Title: A new approach to detect similar proteins from 2D gel electrophoresis images
1A new approach to detect similar proteins from 2D
gel electrophoresis images
- Nawaz Khan and Shahedur Rahman
- Proceedings of the Third IEEE Symposium on
BioInformations and BioEngineering(BIBE03), 2003 - Speaker Ho, Yu An(???)
- Date 2004/6/3
2Outline
- Introduction
- Methodology
- Experiments and results
- Conclusion
3Introduction (1/4)
- GELLAB system (1981)
- Uses the point pattern comparison.
- MELANIE (1997)
- Compares spot clusters.
- Panek and Vohradsky (1999)
- Use the information from the neighbourhood spots
for comparison.
4Introduction (2/4)
- Although the spot in the source and target image
can be identical or similar, but still the
following parameters can very - Background value
- Protein spot intensity
- Protein spot shape
- Noise in the image
5Introduction (3/4)
Triosophosphate isomerase protein spots in two
different images.
6Introduction (4/4)
- This paper presents a novel approach for
identifying the identical or similar protein spot
in 2D gel electrophoresis images by considering
the following factors - 2D gel electrophoresis protein spots differ
significantly in two different images even when
they represent the same protein. - Same or similar protein spots will lie at the
same line of path because of their
electrophoresis mobility and molecular weight. - The intensity of the matched regions in both
images can be different even thought it shows a
correct matching. - The region of similar spot at the target image
must lie at the same or different directional
vector on the line of path.
7Methodology
- Determining the position of the protein spot in
the source image - Defining the region of interest
- Matching the selected protein spot in the target
image - Searching for the protein spot in the
neighbourhood area - Selecting the best matched spot
- Retrieving 3D structure of a protein
81. Determining the position of the protein spot
in the source image (1/3)
Source image divided into four quadrants.
91. Determining the position of the protein spot
in the source image (2/3)
101. Determining the position of the protein spot
in the source image (3/3)
Angle produced with the horizontal axis for any
point of interest on the vertical plane.
112. Defining the region of interest (1/2)
122. Defining the region of interest (2/2)
(a) A set of points defined by the user, (b)
Defining the region of interest.
133. Matching the selected protein spot in the
target image
144. Searching for the protein spot in the
neighbourhood area (1/2)
Non emptied straight line of path in the target
image to determine the neighbourhood protein spot
154. Searching for the protein spot in the
neighbourhood area (2/2)
165. Selecting the best matched spot
17Experiments and results
- Identifying a spot along the line of path
- Identifying a spot of interest in the target
image - Matching on 2D gel electrophoresis image
- Shape comparison
- Retrieving 3D image
181. Identifying a spot along the line of path (1/2)
191. Identifying a spot along the line of path (2/2)
threshold
Identifying a spot along the line of path using
the low intensity values.
202. Identifying a spot of interest in the target
image (1/3)
212. Identifying a spot of interest in the target
image (2/3)
222. Identifying a spot of interest in the target
image (3/3)
233. Matching on 2D gel electrophoresis image (1/2)
243. Matching on 2D gel electrophoresis image (2/2)
254. Shape comparsion
- Source spot
- Detected spot
265. Retrieving 3D image (1/3)
- The following parameters are stored in the target
specific dedicated database - Coordinates
- Intensity values
- Positional orientation
- Average shape radius
275. Retrieving 3D image (2/3)
285. Retrieving 3D image (3/3)
29Conclusion
- This approach reduces the number of candidate
spot to be identified within the image.