mary ann tuli advisory board meeting, cshl 2005 wormbase and the cgc mary ann tuli
TRANSCRIPT
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Mary Ann Tuli Advisory Board Meeting, CSHL 2005
WormBase and the CGCWormBase and the CGC
Mary Ann Tuli
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Growth of genetic dataGrowth of genetic data
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14000
CGC GeneName
Gene Class Allele Strain Multipointdata
WS120 Mar 2004
WS130 Aug 2004
WS140 Mar 2005
WS150 Oct 2005
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
WBGeneWBGene
≈ ?Gene model introduced in April 2004 (WS124)
≈ Name server – streamlining gene tracking
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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
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1400
1450
1500
1550
1600
1650
GeneClasses
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
CGC Gene NamesCGC Gene Names
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CGC Gene Name
WS100 May 2003
WS110 Oct 2003
WS120 May 2004
WS130 Aug 2004
WS140 Mar 2005
WS150 Oct 2005
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Gene Naming PipelineGene Naming Pipeline
Web Form
Submitter
Geneace Curator
CGC
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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
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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
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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
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Developments - StatusDevelopments - Status
≈ After:≈ Status tag introduced in Gene and
Variation model (WS144)≈ Live, Dead or Suppressed
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
The Variation ClassThe Variation Class
Variation ClassWS140
Locus Class Allele Class
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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
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Growth in Allele DataGrowth in Allele Data
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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
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Allele Submission PipelineAllele Submission Pipeline
Web Form
SubmitterNBPGeneace Curator
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Knockout AllelesKnockout Alleles
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WS120WS130
WS140WS150
≈ Mark Edgley≈ Jeff Holmes
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Knockout AllelesKnockout Alleles
0200400600800
10001200140016001800 ≈ Shohei Mitani
NBP
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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
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Strain DataStrain Data
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≈ Sent periodically to WormBase from Theresa Stiernagle
≈ Leads to merges of Gene names and sequences
≈ Leads to updates of tag- genes
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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
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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
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Mary Ann TuliAdvisory Board Meeting, CSHL 2005
Multipoint DataMultipoint Data
0
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4500
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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
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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.
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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.
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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
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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