Ogata lab

Ogata lab is a laboratory to analyze big data of molecular biology in plants & microorganisms using bioinformatics,
especially, correlation network analysis.

★ What is "bioinformatics&quot?

  • It is based on life science and information science.
  • Recently, big data of information on life science require approaches based on information science, which is called "data science".

★ Collaborative researches

  • In Ogata lab, collaborative researches with "wet" researchers are performed such as microbiome analyses in gut & oral flora.

♦ Dog gut microbiome

  • By analyzing gut microbiome of dogs in illness, we search microorganisms that cause particular diseases.

♦ Human oral microbiome

  • By analyzing oral microbiome of young and aged women, we aim to reveal the relationships of the flora with health & mouth odor.

★ Development of bio-tools

  • We develop various tools useful for analyses in life science.
  • Ogata lab publish two tools now.
ConfeitoGUI This tool, one of multiseriate analyses, is used to detect groups from a network in a size-sensitive manner.
MagicSuite This tool is used for " intuitive" next-generation sequencing to any types of query datasets such as DNA (for SNP analysis), RNA (for RNA-Seq), and 16S rDNA (for microbiome), executable on Windows & Macintosh.

★ Bio-database

  • "Bio-database" is a website that publishes datasets of life science curated by bioscience researchers.
  • Ogata lab publishes 3 bio-databases.
  • This is a database to retrieve homologous genes for understanding function & evolution of gene. We publish the database for plants, named "Gcorn plant."
  • Similarity in amino acids between genes (or proteins) leads to predicting gene function.
  • Sequences of amino acids and bases retain information on gene evolution.
    By using such information, we aim to reveal gene evolution along with speciation & duplication throughout the whole organisms.
  • In the near future, we will publish such databases for protozoa ( Gcorn protozoa), fungi (Gcorn fungi), invertebrate (Gcorn invertebrate), vertebrate (Gcorn vertebrate), & mammalian (Gcorn mammalian).
  • This is a database to retrieve gene expression datasets obtained from microarray & next-generation sequencing.
  • Using the database, experimental conditions such as tissues or stresses in which a gene of interest is expressed are retrievable.
  • By integrating with Gcorn database, in the near future, gene expression profiles of homologous genes in other organisms will be available.
This is a database based on 1131 samples of dog gut microbiome. The database was constructed by a Ogata lab member (M2).
This is a database to retrieve plant gene expression based on RNA-seq analyses. The database was constructed by a Ogata lab member (M1).

★ Researches in the near future

♦ Database of trees

  • This database will be designed to integrate phenology, tissue anatomy, & genomics. Dissimilar to other plants’ genes, which tend to be homologous to other plants in the same families, genes of trees have tendencies to be similar over families. We aim to reveal which kinds of genes exist in trees in different families and influence to phenology & tissue anatomy.
  • Trees preserve information on their growth in tree rings, which are retained after their felling. We will analyze big data of such tree rings.
  • Classical instruments such as violin are still made by woods. We will approach a secret of exquisite instruments on the basis of wood structure & molecular biology.
♦ Database of thoroughbreds

  • Thoroughbred horses are precious because of information on lineages through over 400 years. We will associate such information with their genomics. Knowledges from these researches may lead to revealing a secret of speed & health of thoroughbreds.
  • Horse gut microbiome may lead to prompt detection of deseases & mental conditions.
  • By using machine learning & AI, we will challenge big data of horse racing.
The KAGIANA Project (since 2006)
Kazusa: 2006-2009
Yokohama: 2010-2011
Osaka: 2012-2017