1. Oct.27, 2003 Curator Meeting, Oct. 2003 Gene Expression Curation ~WormBase, 2003 ~

2. Oct.27, 2003 Curator Meeting, Oct. 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 ≈ Gene regulation ≈Gene expression in mutant/RNAi background ≈Expression influenced by temperature, chemical...

3. Oct.27, 2003 Curator Meeting, Oct. 2003 WormBase Literature Curation First-Pass CurationJamboree or Textpresso ~7,000 worm papers RNAi gene expression gene function First Pass Curation Second Pass Curation curator extract data from literature data released in WormBase ~7,000 worm papers ~7,000 worm papers ~7,000 worm papers transgene expression interaction Second Pass Curation curator extract data from literature data released in WormBase Textpresso Jamboree

4. Oct.27, 2003 Curator Meeting, Oct. 2003 4,281 worm papers before 2001 Jamboree for papers with expression pattern data ~1,000 papers Manually extract expression pattern data New data released at WormBase fort-nightly 2011 worm papers after 2001 592 papers First Pass curation Curation pipeline for Anatomical and temporal expression data.

5. Oct.27, 2003 Curator Meeting, Oct. 2003 ItemsTotal % of total Expr_pattern2363 from primary research article194282% from meeting abstracts562% from user submission36515% Reporter gene assay139859% Antibody assay40117% In situ hybridization1757% Northern analysis28912% RT PCR713% Western analysis372% Genes With sub-cellular localization Info578 Paper1009 Total genes described1684 Expression Pattern Summary (WS113)

6. Oct.27, 2003 Curator Meeting, Oct. 2003 Gene Summary Page for lin-3

7. Oct.27, 2003 Curator Meeting, Oct. 2003

8. Oct.27, 2003 Curator Meeting, Oct. 2003 ≈ 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. Microarray Data Curation

9. Oct.27, 2003 Curator Meeting, Oct. 2003 Gene Summary Page for cpr-1

10. Oct.27, 2003 Curator Meeting, Oct. 2003

11. Oct.27, 2003 Curator Meeting, Oct. 2003 ≈ 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. Gene Regulation Curation

12. Oct.27, 2003 Curator Meeting, Oct. 2003 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.