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Figure4- Extracted GO subcellular localization subgraphs form a network with expected connectivity patterns
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Figure7 - Methods overview of knowledgebase gene annotation mapping and comparison to Human Protein Database subcellular localization raw data
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Figure8 - Comparison of UniProt-Ensembl knowledgebase annotation data mining extraction performance by GOcats, Map2Slim, and UniProt CV
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Figure10 - Comparing p-values of significantly-enriched annotations using GOcats paths vs excluding has_part edges
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Figure1 - GOcats data flow diagram for subgraph creation and GAF mapping
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Figure2 - Flowchart of the GOcats’ subgraph creation method
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Supplemental
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DATASET
Table2 - Summary of 25 example subcellular locations extracted by GOcats
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DATASET
Table3 - Agreement summary between corresponding GOcats and UniProt CV subgraphs
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Table4 - Agreement summary between corresponding GOcats and Map2Slim subgraphs
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Table5 - Prevalence of potential has_part (HP) relationship mapping errors in GO
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Table6 - Summary of GO term mapping errors resulting from misevaluation of relationships with respect to semantic scoping
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DATASET
Table7 - Summary of 20 subcellular locations used in the HPA raw experimental data extracted by GOcats
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Table8 - Generic location categories used to resolve potential scoping inconsistencies in HPA raw data
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Table9 - Summary of gene location category agreement
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DATASET
Table1 - Prevalence of relationships in the Gene Ontology and suggested semantic correspondence classes to reduce ambiguity
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Figure3 - The has_part relation creates paths with of varying semantic scoping which confuses mapping within GO, simplified
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Figure5- Flowchart of the UniProt subcellular location CV subgraph creation method and inclusion index equation
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Figure6 - Visualizing the degree of overlap between the category subgraphs created by GOcats, Map2Slim, and the UniProt CV, relabeled and reconfigured
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Figure9 - Comparison of HPA knowledgebase derived annotations to HPA experimental data, a_only
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FiguresTablesSupplemental_2018-04-21
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modified on 2018-04-24, 15:30
Categories
Bioinformatics and computational biology not elsewhere classified
Keywords
Bioinformatics
Licence
CC BY 4.0
