Gene-Representing cDNA Clusters Defined by Hybridization of 57,419 Clones from Infant Brain Libraries with Short Oligonucleotide Probes

Drmanac, Snezana; Stavropoulos, N.A.; Labat, Ivan; Vonau, J.; Hauser, Bernard A.; Soares, Marcelo B.; Drmanac, Radoje

doi:10.1006/geno.1996.0517

Cited by 75 publications

(46 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…estimate (e.g., by evaluating control clones of known sequences) the range of positive hybridizations of the probes to be 5%-25%. Two different approaches could lead to the design of probes with higher matching rates: (1) The use of shorter probes than octamers increases matching frequencies statistically; Milosavljevic et al (1996) and Drmanac et al (1996) have shown that it is experimentally possible to hybridize and to evaluate heptamer probes. (2) The pooling of octamer probes is another way to increase matching frequencies.…”

Section: Discussionmentioning

confidence: 99%

“…The method of hybridization of short synthetic oligonucleotide probes to cloned cDNA sequences under high stringency conditions to extract genetic information has been demonstrated by a number of research groups in recent years (Lehrach et al 1990; Lennon and Lehrach 1991;Meier-Ewert et al 1993;Drmanac et al 1996;Milosavljevic et al 1996). Oligonucleotide fingerprinting is an efficient and fast approach to extract parallel gene expression information about all genes that are represented in a cDNA library from a specific tissue under analysis.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Large-Scale Clustering of cDNA-Fingerprinting Data

Herwig

Poustka²,

Müller³

et al. 1999

Genome Res.

194

120

View full text Add to dashboard Cite

Clustering is one of the main mathematical challenges in large-scale gene expression analysis. We describe a clustering procedure based on a sequential k-means algorithm with additional refinements that is able to handle high-throughput data in the order of hundreds of thousands of data items measured on hundreds of variables. The practical motivation for our algorithm is oligonucleotide fingerprinting-a method for simultaneous determination of expression level for every active gene of a specific tissue-although the algorithm can be applied as well to other large-scale projects like EST clustering and qualitative clustering of DNA-chip data. As a pairwise similarity measure between two p-dimensional data points, x and y, we introduce mutual information that can be interpreted as the amount of information about x in y, and vice versa. We show that for our purposes this measure is superior to commonly used metric distances, for example, Euclidean distance. We also introduce a modified version of mutual information as a novel method for validating clustering results when the true clustering is known. The performance of our algorithm with respect to experimental noise is shown by extensive simulation studies. The algorithm is tested on a subset of 2029 cDNA clones coming from 15 different genes from a cDNA library derived from human dendritic cells. Furthermore, the clustering of these 2029 cDNA clones is demonstrated when the entire set of 76,032 cDNA clones is processed.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Large-Scale Clustering of cDNA-Fingerprinting Data

Herwig

Poustka²,

Müller³

et al. 1999

Genome Res.

194

120

View full text Add to dashboard Cite

show abstract

“…ICRFp524), and 20,000 cDNA clones from the adult-liver library (see Resource Availability). Fifty-five thousand clones from the ICRFp524 and 20,000 clones from the ICRFp532 libraries were selected for OFP analysis (Meier-Ewert et al 1993Drmanac et al 1996;Milosavljevic et al 1996;Clark et al 1999). cDNA inserts first were PCR-amplified and spotted onto filters.…”

Section: Resultsmentioning

confidence: 99%

“…Typically, one representative clone is rearrayed for further analysis, such as tag sequencing. OFP technology has been used previously in the mapping of the herpes simplex virus genome (Craig et al 1990), the selection of clones for genomic shotgun sequencing (Radelof et al 1998), and for the characterization and normalization of cDNA libraries (Meier-Ewert et al 1993Drmanac et al 1996;Milosavljevic et al 1996;Poustka et al 1999). Here, we have used OFP to characterize 75,000 cDNAs from zebrafish embryonic and adult liver cDNA libraries, and provide the most extensive validation of OFP to date.…”

mentioning

confidence: 99%

An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library

Clark

Hennig²,

Herwig³

et al. 2001

Genome Res.

View full text Add to dashboard Cite

The zebrafish is a powerful system for understanding the vertebrate genome, allowing the combination of genetic, molecular, and embryological analysis. Expressed sequence tags (ESTs) provide a rapid means of identifying an organism's genes for further analysis, but any EST project is limited by the availability of suitable libraries. Such cDNA libraries must be of high quality and provide a high rate of gene discovery. However, commonly used normalization and subtraction procedures tend to select for shorter, truncated, and internally primed inserts, seriously affecting library quality. An alternative procedure is to use oligonucleotide fingerprinting (OFP) to precluster clones before EST sequencing, thereby reducing the re-sequencing of common transcripts. Here, we describe the use of OFP to normalize and subtract 75,000 clones from two cDNA libraries, to a minimal set of 25,102 clones. We generated 25,788 ESTs (11,380 3Ј and 14,408 5Ј) from over 16,000 of these clones. Clustering of 10,654 high-quality 3Ј ESTs from this set identified 7232 clusters (likely genes), corresponding to a 68% gene diversity rate, comparable to what has been reported for the best normalized human cDNA libraries, and indicating that the complete set of 25,102 clones contains as many as 17,000 genes. Yet, the library quality remains high. The complete set of 25,102 clones is available for researchers as glycerol stocks, filters sets, and as individual EST clones. These resources have been used for radiation hybrid, genetic, and physical mapping of the zebrafish genome, as well as positional cloning and candidate gene identification, molecular marker, and microarray development.

show abstract

“…In [4], the frequency matrix based method was suggested. And an information theoretical method based on Shannon entropy as a quality criterion was used in [5].…”

Section: Introductionmentioning

confidence: 99%

Multi-objective Evolutionary Probe Design Based on Thermodynamic Criteria for HPV Detection

Lee

Kim

Zhang

2004

PRICAI 2004: Trends in Artificial Intelligence

View full text Add to dashboard Cite

Abstract. DNA microarrays are widely used techniques in molecular biology and DNA computing area. It consists of the DNA sequences called probes, which are DNA complementaries to the genes of interest, on solid surfaces. And its reliability seriously depends on the quality of the probe sequences. Therefore, one must carefully choose the probe sets in target sequences. In this paper, the probe design for DNA microarrays is formulated as the multi-objective optimization problem. We propose a multi-objective evolutionary approach, which is known to be suitable for this kind of optimization problem. Since a multi-objective evolutionary algorithm can find multiple solutions at a time, we used thermodynamic criteria to choose the most suitable one. For the experiments, the probe set generated by the proposed method is compared to the sequences used in commercial microarrays, which detects a set of Human Papillomavirus (HPV). The comparison result supports that our approach can be useful to optimize probe sequences.

show abstract

Gene-Representing cDNA Clusters Defined by Hybridization of 57,419 Clones from Infant Brain Libraries with Short Oligonucleotide Probes

Cited by 75 publications

References 0 publications

Large-Scale Clustering of cDNA-Fingerprinting Data

Large-Scale Clustering of cDNA-Fingerprinting Data

An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library

Multi-objective Evolutionary Probe Design Based on Thermodynamic Criteria for HPV Detection

Contact Info

Product

Resources

About