Array: Applied Biosystems AB1700 mouse chip (33315 probes)
30 arrays in total with triple biological replicates
Comprehensive analysis of differential gene expression profiles on
D-galactosamine-induced acute mouse liver injury and regeneration
Heekyoung Chung,a,b Hyun-Jun Kim, a Ki-Seok Jang, a Mingoo Kim,c Jungeun Yang,d Kyung-Sun Kang, b,e
Hyung-Lae Kim, b,f Byung-Il Yoon, b,g Mi-Ock Lee, b,h Byung-Hoon Lee, b,i Ju Han Kim,b,c Yong-Sung Lee,d and Gu Kong a,b*
Affiliation and Addresses:
a Department of Pathology,
and d Department of Biochemistry, College of Medicine, Hanyang
University, Seoul 133-791, Republic of Korea;
b
Toxicogenomics Research Consortium (TGRC), Hanyang University, Seoul 133-791,
Republic of Korea;
c Seoul National University
Biomedical Informatics (SNUBI), Seoul National University College of Medicine,
Seoul 110-799, Republic of Korea;
e
Department of Veterinary Public Health, College of Veterinary
Medicine, Seoul National University, Seoul
151-742, Republic of Korea;
f Department of Biochemistry, College of
Medicine, Ewha Womans University, Seoul 158-710, Republic of Korea;
g
School of Veterinary Medicine, Kangwon National University, Chuncheon 200-701,
Republic of Korea;
h College of Pharmacy and Bio-MAX Institute, Seoul
National University, Seoul 151-742, Republic of Korea; and
i College
of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National
University, Seoul 151-742, Republic of Korea.
*Corresponding Author. Department of Pathology, College of
Medicine, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul, 133-791,
Republic of Korea. Tel: +82-2-2290-8251, Fax: +82-2-2295-1091,
E-mail address: gkong@hanyang.ac.kr (G. Kong).
Key Words: D-galactosamine (GalN); mouse; liver; toxicogenomics; Applied
Biosystems Mouse Genome Survey Microarray
Abstract
Microarray analysis of RNA from D-galactosamine (GalN)-administered mouse livers was performed to establish a global gene expression profile during injury and regeneration stages at two different doses. A single dose of GalN at 266 or 26.6 mg/kg body weight was given intraperitoneally, and the liver samples were obtained after 6, 24, and 72 h. Histopathologic studies enabled the classification of the D-galactosamine effect into injury (6, 24 h) and regeneration (72 h) stages. By using the Applied Biosystems Mouse Genome Survey Microarray, a total of 7,267 out of 33,315 (21.8%) genes were found to be statistically reliable at p < 0.05 by 2-way ANOVA, and 1,469 (4.4%) probes at false discovery rate < 5% by Significance Analysis of Microarray. Among the statistically reliable clones by both analytical methods, 389 genes were differentially expressed when compared with non-treated control, with more than a 1.625-fold difference (which equals 0.7 in log2 scale) at one or more GalN treatment conditions and with less than 1.625-fold difference at all three vehicle-treated conditions. Three hundred thirty six genes and 13 genes were identified as injury- and regeneration-specific genes, respectively, showing that most of the transcriptomic changes were seen during the injury stage. Furthermore, multiple genes involved in protein synthesis and degradation, mRNA processing and binding, and cell cycle regulation showed variable transcript levels upon acute GalN administration.
1. Experimental Design
Array: Applied Biosystems AB1700 mouse chip (33315 probes)
30 arrays in total with triple biological replicates
2. Data
2.1. Raw data
2.2. Normalized data
Download normalized data (33315 probes x 30 samples)
Data are normalized in following procedure.
- Assay Normalized Signals are used.
- Only probes with Flag < 100 are used.
- Missing and filtered valued are imputed with KNN imputation algorithm.
- Values are VSN transformed.
- Arrays are scaled with quantile normalization.
- Normalized valued are rescaled with
3. Diagnostic Plots
3.1. Single-chip diagnostic plots
- AB1700 array has five features: Signal, S/N ratio, Assay normalized signal, SDEV and CV
- Histograms(1~5) show the distributions of each feature in log2 scale.
- Scatterplot(6) show the relationships between features in log2 scale.
- Psedoimageplot(7,8) reconstruct arrays with Signal and S/N ratio features. This plot checks whether features are dependent on the physical position in the array (spatial bias).
3.2. Between-chip diagnostic plots
[View between-chip diagnostic plots]
- Boxplots(1~3) show intensity distribution of 30 arrays at each normalization step.
- Scatterplots(4~18) show intensity relations between 30 arrays at each normalization step (6 arrays in each panel).
- MVAplots(19~38) show M and A relationship between 30 arrays at each normalization step (3 arrays in each panel).
4. Differentially Expressed Genes (DEGs)
4.1. Lists of DEGs
Supplementary Table 1. Microarray results of 7,267 probes found to be statistically reliable at p < 0.05 by 2-way ANOVA
Supplementary Table 2. Microarray results of 4,240 "differentially regulated" probes found to be statistically reliable at p < 0.05 by 2-way ANOVA
Supplementary Table 3. Microarray results of 1,469 probes found to be statistically reliable by SAM at FDR < 5%
Supplementary Table 4. Microarray results of 460 "differentially regulated" probes found to be statistically reliable by SAM at FDR < 5%
Supplementary Table 5. Microarray results of 389 "differentially regulated" probes identified by SAM and 2-way ANOVA
Supplementary Table 6. Microarray results of 138 injury-specific downregulated genes identified by 2-way ANOVA and SAM
Supplementary Table 7. Microarray results of 198 injury-specific upregulated genes identified by 2-way ANOVA and SAM
Supplementary Table 8. Microarray results of 13 regeneration-specific genes identified by 2-way ANOVA and SAM
Supplementary Table 9. GenMAPP result of injuy- or regeneration-specific genes4.2. SOM clustering and Gene ontology and pathway functional enrichment study
SOM clustering was performed on each ANOVA group. Then Enrichment study using
Gene ontology and pathway information was performed on each
cluster.
Broken line graphs show general tendency of expression profile for each cluster.
(Installation of SVG
viewer under Internet Explore is requiered.)
P-value < 0.05
MTC MABI MABx MAxI MAxx MxBI MxBx MxxI Mxxx un 314 C A 679 C A 201 C A 645 C A 977 C A 3697 C A 637 C A 117 C A bf 2 C A 0 C A 0 C A 0 C A 2 C A 264 C A 0 C A 0 C A bh 14 C A 0 C A 0 C A 0 C A 33 C A 2276 C A 0 C A 0 C A by 1 C A 0 C A 0 C A 0 C A 2 C A 872 C A 0 C A 0 C A D = Dose
T = Time
Click C for Cluster viewer, GO enrichement analysis
Click A for ArrayXPath, Pathway enrichment analysis
UN = Unadjusted
BF = Bonferoni multiple test correction
BH = Benjamini :: Hochberg multiple test correction
BY = Benjamini & Yekutieli multiple test correction
Last updated: 2006-06-14
