| Title: |
The innate immune database (IIDB) |
| Authors: |
Korb, M; Rust, AG; Thorsson, V; Battail, C; Li, B; Hwang, D; Kennedy, KA; Roach, JC; Rosenberger, CM; Gilchrist, M; Zak, D; Johnson, C; Marzolf, B; Aderem, A; Shmulevich, I; Bolouri, H |
| Contributors: |
융합생명공학부; 10180943; Hwang, D |
| Publisher Information: |
BIOMED CENTRAL LTD |
| Publication Year: |
2008 |
| Collection: |
Pohang University of Science and Technology (POSTECH): Open Access System for Information Sharing (OASIS) |
| Subject Terms: |
TRANSCRIPTION FACTORS; REGULATORY ELEMENTS; PROMOTERS; IDENTIFICATION; ACTIVATION; DISCOVERY; RESPONSES; PROGRAMS; INSIGHTS; BROWSER |
| Description: |
Background: As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site http:// www.innateImmunity-systemsbiology.org. Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens. Description: We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be ... |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
BMC IMMUNOLOGY; SCI급, SCOPUS 등재논문; SCI; Immunology; https://oasis.postech.ac.kr/handle/2014.oak/9858; 8315; BMC IMMUNOLOGY, v.9, no.7; 000254314500001 |
| Availability: |
https://oasis.postech.ac.kr/handle/2014.oak/9858 |
| Rights: |
BY_NC_ND ; http://creativecommons.org/licenses/by-nc-nd/2.0/kr |
| Accession Number: |
edsbas.C751255F |
| Database: |
BASE |