Mary Ann Tuli Advisory Board Meeting, CSHL 2005

WormBase and the CGCWormBase and the CGC

Mary Ann Tuli

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Growth of genetic dataGrowth of genetic data

0

2000

4000

6000

8000

10000

12000

14000

CGC GeneName

Gene Class Allele Strain Multipointdata

WS120 Mar 2004

WS130 Aug 2004

WS140 Mar 2005

WS150 Oct 2005

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

WBGeneWBGene

≈ ?Gene model introduced in April 2004 (WS124)

≈ Name server – streamlining gene tracking

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Gene ClassesGene Classes

≈ 200 classes with no members

≈ 1692 CGC names not connected to sequences

≈ let and seven TM receptors are largest gene classes

1250

1300

1350

1400

1450

1500

1550

1600

1650

GeneClasses

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

CGC Gene NamesCGC Gene Names

0

1000

2000

3000

4000

5000

6000

7000

CGC Gene Name

WS100 May 2003

WS110 Oct 2003

WS120 May 2004

WS130 Aug 2004

WS140 Mar 2005

WS150 Oct 2005

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Gene Naming PipelineGene Naming Pipeline

E-mail

Web Form

Submitter

Geneace Curator

CGC

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Developments – Tracking Developments – Tracking gene namesgene names

Before:Gene_name: abu-1 Gene_class: abu-1Other_name: pqn-1 Remark“pqn-1 is Other_name of

abu-1 and has been merged into it”

After:Gene_name: abu-1 Gene_class: pqnOther_name: pqn-1 Old_member: pqn-1

Gene_name: pqn-1Former_member_of: pqn

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Developments – Tracking Developments – Tracking gene namesgene names

≈ Former_member_of and Old_member introduced in WS144

≈ WS150 = 663 CGC Other_names in 291 gene classes

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Developments - StatusDevelopments - Status

≈ Before:≈ Live tag only in ?Gene model≈ Absence implied object was Dead≈ Difficult to differentiate between different

statuses

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Developments - StatusDevelopments - Status

≈ After:≈ Status tag introduced in Gene and

Variation model (WS144)≈ Live, Dead or Suppressed

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

The Variation ClassThe Variation Class

Variation ClassWS140

Locus Class Allele Class

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

The Variation ClassThe Variation Class

≈ Type of Variation≈ Deletion≈ Insertion_and_deletion≈ Insertion≈ Substitution≈ Mos_insertion≈ Transposon_insertion≈ SNPs

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Growth in Allele DataGrowth in Allele Data

0

2000

4000

6000

8000

10000

12000

14000

WS120WS130

WS140WS150

Total

Knockouts

≈ Nearly 10,000 manually curated alleles

≈ Most have at least a gene connection

≈ Many have details of the strain carrying the mutation

≈ 1500 have rich annotation≈ Description of lesion≈ Connection to sequence

≈ Submission of Plasterk high throughput chemical mutagenesis/sequencing will result in many new alleles

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Allele Submission PipelineAllele Submission Pipeline

E-mail

Web Form

SubmitterNBPGeneace Curator

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Knockout AllelesKnockout Alleles

0

200

400

600

800

1000

1200

1400

WS120WS130

WS140WS150

≈ Mark Edgley≈ Jeff Holmes

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Knockout AllelesKnockout Alleles

0200400600800

10001200140016001800 ≈ Shohei Mitani

NBP

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Knockout Alleles - plansKnockout Alleles - plans

≈ Possible Web form for collaborators to upload data

≈ Advantages≈ onus on user to provide accurate data≈ More efficient way for us to convey

changes in database conventions

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Strain DataStrain Data

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

10000

≈ Sent periodically to WormBase from Theresa Stiernagle

≈ Leads to merges of Gene names and sequences

≈ Leads to updates of tag- genes

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Strain Data – tag gene classStrain Data – tag gene class

≈ All genes with KO alleles should have name which follows recommendations e.g. unc-12 not R09B3.4

≈ tag- genes assigned…but the list kept growing

≈ No longer assign new tag- genes

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Laboratory DataLaboratory Data

460

470

480

490

500

510

520

530

540

550

WS120WS130

WS140WS150

Labs

≈ Laboratory data sent from the CGC and Caltech

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Multipoint DataMultipoint Data

0

500

1000

1500

2000

2500

3000

3500

4000

4500

5000

WS12

0

WS13

0

WS14

0

WS15

0

Total

Inferred

≈ Process of adding inferred multi_pt_data continues

≈ Script in Jan 2004 to add inferred data.

≈ 1996 ~1,300 genetic marker loci

≈ Mar 2004 – 2,500 markers≈ Oct 2005 – 4,000 markers

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

The Genetic MapThe Genetic Map

≈ Recent transfer of knowledge from Jonathan Hodgkin and Richard Durbin is enabling WormBase to update the genetic map when new information becomes available.

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

The end of the CGC contractThe end of the CGC contract

≈ Subcontract between CGC and Oxford (Jonathan Hodgkin) runs until May 2007.

≈ WormBase needs to prepare for this.

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

Future PlansFuture Plans

≈ Continue to ensure timely incorporation of all data..including alleles!

≈ Streamline submission processing≈ Update Web forms≈ Improve scripts

≈ Improve models

Mary Ann TuliAdvisory Board Meeting, CSHL 2005

CollaboratorsCollaborators

≈ The CGC≈ Jonathan Hodgkin≈ Bob Herman & Theresa Stiernagle

≈ The Knockout Consortium≈ Mark Edgley≈ Jeff Holmes

≈ National BioResource Centre, Japan≈ Shohei Mitani