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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Genomics & Informatics
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Korea Genome Organization
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Volume & Issues
Volume 4, Issue 4 - Dec 2006
Volume 4, Issue 3 - Sep 2006
Volume 4, Issue 2 - Jun 2006
Volume 4, Issue 1 - Mar 2006
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Chromosomal Information of 1,144 Korean BAC Clones
Park, Mi-Hyun ; Lee, Hee-Jung ; Kim, Kwang-Joong ; Jeon, Jae-Pil ; Lee, Hye-Ja ; Kim, Jun-Woo ; Kim, Hung-Tae ; Cha, Hyo-Soung ; Kim, Cheol-Hwan ; Choi, Kang-Yell ; Park, Chan ; Oh, Berm-Seok ; Kim, Ku-Chan ;
Genomics & Informatics, volume 4, issue 4, 2006, Pages 141~146
We sequenced 1,841 BAC clones by terminal sequencing, and 1,830 of these clones were characterized with regard to their human chromosomal location and gene content using Korean BAC library constructed at the Korean Science (KCGS). Sequence analyses of the 1,830 BAC clones was performed for chromosomal assignment: 1,144 clones were assigned to a single chromosome, 190 clones apparently assigned to more than one chromosome, and 496 clones to no chromosome. Evaluating gene content of the 1,144 BAC clones, we found that 706 clones represented 1,069 genes of which 415 genes existed in the BAC clones covering the full sequence of the gene, 180 genes covering a
, and 474 genes covering less than 50% of the gene coverage. The estimated covering size of the KBAC clones was 73,379 kilobases (kb), in total corresponding to 2.3% of haploid human genome sequence. The identified BAC clones will be a public genomic resource for mapped clones for diagnostic and functional studies by Korean scientists and investigators worldwide.
A Comparative Genome-Wide Analysis of GATA Transcription Factors in Fungi
Park, Jong-Sun ; Kim, Hyo-Jeong ; Kim, Soon-Ok ; Kong, Sung-Hyung ; Park, Jae-Jin ; Kim, Se-Ryun ; Han, Hyea-Young ; Park, Bong-Soo ; Jung, Kyong-Yong ; Lee, Yong-Hwan ;
Genomics & Informatics, volume 4, issue 4, 2006, Pages 147~160
GATA transcription factors are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif in the form
followed by a basic region. In fungi, they act as transcriptional activators or repressors in several different processes, ranging from nitrogen source utilization to mating-type switching. Using an in-house bioinformatics portal system, we surveyed 50 fungal and 9 out-group genomes and identified 396 putative fungal GATA transcription factors. The proportion of GATA transcription factors within a genome varied among taxonomic lineages. Subsequent analyses of phylogenetic relationships among the fungal GATA transcription factors, as well as a study of their domain architecture and gene structure, demonstrated high degrees of conservation in type IVa and type IVb zinc finger motifs and the existence of distinctive clusters at least at the level of subphylum. The SFH1 subgroup with a 20-residue loop was newly identified, in addition to six well-defined subgroups in the subphylum Pezizomycotina. Furthermore, a novel GATA motif with a 2f-residue loop (
, designated 'zinc finger type IVc') was discovered within the phylum Basidiomycota. Our results suggest that fungal GATA factors might have undergone multiple distinct modes of evolution resulting in diversified cellular modulation in fungi.
Prediction Model for the Cellular Immortalization and Transformation Potentials of Cell Substrates
Lee, Min-Su ; Matthews Clayton A. ; Chae Min-Ju ; Choi, Jung-Yun ; Sohn Yeo-Won ; Kim, Min-Jung ; Lee, Su-Jae ; Park, Woong-Yang ;
Genomics & Informatics, volume 4, issue 4, 2006, Pages 161~166
The establishment of DNA microarray technology has enabled high-throughput analysis and molecular profiling of various types of cancers. By using the gene expression data from microarray analysis we are able to investigate diagnostic applications at the molecular level. The most important step in the application of microarray technology to cancer diagnostics is the selection of specific markers from gene expression profiles. In order to select markers of Immortalization and transformation we used c-myc and
oncogene-transfected NIH3T3 cells as our model system. We have identified 8751 differentially expressed genes in the immortalization/transformation model by multivariate permutation F-test (95% confidence, FDR<0.01). Using the support vector machine algorithm, we selected 13 discriminative genes which could be used to predict immortalization and transformation with perfect accuracy. We assayed
-transfected 'transformed' cells to validate our immortalization/transformation dassification system. The selected molecular markers generated valuable additional information for tumor diagnosis, prognosis and therapy development.
New Approach to the Analysis of Palindromic Structure in Genome Sequences
Kim, Seok-Won ; Lee, Yong-Seok ; Choi, Sang-Haeng ; Chae, Sung-Hwa ; Kim, Dae-Won ; Park, Hong-Seog ;
Genomics & Informatics, volume 4, issue 4, 2006, Pages 167~169
PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user-defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users.
ESTin: A Program for Building a dbEST Submission File from Massive EST Sequences
Lee, Byung-Wook ;
Genomics & Informatics, volume 4, issue 4, 2006, Pages 170~172
ESTin is an easy-to-use tool that allows EST researchers to build a dbEST submission file with EST sequences and related data. The advantages of ESTin are its user-friendly interface, various editing functions, and rigorous validation function.
A Pattern Summary System Using BLAST for Sequence Analysis
Choi, Han-Suk ; Kim, Dong-Wook ; Ryu, Tae-W. ;
Genomics & Informatics, volume 4, issue 4, 2006, Pages 173~181
Pattern finding is one of the important tasks in a protein or DNA sequence analysis. Alignment is the widely used technique for finding patterns in sequence analysis. BLAST (Basic Local Alignment Search Tool) is one of the most popularly used tools in bio-informatics to explore available DNA or protein sequence databases. BLAST may generate a huge output for a large sequence data that contains various sequence patterns. However, BLAST does not provide a tool to summarize and analyze the patterns or matched alignments in the BLAST output file. BLAST lacks of general and robust parsing tools to extract the essential information out from its output. This paper presents a pattern summary system which is a powerful and comprehensive tool for discovering pattern structures in huge amount of sequence data in the BLAST. The pattern summary system can identify clusters of patterns, extract the cluster pattern sequences from the subject database of BLAST, and display the clusters graphically to show the distribution of clusters in the subject database.
In Silico Identification of 6-Phosphogluconolactonase Genes that are Frequently Missing from Completely Sequenced Bacterial Genomes
Jeong, Hae-Young ; F. Kim, Ji-Hyun ; Park, Hong-Seog ;
Genomics & Informatics, volume 4, issue 4, 2006, Pages 182~187
6-Phosphogluconolactonase (6PGL) is one of the key enzymes in the ubiquitous pathways of central carbon metabolism, but bacterial 6PGL had been long known as a missing enzyme even after complete bacterial genome sequence information became available. Although recent experimental characterization suggests that there are two types of 6PGLs (DevB and YbhE), their phylogenetic distribution is severely biased. Here we present that proteins in COG group previously described as 3-oarboxymuconate cyclase (COG2706) are actually the YbhE-type 6PGLs, which are widely distributed in Proteobacteria and Fimicutes. This case exemplifies how erroneous functional description of a member in the reference database commonly used in transitive genome annotation cause systematic problem in the prediction of genes even with universal cellular functions.