Oct.27, 2003

Curator Meeting, Oct. 2003

Gene Expression CurationGene Expression Curation

~WormBase, 2003 ~

Oct.27, 2003

Curator Meeting, Oct. 2003

What kind of data are considered What kind of data are considered gene expression data?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 ...

Oct.27, 2003

Curator Meeting, Oct. 2003

WormBase Literature CurationWormBase Literature CurationFirst-Pass Curation Jamboree or Textpresso

~7,000 worm papers

RNAigene 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 TextpressoJamboree

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 Curation pipeline for Anatomical and temporal expression data.temporal expression data.

Oct.27, 2003

Curator Meeting, Oct. 2003

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

Expression Pattern SummaryExpression Pattern Summary(WS113)(WS113)

Oct.27, 2003

Curator Meeting, Oct. 2003

Gene Summary Page for lin-3Gene Summary Page for lin-3

Oct.27, 2003

Curator Meeting, Oct. 2003

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 CurationMicroarray Data Curation

Oct.27, 2003

Curator Meeting, Oct. 2003

Gene Summary Page for cpr-1Gene Summary Page for cpr-1

Oct.27, 2003

Curator Meeting, Oct. 2003

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 CurationGene Regulation Curation

Oct.27, 2003

Curator Meeting, Oct. 2003

OntologyOntology

≈ 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.