SEEK ID: https://fairdomhub.org/people/1909
Locations: Netherlands , Not specified
ORCID: Not specified
Joined: 2nd Dec 2020
Expertise: Not specified
Tools: Not specified
Related items
- Programmes (2)
- Projects (3)
- Institutions (2)
- Investigations (3)
- Studies (6)
- Assays (6)
- Data files (35)
- Documents (3)
Projects: Consensus Hallmark Annotation, The evolution of Gene Ontology
Web page: Not specified
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, Endometriosis, 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, Function, control and engineering of microbial methylotrophy, 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, Cancer Systems Biology Consortium (CSBC), 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
Web page: Not specified
This project stored supplementary files that we didn't include in the paper ' Exploring the Evolution of the Gene Ontology and itsImpact on Enrichment Analysis'
Programme: Hallmarks of cancer
Public web page: Not specified
Organisms: Not specified
supplementary materials
Programme: Independent Projects
Public web page: Not specified
Organisms: Not specified
Data and experimental methods to support the work in the following paper:
Establishing Consensus Annotation for the Hallmarks of Cancer, 2020, Yi Chen, F.J.Verbeek and K.Wolstencroft, in submission
Programme: Hallmarks of cancer
Public web page: Not specified
Organisms: Homo sapiens
Submitter: Yi Chen
Studies: Exploring how the concept and structure was influenced during the evolut..., The influence of GO evolution on downstream analysis
Assays: GO evolution - Terms and Annotations, The influence on functional enrichment analysis
Snapshots: No snapshots
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 ...
Snapshots: No snapshots
The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. In this investigation we compare cancer hallmark mapping strategies from different studies, based on Gene Ontology and biological pathway annotation. By analysing the semantic ...
Submitter: Katy Wolstencroft
Studies: Comparing Cancer Hallmark Descriptions, Evolution of Gene Ontology Terms, Prognostic and Hallmark Gene Networks
Assays: Analysing Changes to GO Biological Process, Annotation Consensus and GO Consensus, Hub genes of modules and enriched GO terms, Jaccard Index Prognostic Hallmark Genes, WGCNA Prognostic Hallmark Genes
Snapshots: No snapshots
Submitter: Yi Chen
Investigation: Exploring the Evolution of the Gene Ontology an...
Snapshots: No snapshots
Submitter: Yi Chen
Investigation: Exploring the Evolution of the Gene Ontology an...
Snapshots: No snapshots
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
Snapshots: No snapshots
The hallmarks mapping schemes under comparison were developed over the period of 7 years and therefore were developed using different versions of the Gene Ontology and associated annotation. Understanding which differences between mapping schemes were the result of topological or annotation changes to GO could therefore help to further refine consensus and make results and conclusions more comparable between studies.
Submitter: Katy Wolstencroft
Investigation: Cancer Hallmark Consensus
Snapshots: No snapshots
Multiple studies have devised mapping schemes to associate cancer hallmarks with Gene Ontology terms and biological pathway. This study compares the similarities and differences between them, in order to establish consensus knowledge.
Submitter: Katy Wolstencroft
Investigation: Cancer Hallmark Consensus
Snapshots: No snapshots
This study examines how different hallmark gene datasets intersect with prognostic cancer genes
Submitter: Katy Wolstencroft
Investigation: Cancer Hallmark Consensus
Assays: Hub genes of modules and enriched GO terms, Jaccard Index Prognostic Hallmark Genes, WGCNA Prognostic Hallmark Genes
Snapshots: No snapshots
Submitter: Katy Wolstencroft
Biological problem addressed: Annotation
Investigation: Cancer Hallmark Consensus
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: GO Consensus terms, Genes annotated to selected GO terms belonging ..., Hallmark genes, Mapping from Gene Ontology terms to individual ..., Mapping from MSigDB pathways to GO terms, Mapping from pathways to individual cancer hall..., The number of genes annotated to individual can...
Snapshots: No snapshots
A Jaccard Index of the overlap between prognostic and hallmark genes for 17 cancer types across different mapping schemes. The impact of selecting different mapping schemes was assessed by pairwise comparisons where there were 5 or more shared genes.
Submitter: Katy Wolstencroft
Biological problem addressed: Biological Network Analysis
Investigation: Cancer Hallmark Consensus
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Abbreviations of 17 cancer types, Jaccard index score, prognostic genes of 17 cancer types
Snapshots: No snapshots
this assay include the hub genes of modules from different mapping schemes with highly functional similarities.
Submitter: Yi Chen
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Cancer Hallmark Consensus
Organisms: No organisms
SOPs: No SOPs
Data files: Gene enrichment analysis output of modules, Modules and hub genes, Semantic similarity between pairwise modules
Snapshots: No snapshots
Submitter: Yi Chen
Biological problem addressed: Gene Expression
Investigation: FAIR Functional Enrichment: Assessing and Model...
Study: FAIR Functional Enrichment
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Supplementary file 1: Search Terms, Supplementary file 2: Publications surveyed
Snapshots: No snapshots
Submitter: Yi Chen
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Exploring the Evolution of the Gene Ontology an...
Organisms: No organisms
SOPs: No SOPs
Data files: Reviewed and unreviewed proteins, Statistics of GO and GOA for 3 aspects from Jan..., Statistics of GO and GOA from Jan 2015 to Dec 2021, Top20 nodes with highest Degree Centrality score
Snapshots: No snapshots
Submitter: Yi Chen
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Exploring the Evolution of the Gene Ontology an...
Organisms: No organisms
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
The table shows the number of valid terms, annotations and edges for 3 aspects from Jan 2015 to Dec 2021
Investigations: Exploring the Evolution of the Gene Ontology an...
The table shows the number of terms, annotations and edges from Jan 2015 to Dec 2021.
Investigations: Exploring the Evolution of the Gene Ontology an...
The table shows the top 20 nodes with the highest degree centrality score in BP, MF and CC
Investigations: Exploring the Evolution of the Gene Ontology an...
Downloaded from UniprotKB
Investigations: Exploring the Evolution of the Gene Ontology an...
This file provides a full list of the PubMed IDs used as input to our survey of SARS-CoV2 enrichment analysis results
Creators: None
Submitter: Yi Chen
Investigations: FAIR Functional Enrichment: Assessing and Model...
Studies: FAIR Functional Enrichment
Assays: FAIR Functional Enrichment
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.
Creators: None
Submitter: Yi Chen
Investigations: FAIR Functional Enrichment: Assessing and Model...
Studies: FAIR Functional Enrichment
Assays: FAIR Functional Enrichment
1222 patients
Investigations: Cancer Hallmark Consensus
Studies: Prognostic and Hallmark Gene Networks
Assays: WGCNA Prognostic Hallmark Genes
Investigations: Cancer Hallmark Consensus
For each module, GSEA analysis was conducted by using web-tool g:profiler and only biological process (BP) were retained. Parameters for GSEA are default.
Investigations: Cancer Hallmark Consensus
Calculated by using R package GOSemSim.
Investigations: Cancer Hallmark Consensus
Modules were identified by WGCNA. hub genes of each modules were identified based on intramodular degree.
Investigations: Cancer Hallmark Consensus
Investigations: Cancer Hallmark Consensus
Investigations: Cancer Hallmark Consensus
Including 91 genes and 1222 Breast cancer patient This is an input data for WGCNA
Investigations: Cancer Hallmark Consensus
Studies: Prognostic and Hallmark Gene Networks
Assays: WGCNA Prognostic Hallmark Genes
Including 289 genes and 1222 Breast cancer patient This is an input data for WGCNA
Investigations: Cancer Hallmark Consensus
Studies: Prognostic and Hallmark Gene Networks
Assays: WGCNA Prognostic Hallmark Genes
Including 277 genes and 1222 Breast cancer patients. This is an input data for WGCNA.
Investigations: Cancer Hallmark Consensus
Studies: Prognostic and Hallmark Gene Networks
Assays: WGCNA Prognostic Hallmark Genes
Including 294 genes and 1222 Breast cancer Patient. This is an input data for WGCNA
Investigations: Cancer Hallmark Consensus
Studies: Prognostic and Hallmark Gene Networks
Assays: WGCNA Prognostic Hallmark Genes
Consensus between selected mapping methods.
Investigations: Cancer Hallmark Consensus
Additional file 2
Investigations: Cancer Hallmark Consensus
Additional File 1
Investigations: Cancer Hallmark Consensus
Figures showing the changes of edges and terms.
Investigations: FAIR Functional Enrichment: Assessing and Model...
Studies: FAIR Functional Enrichment
Assays: FAIR Functional Enrichment
Prov-O Representation for an enrichment analysis experiment on differentially expressed RNA-Seq data, analysed with Enrichr and 2021 version of GO. Rectangle represents Activity, eclipse represents entity and rhombus represents agents
Investigations: FAIR Functional Enrichment: Assessing and Model...
Studies: FAIR Functional Enrichment
Assays: FAIR Functional Enrichment