Databases for Microarrays

Vidhya Jagannathan SIB, Lausanne

Overview

Microarray data in a nutshell Why databases? What data to represent? What is a database? Different data models E-R modelling Microarray Databases Standards being developed
Vidhya Jagannathan, SIB, Lausanne

Microarray Experiment

Vidhya Jagannathan, SIB, Lausanne

Microarray Data in a Nutshell

Lots of data to be managed before and after the experiment. Data to be stored before the experiment .

Description of the array and the sample. Direct access to all the cDNA and gene sequences, annotations, and physical DNA resources. Raw Data - scanned images. Gene Expression Matrix - Relative expression levels observed on various sites on the array.

Data to be stored after the experiment

Hence we can see that database software capable of dealing with larger volumes of numeric and image data is required.
Vidhya Jagannathan, SIB, Lausanne

Why Databases?

Tailored to datatype Tailored to the Scientists Intuitive ways to query the data

Diagrams, forms, point and click, text etc.

Query optimisation, indexes, compact physical storage.

Support for efficient answering of queries.

Vidhya Jagannathan, SIB, Lausanne

Data Representation

Goal: Represent data in an intuitive and convenient manner

Without unnecessary replication of information Making it easy to write queries to find required information Supporting efficient retrieval of required information

Vidhya Jagannathan, SIB, Lausanne

What is a Database?

A database is an organised collection of pieces of structured electronic information.

Example 1: Libraires use a database system to keep track of library inventory and loans. Example 2: All airlines use database system to manage their flights and reservations. The collection of records kept for a common purpose such as these is known as a database.

The records of the database normally reside on a hard disk and the records are retrieved into computer memory only when they are accessed. So the reasons are obvious why we need to discuss about a Microarray database.

Vidhya Jagannathan, SIB, Lausanne

Data Models

Describes a container for data and methods to store and retrieve data from that container.

Abstract math algorithms and concepts. Cannot touch a data model. Very useful
Vidhya Jagannathan, SIB, Lausanne

Types of Data Models

Ad-hoc file formats (not really data models!) Relational data model Object-relational data model Object-oriented data model XML (Extensible Markup Language)

Vidhya Jagannathan, SIB, Lausanne

Ad-hoc File Formats

The various 'ad-hoc' file formats in use for microarray data are:

Flat file formats. Spread sheet formats. Not the least - Even MS-Word documents !!!

Very rudimentary method to store data . Sometimes contains redundant information. Extremely inefficient for retrieval of particular subsets of the results.

Vidhya Jagannathan, SIB, Lausanne

Relational Data Model

Most prevalent and used in many databases developed today. The collection of related information is represented as a set of tables. Data value is stored in the intersection of row and column Column values are of the same kind. A Simple data validation. Rows are unique. So no data redundancy and every row is meaningful and can be identified by the unique key. Utilises Structured Query Language (SQL) for data storage, retrival and manipulation.
Vidhya Jagannathan, SIB, Lausanne

Example
Table GENE
GENE_ID GB2VN GB2VN32 CONTIG_ID NT_0106058.3 NT_0106051.3 CONTIG_START 2354807 2308745 CONTIG_END 2360778 2321072 CONTIG_STRAND Complement Complement

Row or Record Field or Column

Vidhya Jagannathan, SIB, Lausanne

Example
GENE
GENE_ID GB2VN CONTIG_ID NT_0106058.3 CONTIG_BEGIN 2354807 CONTIG_END 2360778 CONTIG_STRAND Complement

GB2VN32

NT_0106051.3

2308745

2321072

Complement

CLASSIFICATION
CLASS_ID MSX2 GO:0003677 GENE_ID GB2VN GB2VN32 DESCRIPTION MSH(Drosophila) DNA binding TYPE Gene Molecular function

Vidhya Jagannathan, SIB, Lausanne

Advantages of Relational Model

Allows information to be broken up into logical units and stored in tables. Allows combining data from different tables in different ways to derive useful information. Great for queries involving information from multiple original sources. Can easily gather related information.

e.g. information about a particular gene from multiple datasets/experiments

Vidhya Jagannathan, SIB, Lausanne

Object Oriented Model

Object Oriented Model allows real world data to be represented as objects. Objects encapsulate the data and provide methods to access or manipulate it. Objects with specific structure and set of methods are said to belong to the object class. Allows new classes to be created by extending the description of the parent class. Child classes inherit the data and methods of the parent class.
Vidhya Jagannathan, SIB, Lausanne

Example
OODBMS Biomolecule . String seq Inherits DNA DNA DNA

get_bio_seq()

Inherits Protein Protein Protein

Vidhya Jagannathan, SIB, Lausanne

Example - ArrayExpress
ArrayExpress
ExpressionValue

Sample

Hybridization

Array

Experiment

External links
Ontology e.g., organism taxonomy Reference e.g., publication, web resource Database e.g., gene in SWISS-prot

Vidhya Jagannathan, SIB, Lausanne

Database Design

Entity-Relationship Concept
Entity A Relationship
Examples

Entity B

Vidhya Jagannathan, SIB, Lausanne

Entities

are real world objects

ex: gene ex: gene_id, sequence

contain attributes

are drawn as rectangle boxes that holds the name of the entity and attribute in two different notations as there is no standard!
Gene
sequence gene_id
Vidhya Jagannathan, SIB, Lausanne

Gene gene_id sequence

notation 2

notation 1

Relationship

Relationships provide connections between two or more entities

ex: Which genes were used in which experiment

When two entities are involved in a relationship, it is known as binary relationship. When three entities are invoved in a relationship, it is called as ternary relationship. When more than three entities are involved in a relationship, it is usually broken in to one or more binary or ternary relationships. are drawn as a line linking the involved entities as: Gene used_in
Vidhya Jagannathan, SIB, Lausanne

Experiment

Example E-R Diagram

Gene gene-id sequence
Expt-Exptr

Experimenter Experimenter-Id Name E-mail Dept. Institution Sample Sample-Id Organism Cell-type {Drug-Ids} Array Array-Id Manufacturer Type Batch

Expression-value value

Expt-Sample

Experiment Experiment-Id Date Image

Notation 1 Expt-Array

Multivalued attribute

* Many-to-one

Vidhya Jagannathan, SIB, Lausanne

Object relational data model

Improved relational model by adding some features from object data models. Information is represented as in relational models but column values not restricted to one mutliple values are allowed. Example (sample table in previous slides):
sampe-id organism celltype drug_id d1 d2

s001 s002

ecoli ecoli

c123 c123

ac1 ac3

nm nm

Vidhya Jagannathan, SIB, Lausanne

Queries, queries, queries!!

Given a collection of microarray generated gene expression data, what kind of questions the users wish to pose. Constructing an extensive list of possible interesting queries and data mining problems that has to be supported by the database will facilitate the design process.
Vidhya Jagannathan, SIB, Lausanne

Queries, queries, queries!!

Query to the data

Which genes are linked ? Which genes are expressed similarly to my gene XYZ? Which genes have a changed the expression in a second condition ? Which genes are co-expressed in differing conditions ? classification (of tumors, diseased tissues etc.): which patterns are characteristic for a certain class of samples, which genes are involved?

Vidhya Jagannathan, SIB, Lausanne

More Queries !!!

Queries that add a link in additional knowledge

functional classification of genes: Are changes clustered in particular classes? metabolic pathway information: Is a certain pathway/route in a pathway affected? disease information & clinical follow up: correlation to expression patterns. phenotype information for mutants: Are there correlations between particular phenotypes and expression patterns?

Vidhya Jagannathan, SIB, Lausanne

More Queries !!!

in what region is the interesting gene located in the genome? is there synteny in this region with other species? is there a known trait that maps to this region?

Vidhya Jagannathan, SIB, Lausanne

Query Language

Language in which user requests information from the database.

SQL Data definition helps you implement your model and data manipulation helps you modify and retrive data Advantages: Can specify query declaratively and let database system figure out best way of finding answers Supports queries of medium complexity Specialized languages SQL language statements are not abstract but very close to spoken language.
Vidhya Jagannathan, SIB, Lausanne

Basic SQL Queries

Find the image for experiment number 1345 select image from experiment where experiment-id = 1345; Find the experiment-id and image of all experiments involving e-coli
select experiment-id, image from experiment, sample where experiment.sample-id = sample.sample-id and sample.organism = `e.coli; All combinations of rows from the relations in the from clause are considered, and those that satisfy the where conditions are output

Vidhya Jagannathan, SIB, Lausanne

Interfacing

SQL queries are carried out on terminal screen which

is not very useful and user friendly for an end user, so applications are created to interface more friendly staments with the SQL statements

More complex queries (e.g. data mining such as

A web form is a typical example of interface for SQL Applications for data loading.

classification and clustering) are very imporatant part of the Microarray Analyis Protocol It is very important to interface the various applications we use to analyse the retrieved data with database.
Vidhya Jagannathan, SIB, Lausanne

Vidhya Jagannathan, SIB, Lausanne

Gene Expression Databases Require Integration

There are many different types of data presenting numerous relationships.

There are a number of Databases with lots of information.

Experiments need to be compared because the experiments are very difficult to perform and very expensive.
Solution: Make all the databases talk the same language. XML was the choice of data interchange format.

Vidhya Jagannathan, SIB, Lausanne

Why XML?

Why XML ?: XML provides the method for defining the meaning or semantics of data. Example : A XML file of the earlier table we defined
<gene_features> <gene_id>GBVN32</gene_id> <contig_id>NT_010651</contig_id> <contig_start>2354807</contig_start> <contig_end>2360778</contig_end> <contig_strand>Complement</contig_strand> </gene_features>

Vidhya Jagannathan, SIB, Lausanne

Mapping XML to Relational Database

The Data Structure in XML is defined in Document Type Descrciptor as follows

<!ELEMENT <!ELEMENT <!ELEMENT <!ELEMENT <!ELEMENT gene_id (#PCDATA)> contig_id (#PCDATA)> contig_start (#PCDATA)> contig_end (#PCDATA)> contig_sequence (#PCDATA)>

This kind of DTD also helps us to have control over the vocabulary used. SQL:
create table gene ( gene_id varchar(5) primary key, contig_id varchar(10) not null, contig_start integer not null, contig_end integer not null, contig_sequence text not null);

So the DTD can be directly mapped into a relational database.

Vidhya Jagannathan, SIB, Lausanne

MAGE-ML As Data Interchage Format

Expression Data

Converter (program)

MAGE-ML

Databases
Vidhya Jagannathan, SIB, Lausanne

Existing Microarray Databases

Several gene expression databases exist:Both commercial and non-commercial. Most focus on either a particular technolgy or a particular organism or both. Commercial databases:

Rosetta Inpharmatics and Genelogic, the specifics of their internal structure is not available for internal scrutiny due to their proprietary nature.

Some non-commercial efforts to design more general databases merit particular mention. We will discuss few of the most promising ones

ArrayExpress - EBI The Gene expression Omnibus (GEO) - NLM The Standford microarray Database ExpressDB - Harvard Genex - NCGR Vidhya Jagannathan, SIB, Lausanne

Vidhya Jagannathan, SIB, Lausanne

ArrayExpress

Public repository of microarray based gene expression data. Implemented in Oracle at EBI. Contains:

several curated gene expression datasets possible introduction of an image server to archive raw image data associated with the experiments.

Accepts submissions in MAGE-ML format via a webbased data annotation/submission tool called MIAMExpress.
A demo version of MIAMExpress is available at: http://industry.ebi.ac.uk/~parkinso/subtool/subtype.html Provides a simple web-based query interface and is directly linked to the Expression Profiler data analysis tool which allows expression data clustering and other types of data exploration directly through the web. Vidhya Jagannathan, SIB, Lausanne

Gene Express Omnibus

The Gene Expression Omnibus ia a gene expression database hosted at the National library of Medicine It supports four basic data elements

Platform ( the physical reagents used to generate the data) Sample (information about the mRNA being used) Submitter ( the person and organisation submitting the data) Series ( the relationship among the samples).

It allows download of entire datasets, it has not ability to query the relationships Data are entered as tab delimited ASCII records,with a number of columns that depend on the kind of array selected. Supports Serial Analysis of Gene Expression (SAGE) data.
Vidhya Jagannathan, SIB, Lausanne

Stanford Microarray Database

Contains the largest amount of data. Uses relational database to answer queries. Associated with numerious clustering and analysis features. Users can access the data in SMD from the web interface of the package. Disadvantage :

It supports only Cy3/Cy5 glass slide data It is designed to exclusively use an oracle database Has been recently released outside without anykind of support !!
Vidhya Jagannathan, SIB, Lausanne

MaxdSQL

Minor changes to the ArrayExpress object data model allowed it to be instantiated as a relational database, and MaxdSQL is the resulting implementation. MaxdSQL supports both Spotted and Affymetrix data and not SAGE data. MaxdSQL is associated with the maxdView, a java suite of analysis and visualisation tools.This tool also provides an environment for developing tools and intergrating existing software. MaxdLoad is the data-loading application software.

Vidhya Jagannathan, SIB, Lausanne

Vidhya Jagannathan, SIB, Lausanne

GeneX

Open source database and integrated tool set released by NCGR http://www.ncgr.org. Open source - provides a basic infrastructure upon which others can build. Stores numeric values for a spot measurement (primary or raw data), ratio and averaged data across array measurements. Includes a web interface to the database that allow users to retrieve:

Entire datasets, subsets Guided queries for processing by a particular analysis routine Download data in both tab delimited form and GeneXML format ( more descriptions later)

Vidhya Jagannathan, SIB, Lausanne

Vidhya Jagannathan, SIB, Lausanne

ExpressDB

ExpressDB is a relational database containing yeast and E.coli RNA expression data. It has been conceived as an example on how to manage that kind of data. It allows web-querying or SQL-querying. It is linked to an integrated database for functional genomics called Biomolecule Interaction Growth and Expression Database (BIGED). BIGED is intended to support and integrate RNA expression data with other kinds of functional genomics data

Vidhya Jagannathan, SIB, Lausanne

Survey of existing microarray systems

This survey is based on the article published in
BRIEFINGS IN BIOINFORMATICS, Vol 2, No 2, pp 143-158, May 2001:
A comparison of microarray databases

Vidhya Jagannathan, SIB, Lausanne

The Microarray Gene Expression Database Group (MGED)

History and Future:

Founded at a meeting in November, 1999 in Cambridge, UK. In May 2000 and March 2001: development of recommendations for microarray data annotations (MAIME, MAML). MGED 2nd meeting:

establishment of a steering committee consisting of representatives of many of the worlds leading microarray laboratories and companies

MGED 4th meeting in 2002:

MAIME 1.0 will be published MAML/GEML and object models will be accepted by the OMG concrete ontology and data normalization recommendations will be published. information can be obtained from http://www.mged.org

Vidhya Jagannathan, SIB, Lausanne

The Microarray Gene Expression Database Group (MGED)

Goals:

Facilitate the adoption of standards for DNA-array experiment annotation and data representation. Introduce standard experimental controls and data normalization methods. Establish gene expression data repositories. Allow comparision of gene expression data from different sources.
Vidhya Jagannathan, SIB, Lausanne

MGED Working Groups

Goals:

MIAME: Experiment description and data representation standards - Alvis Brazma

MAGE: Introduce standard experimental controls and data normalization methods - Paul Spellman. This group includes the MAGE-OM and MAGE-ML development. OWG: Microarray data standards, annotations, ontologies and databases - Chris Stoeckert NWG: Standards for normalization of microarray data and cross-platform comparison - Gavin Sherlock

Vidhya Jagannathan, SIB, Lausanne

References

URL:
Tutorial on Information Management for Genome Level Bioinformatics, Paton and Goble, at VLDB 2001: http://www.dia.uniroma3.it/~vldbproc/#tutEuropea European Molecular Biology Network http://www.embnet.org/ Univ. Manchester site (with relational version of Microarray data representation, and links to other sites) http://www.bioinf.man.ac.uk Database textbook with absolutely no bioinformatics coverage For Microarray Data http://linkage.rockefeller.edu/wli/microarray/

Vidhya Jagannathan, SIB, Lausanne