# Presentation: 320554

## The Integrated Molecular Analysis of Genomes and their Expression Consortium’s Data Mining Tools:  Introducing the IQ

**The Integrated Molecular Analysis of Genomes and their Expression Consortium’s Data Mining Tools:  Introducing the IQ**

- Peg Folta
- Lawrence Livermore National Laboratory
- 3/12/02

- TRANSCRIPTOME 2002
- Seattle, WA

## I.M.A.G.E. maintains world’s largest publicly available cDNA collection

- 5,819,514 clones arrayed

- I.M.A.G.E. clones account for 64% of human ESTs in GenBank

- cumulative

- arrayed

- *

## The I.M.A.G.E. collection has been shaped by projects (C-GAP, MGC...)

- Species

- Library Method

- Developmental state

- Tissue

- Clone sequence

## Informatics focus this year was on tools to characterize and query the collection.

- IMAGEne – mature clustering tool
- IMAGEne Tissue – allows searching of tissue type dominance in clusters
- IQ – Intelligent Query tool allows mining of I.M.A.G.E. data
- Library/plate query – allows selective searching of libraries and plates
- Problem report and query – allows users to report or query problems related to I.M.A.G.E. clones

## IMAGEne-Human Process

- 2,289,020
- Quality
- I.M.A.G.E
- sequences

- 14,566
- NCBI
- Ref Seq

- IMAGEne

- 1,676,516
- Sequences

- 623,294
- Sequences

- Remaining
- Sequences

**>50 basepairs of contiguous, non-repeat sequence**

- 14,566

- Candidate
- Clusters
- w/consensus

- 67,521

- 268,472

- 279,262
- Lower quality
- I.M.A.G.E
- Sequences

## Initial query page, construct the query.

## Clusters matching query results, chose your cluster.

## Display of cluster

## Known gene clusters with full length I.M.A.G.E. clones have doubled in number.

- Cluster
- coverage

- Avg. gene
- length

**3392**

**2763**

**3380**

**1896**

**1578**

## Known Gene Cluster distribution of full length clones

- avg. length = 948

## Candidate gene clusters consensus sequence and contigs are generated by CAP4

- 61,314

- 4,971

- 824

- 95

- 227

- 40

## Candidate Gene cluster characteristics.

## Singleton:  Wheat within the chaff

-  305 full insert sequences are singletons.
-  62,143 singletons have a 3’ PolyA site.

- Avg. length is 547

## IMAGEne Tissue query allows searching for tissue proportions within clusters.

## Introducing the Intelligent Query - IQ

- For a given category (currently clone and library) a user can specify a query based on key database attributes.
- The user can specify the fields returned.
- Various result format options (HTML, text)
- Initial version was rolled out last summer
- New functionality to be added this year (additional categories, etc.)

## Specify a clone-based query.

## Next specify what clone centric results will be provided and in what format.

## HTML version of clone-based query results.

## Specify a library-based query.

## Similarly specify what library centric results will be provided.

## HTML version of library-based query results.

## Other tools to mine I.M.A.G.E. information

- Query plates from libraries.

- Query for reported problems.

## Quality control for historical collection

| Plates | Source | Well Error Rate |
| --- | --- | --- |
| 1-3705 | Incyte | 13 |
|  | LLNL Master  | 10 |
|  | Research Genetics | 12 |
|  | Resource Center of HumanGenome Project | 10 |
|  | ATTC | 11 |
| 3,796-6000 | Incyte | 7 |
|  | LLNL Master  | 7 |
|  | Research Genetics | 10 |
|  | Resource Center of Human Genome Project | 12 |

## QC on-going

| Months | Well error rate | Plate Error Rate | Well error rate | Plate Error Rate |
| --- | --- | --- | --- | --- |
| 6/2000 | 1  (1,3) | 0 | 7  (4,11) | 2 |
| 10/2000 | 1  (0,3) | 0 | 1  (0,3) | 2 |
| 12/00 | 0  (0,2) | 2 | 1  (0,3) | 2 |
| 1/01 | 2  (1,4) | 0 | 6  (4,11) | 3 |
| 2/01 | 1  (0,3) | 0 | 2  (1,5) | 2 |
| 3/01 | 2  (1,5) | 2 | 2  (1,5) | 0 |
| 4/01 | 1  (0,3) | 2 | 2  (1,4) | 0 |
| 5/01 | 0  (0,1) | 0 | 2  (1,5) | 0 |
| 6/01 | 1  (0,3) | 0 | 1  (0,4) | 0 |
| 7/01 | 1   (0,4) | 0 | 2  (1,6) | 0 |
| 8/01 | 2  (1,3) | 0 | 3  (2,6) | 0 |

- LLNL Replication

- Master vs. GenBank

## Ongoing QC results

- On-going
- Comparing master to GenBank

- Error in replication @ LLNL

## Next for I.M.A.G.E. Informatics

- Extensive expansion of query tools and data access
- IMAGEne non-species specific
- Analysis of human cluster candidate genes and singletons
- Redo of web site, easier to navigate
- MUCH influenced by public needs.....you have a say!

## Acknowledgements

- LLNL
- Christa Prange, I.M.A.G.E. PI
- Tim Harsch, Amber Johnston, Julie Amundson
- Sponsors
- DOE, Marv Stodolsky
- NIH, Bob Strausberg

- image.llnl.gov