Computer analysis of two‐dimensional gels: Automatic matching

Miller, Mark J.; Olson, Arthur D.; Thorgeirsson, Snorri S.

doi:10.1002/elps.1150050510

Cited by 49 publications

(11 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Soft community matching can be done so as to minimize the distance between the two matrices [27]. In computer vision, community matching has been Table 1: Table of Notations done by using cluster features like position, intensity, shape and average gray-scale difference [23], and degree of match between surrounding clusters [28]. Words-based communities could be matched using TF-IDF similarity [9].…”

Section: Related Workmentioning

confidence: 99%

Integrating community matching and outlier detection for mining evolutionary community outliers

Gupta

Gao²,

Sun

et al. 2012

Proceedings of the 18th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

View full text Add to dashboard Cite

Temporal datasets, in which data evolves continuously, exist in a wide variety of applications, and identifying anomalous or outlying objects from temporal datasets is an important and challenging task. Different from traditional outlier detection, which detects objects that have quite different behavior compared with the other objects, temporal outlier detection tries to identify objects that have different evolutionary behavior compared with other objects. Usually objects form multiple communities, and most of the objects belonging to the same community follow similar patterns of evolution. However, there are some objects which evolve in a very different way relative to other community members, and we define such objects as evolutionary community outliers. This definition represents a novel type of outliers considering both temporal dimension and community patterns. We investigate the problem of identifying evolutionary community outliers given the discovered communities from two snapshots of an evolving dataset. To tackle the challenges of community evolution and outlier detection, we propose an integrated optimization framework which conducts outlier-aware community matching across snapshots and identification of evolutionary outliers in a tightly coupled way. A coordinate descent algorithm is proposed to improve community matching and outlier detection performance iteratively. Experimental results on both synthetic and real datasets show that the proposed approach is highly effective in discovering interesting evolutionary community outliers.

show abstract

Section: Related Workmentioning

confidence: 99%

Integrating community matching and outlier detection for mining evolutionary community outliers

Gupta

Gao²,

Sun

et al. 2012

Proceedings of the 18th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

View full text Add to dashboard Cite

show abstract

“…Subsequently, additional spots surrounding the landmark spots were matched by shifting the overlaid images to accomodate slight variations between gels. Cross-matching of spots on multiple gels established a data base which was automatically searched by the software to identify and display polypeptides present (or absent) on specified gels [21].…”

Section: Analysis Of Polypeptide Patternsmentioning

confidence: 99%

Polypeptide composition of normal and neoplastic human breast tissues and cells analyzed by two-dimensional gel electrophoresis

Maloney

Paine

Russo

1989

Breast Cancer Res Tr

View full text Add to dashboard Cite

The protein populations of epithelial cells cultured from two neoplastic and five non-neoplastic human breast tissues were resolved and displayed by two-dimensional polyacrylamide gel electrophoresis and silver-staining. With a computer-based image analysis system, we identified eight polypeptides which are present in both of the neoplastic cell lines, but absent from all five of the cultures of non-neoplastic breast cells. The eight polypeptides are not unique to cells cultured from neoplastic breast, because they are also found in cells cultured from non-breast tissues, both neoplastic and non-neoplastic. Two of the eight polypeptides (approximately Mr 25,000/pI 4.4 and approximately Mr 31,000/pI 5.5) are present in the patterns of whole tissue samples from infiltrating ductal carcinomas and absent in most normal breast tissue.

show abstract

“…Computer algorithms for 2D gel analysis, which address these problems, are the subject of an extensive literature (2,(8)(9)(10)(11)(12)(13)(14).…”

Section: Peak Finding and Matchingmentioning

confidence: 99%

Apparatus for direct counting of beta-rays from two-dimensional protein gels: measurement of changes in protein synthesis due to changes in density of Chinese hamster ovary cells.

Anderson¹,

Puck²,

Shera³

1987

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

A method is described for scanning twodimensional protein gels that utilizes direct counting of a-rays instead of autoradiography. The methodology is compared with autoradiographic results and data are presented demonstrating changed patterns of protein synthesis accompanying changes in cell density. The method is rapid and permits identification of differences in protein abundance of -10% for a substantial fraction of the more prominent proteins. A modulation effect of >5 standard deviations is shown to occur for an appreciable number of the proteins that accompany the inhibition of cell growth due to contact inhibition. The method promises application to a variety of biochemical and genetic problems designed to delineate changes in protein synthesis accompanying changes in genome, molecular environment, history, and state of differentiation of the cell populations studied.The combination of somatic cell genetics and recombinant DNA methodologies has made possible an enormous increase in the elucidation of the structure of the mammalian cell genome. However, perhaps the central unsolved problem of human genetics revolves around the following question: How are the cells of the different tissues, despite their possession of identical chromosomal and DNA structures, able to produce different and specific patterns of protein biosynthesis? Understanding of this process will illuminate the regulatory mechanisms that govern gene expression and the molecular dynamics of disease in the various tissues. Therefore, it becomes necessary to be able to study the spectrum of protein biosynthesis of different cell populations and to correlate changes in this pattern with changes in the DNA state, the molecular environment, and the differentiation history of the cell, with precision.The two-dimensional (2D) gel technique pioneered by O'Farrell (1) offers great power in elucidating protein biosynthetic patterns since it permits examination of large numbers of the proteins synthesized by any cell population. The present study was undertaken to eliminate the necessity of employing autoradiography to visualize the points of deposition in the gel of the peptides containing radioactively labeled amino acids and to measure changes in quantity with precision. An exposure of autoradiographic films can be time consuming and a linear relationship between the amount of film blackening and quantity of peptide deposited is obtained only over a relatively limited range of intensities, making quantitative comparisons difficult. Quantification using autoradiography requires a series of autoradiographs with different exposure times (2).We describe here a method for detection and quantitation of radiolabeled peptides in 2D gels, in which the a-rays are counted directly. The methodology is described, its results are compared with the autoradiographic technique, and some representative biological findings are reported. In this study we have concentrated attention on the group of the most abundant proteins synthesized by the Chinese hamster ...

show abstract

Computer analysis of two‐dimensional gels: Automatic matching

Cited by 49 publications

References 13 publications

Integrating community matching and outlier detection for mining evolutionary community outliers

Integrating community matching and outlier detection for mining evolutionary community outliers

Polypeptide composition of normal and neoplastic human breast tissues and cells analyzed by two-dimensional gel electrophoresis

Apparatus for direct counting of beta-rays from two-dimensional protein gels: measurement of changes in protein synthesis due to changes in density of Chinese hamster ovary cells.

Contact Info

Product

Resources

About