Database

SBM DB

Systems Biology and Medicine Database

SBM DB is comprehensive database of Gene Expression Profiles, which enable to compare the transcriptome of various tissues, organs and experiments. mRNA expression levels of thousands of genes are measured with oligo-nucleotide DNA microarray "GeneChip". All gene expression data in this database is produced by LSBM (Laboratory for Systems Biology and Medicine) and the collaborators.
We provide 3 types of Databases.

Reference database for gene Expression Analysis HUVEC Database for Vascular Endothelial research Protein Expression Database using Immunohistochemistory
RefExA

Comprehensive gene expression database of Human normal tissues, normal cultured cells and cancer cell lines with GeneChip HG-U133A, can help investigation of Human disease.

HUVEC DB

Database for HUVEC (Human Umbilical Vein Endothelial Cells) gene expression with stimuli by TNF&alpha etc..

IHC DB

Database for Nuclear receptor protein expression and localization in each normal organ (rat tissues) using antibody and immunohistochemical staining.

The Objective

SBM-DB aims to investigate mainly Human disease and other mammalian's. Analysis from comprehensive gene expression profiles may help to define out the causes of disease in molecular level.

Experimental Procedure

Experimental procedures for GeneChip were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, each 10 mg RNA are used to synthesize biotin-labeled cRNA, which was then hybridized to the high-density oligonucleotide array (GeneChip Human U133 array; Affymetrix, Santa Crara, CA). After washing, arrays were stained with streptavidin-phycoerythrin and analyzed by a Hewlett-Packard Scanner to collect image data.

Data Analysis

GeneChip Analysis Suite software version 5.0 was used to calculate the Signal value, and Detection Call (called "Average Difference", "Absolute Call" in previous MAS4.0).

Probe Information

Each Probeset have a GenBank Accession number, and we mapped with UniGene ClusterID. (Human Unigene Build #148, 1 April, 2002)

Term of Use

  1. User should obey the basis of these database objectives.
  2. Data should not be used for commercial pursuits.
  3. Data should not be transferred without permission.
  4. Data using the part of database should not be published without contact to the researcher who is responsible for the experiment.
  5. We do not guarantee the accuracy and reliability of our data, and are not responsible for the consequences of the possible errors.

Copyright

The experiment data and all other information in this websites are protected by copyright laws. On the occasion of the duplicate of this information, permission is required.

History

Update Edited

2003/08/25 from HNT-DB to RefExA

  • Rename HNT-DB to RefExA due to increased samples.
    from HNT-DB (Human Normal Tissue Database)
    to RefExA (Reference database for gene Expression Analysis)
  • Gene annotation is update to UniGene Hs build#161
  • Add annotation of NetAffx(TM) of Analysis Center (Affymetrix inc.)
  • Improvements of web interface. (graphical panel, bar graph, etc.)

2003/07/08 Renewal in Human Normal Tissue DB (HNT DB)

  • 40 normal tissues + 17 normal cells + 23 cancer cell lines
  • Gene annotation is update to UniGene build #159

2003/04/11 LSBM Website renewal. Interface of SBM-DB has been improved.

2002/07/15 Update to 35 Human Normal Tissues, and interface is reformed

2002/04/16 Open Human Normal 30 Tissue Database

Grant

SBM-DB is supported from the Grant(s) following, - Grant-in-Aid for Publication of Scientific Research Results, KAKENHI, JSPS (2003.4-2004.3)

Inquiry

If you have any questions or comments about this site or database, please e-mail to
dbadmin@genome.rcast.u-tokyo.ac.jp