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Gene Expression Curation

Gene Expression Curation. ~WormBase, 2003 ~. What kind of data are considered gene expression data?. Anatomical and temporal expression analysis Reporter gene analysis (GFP, LacZ …) Antibody staining In situ hybridization Northern, Western, RT PCR on staged animals. Microarray/SAGE

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Gene Expression Curation

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  1. Gene Expression Curation ~WormBase, 2003 ~ Curator Meeting, Oct. 2003

  2. What kind of data are considered gene expression data? • Anatomical and temporal expression analysis • Reporter gene analysis (GFP, LacZ …) • Antibody staining • In situ hybridization • Northern, Western, RT PCR on staged animals. • Microarray/SAGE • Gene regulation • Gene expression in mutant/RNAi background • Expression influenced by temperature, chemical ... Curator Meeting, Oct. 2003

  3. WormBase Literature Curation First-Pass Curation Jamboree or Textpresso ~7,000 worm papers ~7,000 worm papers ~7,000 worm papers ~7,000 worm papers First Pass Curation Jamboree Textpresso Textpresso gene function transgene interaction RNAi expression gene expression Second Pass Curation Second Pass Curation curator extract data from literature curator extract data from literature data released in WormBase data released in WormBase Curator Meeting, Oct. 2003

  4. Curation pipeline for Anatomical and temporal expression data. 2011 worm papers after 2001 4,281 worm papers before 2001 Jamboree for papers with expression pattern data First Pass curation 592 papers ~1,000 papers Manually extract expression pattern data New data released at WormBase fort-nightly Curator Meeting, Oct. 2003

  5. Expression Pattern Summary(WS113) Items Total % of total Expr_pattern 2363 from primary research article 1942 82% from meeting abstracts 56 2% from user submission 365 15% Reporter gene assay 1398 59% Antibody assay 401 17% In situ hybridization 175 7% Northern analysis 289 12% RT PCR 71 3% Western analysis 37 2% Genes With sub-cellular localization Info 578 Paper 1009 Total genes described 1684 Curator Meeting, Oct. 2003

  6. Gene Summary Page for lin-3 Curator Meeting, Oct. 2003

  7. Curator Meeting, Oct. 2003

  8. Microarray Data Curation • At least 3 types of data • Affymetrix type (2 papers) - 2 curated • PCR product based (17 papers) - 5 curated • cDNA based (2 papers) - 0 curated • Same data model for all types of microarray. • Microarray results dynamically mapped to genome. • No raw data. WormBase only stores and displays microarray data that are calculated, finalized and published in literature. • Clustering results are curated. • Progress • 595,451 individual expression level data points • 2 sets of Affymetrix type data, 20 experiments • 5 sets of PCR product based data, 14 experiments • 175 Clusters from 3 papers. Curator Meeting, Oct. 2003

  9. Gene Summary Page for cpr-1 Curator Meeting, Oct. 2003

  10. Curator Meeting, Oct. 2003

  11. Gene Regulation Curation • Regulation on gene expression • Allele, RNAi or Transgene regulate expression of another gene. • Cis regulatory sequence analysis. • Chemical or temperature regulated gene expression. • Curation just started. • WS113 will contain 34 regulation data from 18 papers. • Follow First-Pass curation pipeline. Try to finish 2003 papers first, then earlier papers. Curator Meeting, Oct. 2003

  12. Ontology • Temporal • Complete Developmental Life Stage Ontology with 69 terms • Applied to all gene expression curation, including expression pattern, microarray and gene regulation. • Anatomical • Complete Anatomy Ontology with ~5,000 terms • Will be applied to future curation on expression pattern and gene regulation. • Old expression and gene regulation data will be updated with anatomy ontology. Curator Meeting, Oct. 2003

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