This document discusses microarray data analysis and the tools used. It explains that microarrays measure thousands of genes simultaneously and produce large amounts of data requiring processing. Several software tools are described that help with steps like image processing, normalization, and visualizing expression data on biological pathways. Microarray technology has major applications in identifying genes and determining gene expression levels, and it is used in medical, comparative genomics, and functional genomics research.

1. Presented by
Er. Ritesh Kumar
Department of Biotechnology
er.riteshkumar007@gmail.com
Biotechnology – 3rd Year
Unit -1st

2. Microarray data analysis
• Micro-array also known as DNA chip, Gene
Chip to measure 1000 of genes
simultaneously.
• Micro array helps in estimating the amount of
protein in the cell and a lots of information
can be derived from this technology.
• Microarray data analysis is the final step in
reading and processing data produced by
a microarray chip.

3. • Samples undergo
various processes
including purification
and scanning using the
microchip, which then
produces a large
amount of data that
requires processing via
computer software.

5. DNA micro array technology is used for two
major applications:-
 To identify the genes.
 To determine the expression level of genes.
 The micro-array technology is a combination of wet
lab techniques, statistical analysis and application
information to the data.

6. Tools for micro array
• A microarray experiment generates a large volume of data,
originally as image files which are later analyzed into
meaningful results.
• The whole process involves a number of steps and a number of
software and tools to obtain dependable expression values for
each gene.
– Soft finder
– SAGE (Serial Analysis of gene expression)
– MADAM (Micro array data manager)
– MIDAS (Micro array data analysis system)
– SNOMAD
– GenMAPP

7. Soft finder
• It is a tool for micro array
image processing using
TIFF(Text Image file
format) file generated by
micro array scans.
SAGE
• It is a tool that allow the
digital analysis of overall
gene expression pattern
because SAGE doesn’t
require a pre-existing probe,
it can be used to identify
and quantitate new gene.
Tools for micro array

8. MADAM
• This program provide data
entry form, data report form
& other application which is
necessary to maintain an
micro-array data for further
analysis.
MIDAS
• It is a part of TM group of
software. The software is
designed to process the raw
expression values from
Spot-finder, perform
normalization, and data
adjustment techniques along
with various filtration
options.
Tools for micro array

9. • SNOMAD is a web-based
tool and has various
normalization options for
two-channel and single-
channel experiments. The
data need to be uploaded in
appropriate format and the
choice of normalization
techniques selected.
• GenMAPP is a computer
application designed to
visualize gene expression
and other genomic data on
maps representing
biological pathways and
groupings of genes.
Tools for micro array
SNOMAD GenMAPP

10. • 4DXpress -- expression database in four dimensions. A database for cross-
species expression pattern comparisons.
• Allen Brain Atlas -- A Genome-wide atlas of gene expression in the adult
mouse brain. Access interactive, genome-wide image database of gene
expression in the mouse brain.
• ArrayExpress -- A public repository for microarray gene expression data at
the EBI. Submit or search annotated microarray data.
• DAVID -- A Database for Annotation, Visualization and Integrated
Discovery
• TMAD -- The Stanford Tissue Microarray Database Find annotated tissue
images and associated expression data.
Some other tools for micro array
analysis are:-

11. • Medical Applications:- To identify genes involved in
disease, comparing gene expression between the healthy cells
and diseased person.
• Comparative Genomics:- Micro-array data from different
species. It can be used to study genomic preference between
species.
• Functional Genomics:- Micro-array is used in the area of
functional genomic and gene annotation i.e., determination of
the function of large number of genes.
• Protein & Peptide micro-array:- This technique is also used
to identify protein - protein enzyme substrate and protein
molecule interaction.
Applications of micro array technology