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Series GSE4603 Query DataSets for GSE4603
Status Public on Apr 01, 2007
Title Molecular factors governing liver pathology in abcb4 (-/-) mice
Organism Mus musculus
Experiment type Expression profiling by array
Summary Molecular factors governing liver pathology in abcb4 (-/-) mice.

Dr. Nakken, Karl Esten, Dr. Berge, Knut E., Dr. Knut J. Labori, Ståle Nygård, Dr. Terese Haaland , professor Morten G. Ræder. Institute for Experimental Medical Research and Department of Pathology, Ulleval University Hospital, Oslo, Norway and Institute for Medical Genetics, National Hospital, Oslo, Norway; E-mail: k.e.nakken@medisin.uio.no.

Background and Aims: Abcb4 (mdr2) (-/-) mice secrete phosphatidylcholine-free bile and develop chronic cholangitis. This study aims at identifying differentially transcribed genes that govern liver pathology during this disease.
Methods: Hepatic gene transcription was measured in 3, 6, 9 and 20 week old abcb4 (-/-) mice (FVB.129P2-abcb4tm1Bor/J) using cDNA microarrays; FVB/NJ abcb4 (+/+) mice serving as controls. Altered gene transcriptions were verified by real-time polymerase chain reaction. Attention focused on genes coding for chemokines and cytokines of potential pathogenic importance and on matrix housekeeping genes, growth factors and genes regulating wound healing, epithelial morphogenesis and tissue development. Disease phenotype was characterized by histopathology scoring.
Results: Transcription of serpina3 genes showed early downregulation. Genes exhibiting upregulated transcription included: Cxcl10, Ccl2, Ccl20, Ctgf, Elf3, Lgals3, Mmp12, Mmp15, Spp1, Loxl2, Pdgfa, Pdgfrb, Sparc, Tgfbi, Tgfbr2.
Conclusions: During early phases of chronic cholangitis in abcb4 (-/-) mice, hepatic downregulation of serpina3 genes and enhanced transcription of genes sustaining inflammatory processes contribute to fashioning the portal tract pathology. Later, enhanced transcription of genes governing tissue repair consolidate the portal tract pathology.
Keywords: Disease state analysis, time course
 
Overall design A time-series where 5 male mice were sacrificed at time-points 3,6,9 and 20 weeks, both sick knockouts and healthy controls. Including one dye-swap there were a total of 6 arrays at each time-point.
 
Contributor(s) Nakken KE, Nygård S, Berge KE, Arnkværn K, Haaland T, Labori KJ, Ræder MG
Citation(s) 17852852
Submission date Apr 04, 2006
Last update date Dec 06, 2012
Contact name Esten Nakken
E-mail(s) esten.nakken@medisin.uio.no, stale.nygard@medisin.uio.no
Organization name Institute for Experimental Medical Research
Department Ulleval university Hospital
Street address Kirkeveien 166
City Oslo
ZIP/Postal code 0407
Country Norway
 
Platforms (1)
GPL891 Agilent-011978 Mouse Microarray G4121A (Feature Number version)
Samples (24)
GSM102853 3 weeks sample 1
GSM102854 3 weeks sample 2
GSM102855 3 weeks sample 3
Relations
BioProject PRJNA94395

Regulated genes in abcb4 knockout mice header descriptions
ID (GeneBank)
Symbol
Fold change, 3weeks
Fold change, 6weeks
Fold change, 9weeks
Fold change, 20weeks
log2 fold change, 3weeks
log2 fold change, 6weeks
log2 fold change, 9weeks
log2 fold change, 20weeks
p-value, 3weeks
p-value, 6weeks
p-value, 9weeks
p-value, 20weeks
description

Data table
ID (GeneBank) Symbol Fold change, 3weeks Fold change, 6weeks Fold change, 9weeks Fold change, 20weeks log2 fold change, 3weeks log2 fold change, 6weeks log2 fold change, 9weeks log2 fold change, 20weeks p-value, 3weeks p-value, 6weeks p-value, 9weeks p-value, 20weeks description
BC028765 0610010O12Rik 1.46 2.54 2.76 2.81 0.55 1.34 1.46 1.49 0.015689 0.000309 0.000677 0.000193 Mus musculus RIKEN cDNA 0610010O12 gene, mRNA (cDNA clone MGC:41247 IMAGE:1195860), complete cds. [BC028765]
NM_025326 0610011I04Rik 2.63 2.07 2.46 2.03 1.40 1.05 1.30 1.02 0.001056 0.000049 0.000052 0.000522 Mus musculus RIKEN cDNA 0610011I04 gene (0610011I04Rik), mRNA [NM_025326]
NM_026159 0610039N19Rik 0.62 0.31 0.39 0.50 -0.69 -1.70 -1.34 -0.99 0.007211 0.000100 0.000476 0.001557 Mus musculus RIKEN cDNA 0610039N19 gene (0610039N19Rik), mRNA [NM_026159]
AK017585 1100001D19Rik 2.04 1.68 2.07 1.90 1.03 0.75 1.05 0.93 0.000500 0.001326 0.000573 0.000814 Mus musculus 8 days embryo whole body cDNA, RIKEN full-length enriched library, clone:5730420D13 product:hypothetical protein, full insert sequence. [AK017585]
NM_183249 1100001G20Rik 0.15 0.47 0.42 0.65 -2.75 -1.10 -1.24 -0.63 0.000330 0.001092 0.000637 0.008968 Mus musculus RIKEN cDNA 1100001G20 gene (1100001G20Rik), mRNA [NM_183249]
NM_028643 1110008L20Rik 1.78 2.60 2.38 2.18 0.84 1.38 1.25 1.12 0.000417 0.000225 0.001250 0.000474 Mus musculus RIKEN cDNA 1110008L20 gene (1110008L20Rik), mRNA [NM_028643]
NM_026807 1110033F04Rik 1.00 0.57 0.33 0.61 0.00 -0.81 -1.62 -0.71 0.951064 0.002282 0.000568 0.006138 Mus musculus RIKEN cDNA 1110033F04 gene (1110033F04Rik), mRNA [NM_026807]
NM_028766 1200015A22Rik 1.15 2.24 1.97 1.77 0.20 1.17 0.98 0.82 0.051905 0.000706 0.001680 0.000548 Mus musculus RIKEN cDNA 1200015A22 gene (1200015A22Rik), mRNA [NM_028766]
NM_152811 1300012D20Rik 0.45 0.61 0.35 0.49 -1.16 -0.71 -1.53 -1.03 0.007585 0.006525 0.000342 0.001264 Mus musculus RIKEN cDNA 1300012D20 gene (1300012D20Rik), mRNA [NM_152811]
NM_025829 1300018P11Rik 1.32 1.99 2.05 2.10 0.40 0.99 1.04 1.07 0.005056 0.000256 0.000577 0.000200 Mus musculus RIKEN cDNA 1300018P11 gene (1300018P11Rik), mRNA [NM_025829]
NM_028166 1600014C10Rik 2.08 1.33 1.29 1.25 1.06 0.41 0.37 0.32 0.000510 0.002518 0.002658 0.022701 Mus musculus RIKEN cDNA 1600014C10 gene (1600014C10Rik), mRNA [NM_028166]
NM_019975 1600020H07Rik 0.34 0.41 0.39 0.43 -1.54 -1.28 -1.36 -1.23 0.001315 0.000612 0.000668 0.000433 Mus musculus RIKEN cDNA 1600020H07 gene (1600020H07Rik), mRNA [NM_019975]
NM_029639 1600029D21Rik 3.36 5.85 4.06 3.13 1.75 2.55 2.02 1.64 0.000170 0.000095 0.000100 0.001673 Mus musculus RIKEN cDNA 1600029D21 gene (1600029D21Rik), mRNA [NM_029639]
NM_175329 1620401E04Rik 0.67 0.50 0.47 0.73 -0.58 -0.99 -1.10 -0.46 0.015273 0.002084 0.000385 0.011026 Mus musculus RIKEN cDNA 1620401E04 gene (1620401E04Rik), mRNA [NM_175329]
AK005902 1700012F10Rik 1.01 0.64 0.48 0.57 0.02 -0.65 -1.06 -0.80 0.699209 0.003132 0.003975 0.003815 Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:1700012F10 product:hypothetical Trp-Asp repeat (WD-repeat) structure containing protein, full insert sequence. [AK005902]
AK005933 1700012P22Rik 1.92 3.88 2.00 1.83 0.94 1.96 1.00 0.87 0.001136 0.000312 0.003017 0.011167 Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:1700012P22 product:hypothetical protein, full insert sequence. [AK005933]
NM_023707 1810009J06Rik 0.95 0.62 0.54 0.49 -0.07 -0.69 -0.88 -1.03 0.102603 0.001744 0.003953 0.001459 Mus musculus RIKEN cDNA 1810009J06 gene (1810009J06Rik), mRNA [NM_023707]
NM_023056 1810009M01Rik 2.53 2.24 2.69 2.26 1.34 1.16 1.43 1.17 0.000679 0.000517 0.000068 0.000717 Mus musculus RIKEN cDNA 1810009M01 gene (1810009M01Rik), mRNA [NM_023056]
NM_028994 1810010O14Rik 0.98 0.56 0.37 0.43 -0.03 -0.84 -1.44 -1.21 0.624396 0.003250 0.001369 0.001246 Mus musculus RIKEN cDNA 1810010O14 gene (1810010O14Rik), mRNA [NM_028994]
NM_026947 1810022C23Rik 0.79 0.42 0.53 0.75 -0.34 -1.25 -0.93 -0.41 0.031619 0.000305 0.000537 0.019838 Mus musculus RIKEN cDNA 1810022C23 gene (1810022C23Rik), mRNA [NM_026947]

Total number of rows: 443

Table truncated, full table size 77 Kbytes.




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