fields] OR "SARS-CoV"[All Fields] OR "Orthocoronavirinae"[All Fields] OR "MERS-CoV"[All Fields] OR "Severe Acute Respiratory Syndrome"[All Fields] OR "Middle East Respiratory Syndrome"[All Fields] OR ("SARS"[All Fields] AND "virus"[All Fields]) OR "soluble ACE2"[All Fields] OR ("ACE2"[All Fields] AND "virus"[All Fields]) OR ("ARDS"[All Fields] AND "virus"[All Fields]) OR ("angiotensin-converting enzyme 2"[All Fields] AND "virus"[All Fields])) AND ("functional enrichment analysis"[All Fields] OR "over-representation analysis"[All Fields] OR "functional class scoring"[All Fields] OR "gene set enrichment analysis"[All Fields])) AND ("2020/02/01"[PubDate] : "3000/12/31"[PubDate])Export PNG
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Created: 28th Nov 2022 at 13:04
Last updated: 13th Jan 2023 at 08:31
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Version 1 (earliest) Created 28th Nov 2022 at 13:04 by Yi Chen
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Projects: Consensus Hallmark Annotation, FAIR Functional Enrichment, The evolution of Gene Ontology
Institutions: University of Leiden, LIACS
Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, ., PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing, Conspicuous chloroplast with LHC‒PSI/II‒megacomplex and diverse PBPs in the marine dinoflagellate Prorocentrum cordatum, icpm-kth, SDBV/HITS, sample project, TestingSeek, Genomic Medicine, Remodeling of cIV, Virtual Human Platform for Safety Assessment, PROMISEANG, URGI, Matsutake, UNDESIRABLE EFFECTS OF POST COVID-19 VACCINATION: A DESCRIPTIVE STUDY, WINTER 2022, Semantic Table Interpretation in Chemistry, MS identification of L infantum proteins related to their drug resistance patterns for new drug targets identification and ecotoxicological evaluations of their environmental and interspecies impact, the Supplementary materials for paper, ToxiGen - Reproductive toxicity and transgenerational effects of petroleum mixtures in fish, PhotoBoost, Measurement of Fisheries Provisioning Services and its Pressure to Support Sustainability of Fisheries in The Jatigede Reservoir, Indonesia, FIsh data on 2022 in the Jatigede Reservoir, ImmPort - data sharing, MESI-Review 2024, REWIRED: comparative RNA-seq and ATAC-seq in six salmonids and six outgroup telest fishes, REWIRED, Data Repository, APPN Test Project, Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation, BIDS, BioRECIPE representation format, UMass Chan BioImage DMS Core_FAIR Metadata Templates, FUNCEMM, Pectobacterium pangenome, New Optical Coherence Tomography Biomarkers Identified with Deep Learning for Risk Stratification of Patients with Age-related Macular Degeneration, Virulence-related genes expression in planktonic mixed cultures of Candida albicans and non-albicans Candida species, Screening of Secondary Plant Metabolites on Antihelmintic Activity in Ascaris scum, Munich Cluster for Systems Neurology, Test project May 2024, Biospecimen Collection Protocol, Winter Wheat (Triticum aestivum L.) Grain Yield, Quality, and Net Photosynthesis When Grown Under Semi-Transparent Cadmium Telluride Photovoltaic Modules Near Maturity, Benefit for All FAIR Data, Implementation of Nanopore Sequencing for Detection of Treatment Induced Transcriptomic and Epitranscriptomic Changes in Leukaemic Tumour Models, DPL, Glycogen Metabolism in bacteria, ILS Ceramide Ring Trial, Project Test, DeepCurate, Revisiting mutational resistance to ampicillin and cefotaxime in Haemophilus influenzae, Biochemical characterization of the feedforward loop between CDK1 and FOXM1 in epidermal stem cells, Drug Discovery and Biotechnology Standard Operating Procedures, EDITH (Ecosystem Digital Twins in Health) test project, Fluid flow project, Smart Garden Watering System, The role of different fatty acids, AQUACIRCLE, IDIM, Sampling vicinity of industrial settings for pathogens and GMO identification, RNA-seq data for paper, RNA-seq data, Academic Scientific Research Group, SYLOBIO, 3T3 murine fibroblast as feeder-layer, Comparative Analysis of decell efficiency and structural integrity of vessels for tissue engineering aplications, S. cerevisiae fed-batch fermentation, Alters-Krebs-Korrelation anhand der Patienteneingänge 2024, Cassava Gates Curation, GWI-HDMT stemcells, HubMOL, test, Lipopeptide research @ VIB, PRIN 2022 - High-resolution study of translational dynamics in human epithelial stem cells, Automated Hepatic Vessel Segmentation in Whole-Slide Images Using U-Net Variants with Attention and SE Blocks, Diverse Metabolic Control of Phosphoglucomutases by Bisphosphorylated Sugars in Heterotrophic Bacteria, GENBioDORA, Preclinical Imaging and Testing Core at MIT Koch Institute, Ultrasound Guided Injection Protocol Development, BullNet, TERRACOTA, B.Ed Colleges in Bangalore, LIRA, reNEW, Cross-Feeding B.theta, Surgery Analyzer, Pseudomonas aeruginosa and its vesicles, FAIRe Tests BMDS, LabscriptAI, Principais cânceres que afetam mulheres no Brasil, DKDM: Diabetic Kidney Disease Map, NGID, From waste to taste: exploring innovative food applications of postharvest fish losses_WASTE2TASTE, Controlled Carbon Loss: Threshold-Dependent Overflow Metabolism in Synechocystis, Giulia Malpezzi PhD raw data, Pro-Inflammatory Response BLE by Mmm, Phage infection in Nitrosomonas europaea, Creative Biogene, 25TST, Biodiversity and enzymatic activity of soil and root-associated microbiome in the oak dominated forests along Eastern Sierra Madre in Mexico during the transition from the period of extreme drought and increased rainfall, BlueTekna research group, PhD project_ValeriaLaGatta, Thesis student-FrancescaFilippelli, Quantifizierung des Zusammenhanges zwischen Leberperfusion und -funktion bei erweiterter Leberresektion - Ein systemmedizinischer Ansatz (QuaLiPerF), Defining the role of fibroblasts in skin expansion, Proteo-Lipidomics Serum Signatures associated with Bevacizumab response in High Grade Serous Ovarian Carcinoma, EtAcMem, BIDS-Training-Project, Thymidylate synthase dimer disrupters induce DNA damage, halt cell growth and overcome drug resistance in colorectal cancer, HIPPO PATHWAY, CureQ demo, Test project 25062026
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supplementary materials
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This investigation serves as supplementary material for a SWAT4HCLS publication that describes minimum metadata and provenance requirements for reproducible enrichment analysis results.
Functional enrichment analysis is an essential downstream process in high throughput omics studies, such as transcriptomics and proteomics. By using the Gene Ontology (GO) and its annotations (GOA), underlying functional patterns of over-representation can be identified, leading to ...
This study describes the results of a survey on enrichment analysis tool usage and provenance reporting for a corpus of SARS-CoV2 data.
Submitter: Yi Chen
Investigation: FAIR Functional Enrichment: Assessing and Model...
Assays: FAIR Functional Enrichment
Submitter: Yi Chen
Biological problem addressed: Gene Expression
Investigation: FAIR Functional Enrichment: Assessing and Model...
Study: FAIR Functional Enrichment
