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We developed computational measures to assess the functional implications of variations on regulatory motifs and to compare the functions of related sites.

Lapidot Michal et al.

PLoS Genetics 4 (3), 01 Mar 2008

We predict the effects of nucleotide variations within motifs on gene expression patterns.

Lapidot Michal et al.

PLoS Genetics 4 (3), 01 Mar 2008

Our results should facilitate the prediction of the expression outcomes of binding site variations.

Lapidot Michal et al.

PLoS Genetics 4 (3), 01 Mar 2008

Yet genomes contain genes with natural variations on motifs, while micro-array data provide the expression pattern of those genes.

Lapidot Michal et al.

PLoS Genetics 4 (3), 01 Mar 2008

We compared the expression of genes containing motifs to the expression of genes that contain motif variations, and assessed how drastically each substitution affected expression.

Lapidot Michal et al.

PLoS Genetics 4 (3), 01 Mar 2008

2008 Background With the recent growth of information on sequence variations in the human genome, predictions regarding the functional effects and relevance to disease phenotypes of coding sequence variations are becoming increasingly important.

Hong-Hee Won et al.

PLoS ONE 3 (10), 30 Oct 2008

The aims of this study were to catalog protein-coding sequence variations (CVs) occurring in genetic variation databases and to use bioinformatic programs to analyze CVs.

Hong-Hee Won et al.

PLoS ONE 3 (10), 30 Oct 2008

By cataloging the coding sequence variations using these databases, we found that 4.36% of CVs from HGMD are concurrently registered in dbSNP (8.11% of CVs from dbSNP are concurrent in HGMD).

Hong-Hee Won et al.

PLoS ONE 3 (10), 30 Oct 2008

This is the first study to compare human sequence variations in HGMD, dbSNP and HapMap at the genome-wide level.

Hong-Hee Won et al.

PLoS ONE 3 (10), 30 Oct 2008

Unprecedented advancements in molecular technology and major initiatives such as the Human Genome Project and the International Haplotype Map Project have created a need for methods to interpret the myriad sequence variations in the human genome, and to catalog disease-causing mutations.

Hong-Hee Won et al.

PLoS ONE 3 (10), 30 Oct 2008

In addition, progress in sequencing technology has allowed mutational analysis of more than 10,000 genes in a single individual and has accelerated research on disease-associated allelic variations at the whole genome sequencing level [2] .

Hong-Hee Won et al.

PLoS ONE 3 (10), 30 Oct 2008

The human genome is estimated to have up to 200,000 amino acid-substituting variations in the protein-coding sequences (CVs), also called nonsynonymous single nucleotide polymorphisms (nsSNPs) [3] .

Hong-Hee Won et al.

PLoS ONE 3 (10), 30 Oct 2008

Among five accessions 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis, identifying 60 genes that were differentially expressed in different accession backgrounds in an organ-dependent manner.

Wenqiong J Chen et al.

Genome Biology 6 (4), 2005

To understand the transcriptional basis of natural variation, we have studied genome-wide variations in transcription and characterized the genetic variations in regulatory elements among Arabidopsis accessions.

Wenqiong J Chen et al.

Genome Biology 6 (4), 2005

Among five accessions (Col-0, C24, L er , WS-2, and NO-0) 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis.

Wenqiong J Chen et al.

Genome Biology 6 (4), 2005

Genes that show substantial genetic variation in mRNA level are those with functions in signal transduction, transcription and stress response, suggesting the existence of variations in the regulatory mechanisms for these genes among different accessions.

Wenqiong J Chen et al.

Genome Biology 6 (4), 2005

While relatively fewer sequence variations were detected on average in the coding regions of these genes, a number of differences were identified from the upstream regions, several of which alter potential cis -regulatory elements.

Wenqiong J Chen et al.

Genome Biology 6 (4), 2005

Copy number variations (CNVs) are deletions, insertions, duplications, and more complex variations ranging from 1 kb to sub-microscopic sizes.

Tae-Wook Kang et al.

BMC Genomics 9 (7), 18 Oct 2008

Conclusion CNVs are recently-recognized structural variations among individuals, and more CNVs need to be identified from diverse populations.

Tae-Wook Kang et al.

BMC Genomics 9 (7), 18 Oct 2008

Understanding variations in the human genome is the key to unraveling the phenotypic diversity among individuals and understanding various human diseases.

Tae-Wook Kang et al.

BMC Genomics 9 (7), 18 Oct 2008

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