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MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics.

Dhandapani VIGNESH ; Paul PARAMESWARI ; Su Bin IM ; Hae Jin KIM ; Yong Pyo LIM

Genomics & Informatics.2011;9(1):39-43.

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.
Clone Cells ; Cloning, Organism ; Gene Silencing ; MicroRNAs ; Repression, Psychology ; RNA ; RNA, Messenger ; Sequence Alignment

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ManBIF: a Program for Mining and Managing Biobank Impact Factor Data.

Ki Jin YU ; Jungmin NAM ; Yun HER ; Minseock CHU ; Hyungseok SEO ; Junwoo KIM ; Jaepil JEON ; Hyekyung PARK ; Kiejung PARK

Genomics & Informatics.2011;9(1):37-38.

Biobank Impact Factor (BIF), which is a very effective criterion to evaluate the activity of biobanks, can be estimated by the citation information of biobanks from scientific papers. We have developed a program, ManBIF, to investigate the citation information from PDF files in the literature. The program manages a dictionary for expressions to represent biobanks and their resources, mines the citation information by converting PDF files to text files and searching with a dictionary, and produces a statistical report file. It can be used as an important tool by biobanks.
Mining

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Finding Interesting Genes Using Reliability in Various Gene Expression Models.

Eun Kyung LEE ; Dianne COOK ; Heike HOFFMAN

Genomics & Informatics.2011;9(1):28-36.

Most statistical methods for finding interesting genes are focusing on the summary values with large fold-changes or large variations. Very few methods consider the probe level data. We developed a new measure to detect reliability that incorporates the probe level data. This reliability measure is useful for exploring the microarray data without ignoring the probe level data. It is easy to calculate, and it can be used for all the other statistical methods as a good guideline to find real differentially expressed genes. Instead of filtering out genes before the analysis, we use whole genes in the analysis and make decisions with new reliability measures.
Gene Expression ; Quality Control

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Standard-based Integration of Heterogeneous Large-scale DNA Microarray Data for Improving Reusability.

Yong JUNG ; Hwa Jeong SEO ; Yu Rang PARK ; Jihun KIM ; Sang Jay BIEN ; Ju Han KIM

Genomics & Informatics.2011;9(1):19-27.

Gene Expression Omnibus (GEO) has kept the largest amount of gene-expression microarray data that have grown exponentially. Microarray data in GEO have been generated in many different formats and often lack standardized annotation and documentation. It is hard to know if preprocessing has been applied to a dataset or not and in what way. Standard-based integration of heterogeneous data formats and metadata is necessary for comprehensive data query, analysis and mining. We attempted to integrate the heterogeneous microarray data in GEO based on Minimum Information About a Microarray Experiment (MIAME) standard. We unified the data fields of GEO Data table and mapped the attributes of GEO metadata into MIAME elements. We also discriminated non-preprocessed raw datasets from others and processed ones by using a two-step classification method. Most of the procedures were developed as semi-automated algorithms with some degree of text mining techniques. We localized 2,967 Platforms, 4,867 Series and 103,590 Samples with covering 279 organisms, integrated them into a standard-based relational schema and developed a comprehensive query interface to extract. Our tool, GEOQuest is available at http://www.snubi.org/software/GEOQuest/
Data Mining ; DNA ; Gene Expression ; Mining ; Oligonucleotide Array Sequence Analysis

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Genetic Association between Eotaxin Genes and Asthma and Its Relationship to Birth Season in Korean Children.

Insung AHN ; Se Eun BAE ; Jeong Hee KIM ; Byong Kwan SON ; Hyeon S SON ; Sung Il CHO

Genomics & Informatics.2011;9(1):12-18.

Asthma is a chronic disease associated with airway constriction due to inflammation caused by eosinophils, mast cells, and T lymphocytes, leading to serious chronic illness in children. The eotaxin gene family has been shown to play an important role in the pathogenesis of asthma. We hypothesized that the distinctive variations among the four seasons in Korea may affect the expression of eotaxin polymorphisms, especially in children. We examined the possible effects of birth season (spring, March-May; summer, June-August; fall, September-November; and winter, December-February) on the phenotype of asthma in children. All SNP data sets of the eotaxin-2 and eotaxin-3 genes were collected from 78 asthma patients and 101 controls. Here, we investigated the effects of birth season on the expression of eotaxin-2 and eotaxin-3 in Korean children. Using the HAPLOTYPE procedure with the HTR method in SAS/Genetics, we showed that children born in spring and summer show significant haplotypes in both the eotaxin-2 and eotaxin-3 genes. Thus, the expression of polymorphisms in eotaxin-2 and eotaxin-3 may vary by season.
Asthma ; Chemokine CCL24 ; Child ; Chronic Disease ; Constriction ; Eosinophils ; Haplotypes ; Humans ; Inflammation ; Korea ; Mast Cells ; Parturition ; Phenotype ; Seasons ; T-Lymphocytes

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Recent Progresses in the Linguistic Modeling of Biological Sequences Based on Formal Language Theory.

Hyun Seok PARK ; Bulgan GALBADRAKH ; Young Mi KIM

Genomics & Informatics.2011;9(1):5-11.

Treating genomes just as languages raises the possibility of producing concise generalizations about information in biological sequences. Grammars used in this way would constitute a model of underlying biological processes or structures, and that grammars may, in fact, serve as an appropriate tool for theory formation. The increasing number of biological sequences that have been yielded further highlights a growing need for developing grammatical systems in bioinformatics. The intent of this review is therefore to list some bibliographic references regarding the recent progresses in the field of grammatical modeling of biological sequences. This review will also contain some sections to briefly introduce basic knowledge about formal language theory, such as the Chomsky hierarchy, for non-experts in computational linguistics, and to provide some helpful pointers to start a deeper investigation into this field.
Biological Processes ; Computational Biology ; Generalization (Psychology) ; Genome ; Linguistics ; Natural Language Processing

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Post-GWAS Strategies.

Sangsoo KIM ; Jong BHAK

Genomics & Informatics.2011;9(1):1-4.

Genome-wide association (GWA) studies are the method of choice for discovering loci associated with common diseases. More than a thousand GWA studies have reported successful identification of statistically significant association signals in human genomes for a variety of complex diseases. In this review, I discuss some of the issues related to the future of GWA studies and their biomedical applications.
Genome, Human ; Genome-Wide Association Study ; Humans

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Mining the Proteome of Fusobacterium nucleatum subsp. nucleatum ATCC 25586 for Potential Therapeutics Discovery: An In Silico Approach.

Abdul Musaweer HABIB ; Md Saiful ISLAM ; Md SOHEL ; Md Habibul Hasan MAZUMDER ; Mohd Omar Faruk SIKDER ; Shah Md SHAHIK

Genomics & Informatics.2016;14(4):255-264. doi:10.5808/GI.2016.14.4.255

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.
Anti-Bacterial Agents ; Bacteria ; Binding Sites ; Colonic Neoplasms ; Colorectal Neoplasms ; Computer Simulation* ; Drug Delivery Systems ; Drug Discovery ; Fusobacterium nucleatum* ; Fusobacterium* ; Genes, Essential ; Genome ; Genome, Human ; Genomics ; Humans ; Ligands ; Mass Screening ; Mining* ; Proteome*

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Drug Target Identification and Elucidation of Natural Inhibitors for Bordetella petrii: An In Silico Study.

Surya Narayan RATH ; Manisha RAY ; Animesh PATTNAIK ; Sukanta Kumar PRADHAN

Genomics & Informatics.2016;14(4):241-254. doi:10.5808/GI.2016.14.4.241

Environmental microbes like Bordetella petrii has been established as a causative agent for various infectious diseases in human. Again, development of drug resistance in B. petrii challenged to combat against the infection. Identification of potential drug target and proposing a novel lead compound against the pathogen has a great aid and value. In this study, bioinformatics tools and technology have been applied to suggest a potential drug target by screening the proteome information of B. petrii DSM 12804 (accession No. PRJNA28135) from genome database of National Centre for Biotechnology information. In this regards, the inhibitory effect of nine natural compounds like ajoene (Allium sativum), allicin (A. sativum), cinnamaldehyde (Cinnamomum cassia), curcumin (Curcuma longa), gallotannin (active component of green tea and red wine), isoorientin (Anthopterus wardii), isovitexin (A. wardii), neral (Melissa officinalis), and vitexin (A. wardii) have been acknowledged with anti-bacterial properties and hence tested against identified drug target of B. petrii by implicating computational approach. The in silico studies revealed the hypothesis that lpxD could be a potential drug target and with recommendation of a strong inhibitory effect of selected natural compounds against infection caused due to B. petrii, would be further validated through in vitro experiments.
Biotechnology ; Bordetella* ; Communicable Diseases ; Computational Biology ; Computer Simulation* ; Curcumin ; Drug Delivery Systems ; Drug Resistance ; Genome ; Humans ; In Vitro Techniques ; Mass Screening ; Proteome ; Tea

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Tissue Specific Expression Levels of Apoptosis Involved Genes Have Correlations with Codon and Amino Acid Usage.

Mohammadreza HAJJARI ; Iman SADEGHI ; Abbas SALAVATY ; Habib NASIRI ; Maryam Tahmasebi BIRGANI

Genomics & Informatics.2016;14(4):234-240. doi:10.5808/GI.2016.14.4.234

Different mechanisms, including transcriptional and post transcriptional processes, regulate tissue specific expression of genes. In this study, we report differences in gene/protein compositional features between apoptosis involved genes selectively expressed in human tissues. We found some correlations between codon/amino acid usage and tissue specific expression level of genes. The findings can be significant for understanding the translational selection on these features. The selection may play an important role in the differentiation of human tissues and can be considered for future studies in diagnosis of some diseases such as cancer.
Apoptosis* ; Codon* ; Diagnosis ; Gene Expression Regulation ; Humans

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