Zonal Gene Expression and Gene Regulatory Network Responses in Centrilobular and Periportal Hepatocytes Following Repeated Exposure to TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin)
gb:NM_133594.1 /DB_XREF=gi:19424297 /GEN=Smt3h2 /FEA=FLmRNA /CNT=51 /TID=Rn.5958.1 /TIER=FL+Stack /STK=35 /UG=Rn.5958 /DEF=Rattus norvegicus SMT3 suppressor of mif two 3 homolog 2 (yeast) (Smt3h2), mRNA. /PROD=SMT3 suppressor of mif two 3 homolog 2 (yeast) /FL=gb:NM_133594.1 gb:L79949.1
NM_133594
Rn.5958
Rn.154659
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae)
Sumo2
chr10q32.3
full length
ENSRNOG00000003670
690244
F1LN30 /// F1M2K3 /// P61959
---
NP_598278
NM_133594
0016925 // protein sumoylation // inferred from direct assay /// 0034613 // cellular protein localization // inferred from direct assay /// 0045892 // negative regulation of transcription, DNA-dependent // inferred from mutant phenotype
0005634 // nucleus // inferred from electronic annotation
0005515 // protein binding // inferred from physical interaction /// 0031625 // ubiquitin protein ligase binding // inferred from sequence or structural similarity
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
cell division cycle 37 homolog (S. cerevisiae)
Cdc37
chr8q13
full length
ENSRNOG00000033426
114562
D3ZA91 /// F1LRF0 /// Q63692
---
NP_446195
NM_053743
0051726 // regulation of cell cycle // inferred from expression pattern /// 0060334 // regulation of interferon-gamma-mediated signaling pathway // inferred from electronic annotation /// 0060334 // regulation of interferon-gamma-mediated signaling pathway // not recorded /// 0060338 // regulation of type I interferon-mediated signaling pathway // inferred from electronic annotation /// 0060338 // regulation of type I interferon-mediated signaling pathway // not recorded
0005737 // cytoplasm // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005829 // cytosol // inferred from electronic annotation /// 0005829 // cytosol // not recorded /// 0032587 // ruffle membrane // inferred from direct assay /// 0043234 // protein complex // inferred from direct assay
0019901 // protein kinase binding // inferred from electronic annotation /// 0019901 // protein kinase binding // inferred from physical interaction /// 0031072 // heat shock protein binding // not recorded /// 0031072 // heat shock protein binding // inferred from electronic annotation /// 0031435 // mitogen-activated protein kinase kinase kinase binding // inferred from physical interaction /// 0043422 // protein kinase B binding // inferred from physical interaction /// 0051087 // chaperone binding // inferred from physical interaction /// 0051879 // Hsp90 protein binding // inferred from electronic annotation /// 0051879 // Hsp90 protein binding // not recorded
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
coatomer protein complex, subunit beta 2 (beta prime)
Copb2
---
full length
---
60384
O35142 /// P97704 /// Q5M7X1
---
NP_068533
NM_021765
0006810 // transport // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0006891 // intra-Golgi vesicle-mediated transport // not recorded /// 0015031 // protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from electronic annotation
0000139 // Golgi membrane // inferred from direct assay /// 0000139 // Golgi membrane // inferred from electronic annotation /// 0005737 // cytoplasm // not recorded /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from direct assay /// 0005794 // Golgi apparatus // not recorded /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0015629 // actin cytoskeleton // not recorded /// 0016020 // membrane // inferred from electronic annotation /// 0030117 // membrane coat // inferred from electronic annotation /// 0030126 // COPI vesicle coat // not recorded /// 0030663 // COPI coated vesicle membrane // inferred from electronic annotation /// 0031410 // cytoplasmic vesicle // inferred from electronic annotation
0005080 // protein kinase C binding // inferred from physical interaction /// 0005198 // structural molecule activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction
gb:NM_053864.1 /DB_XREF=gi:17865350 /GEN=Vcp /FEA=FLmRNA /CNT=53 /TID=Rn.3820.1 /TIER=FL+Stack /STK=16 /UG=Rn.3820 /LL=116643 /DEF=Rattus norvegicus valosin-containing protein (Vcp), mRNA. /PROD=valosin-containing protein /FL=gb:NM_053864.1 gb:U11760.1
NM_053864
Rn.3820
Rn.98891
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
valosin-containing protein
Vcp
chr5q22
full length
ENSRNOG00000034242
116643
P46462
---
NP_446316
NM_053864
0006200 // ATP catabolic process // inferred from direct assay /// 0006302 // double-strand break repair // inferred from electronic annotation /// 0006302 // double-strand break repair // not recorded /// 0006511 // ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0006511 // ubiquitin-dependent protein catabolic process // not recorded /// 0006810 // transport // inferred from electronic annotation /// 0006888 // ER to Golgi vesicle-mediated transport // inferred from mutant phenotype /// 0006919 // activation of cysteine-type endopeptidase activity involved in apoptotic process // inferred from electronic annotation /// 0006919 // activation of cysteine-type endopeptidase activity involved in apoptotic process // not recorded /// 0006974 // response to DNA damage stimulus // not recorded /// 0006974 // response to DNA damage stimulus // inferred from electronic annotation /// 0030970 // retrograde protein transport, ER to cytosol // inferred from electronic annotation /// 0030970 // retrograde protein transport, ER to cytosol // not recorded /// 0031334 // positive regulation of protein complex assembly // inferred from electronic annotation /// 0031334 // positive regulation of protein complex assembly // not recorded /// 0032436 // positive regulation of proteasomal ubiquitin-dependent protein catabolic process // inferred from mutant phenotype /// 0032436 // positive regulation of proteasomal ubiquitin-dependent protein catabolic process // not recorded /// 0032436 // positive regulation of proteasomal ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0045732 // positive regulation of protein catabolic process // not recorded /// 0045732 // positive regulation of protein catabolic process // inferred from electronic annotation /// 0051260 // protein homooligomerization // inferred from direct assay /// 0070842 // aggresome assembly // inferred from electronic annotation /// 0070842 // aggresome assembly // not recorded
0000502 // proteasome complex // inferred from electronic annotation /// 0000502 // proteasome complex // not recorded /// 0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // not recorded /// 0005730 // nucleolus // not recorded /// 0005737 // cytoplasm // not recorded /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005783 // endoplasmic reticulum // inferred from direct assay /// 0005783 // endoplasmic reticulum // not recorded /// 0005783 // endoplasmic reticulum // inferred from electronic annotation /// 0005792 // microsome // inferred from direct assay /// 0005792 // microsome // inferred from electronic annotation /// 0005829 // cytosol // inferred from direct assay /// 0005829 // cytosol // not recorded /// 0005829 // cytosol // inferred from electronic annotation /// 0043234 // protein complex // not recorded /// 0043234 // protein complex // inferred from electronic annotation
0000166 // nucleotide binding // inferred from electronic annotation /// 0005102 // receptor binding // inferred from direct assay /// 0005515 // protein binding // inferred from physical interaction /// 0005524 // ATP binding // inferred from direct assay /// 0005524 // ATP binding // inferred from electronic annotation /// 0008289 // lipid binding // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation /// 0016887 // ATPase activity // inferred from direct assay /// 0017111 // nucleoside-triphosphatase activity // inferred from electronic annotation /// 0019903 // protein phosphatase binding // inferred from electronic annotation /// 0019903 // protein phosphatase binding // not recorded /// 0019904 // protein domain specific binding // inferred from electronic annotation /// 0019904 // protein domain specific binding // not recorded /// 0031593 // polyubiquitin binding // inferred from electronic annotation /// 0031593 // polyubiquitin binding // not recorded /// 0032403 // protein complex binding // inferred from physical interaction /// 0042802 // identical protein binding // inferred from direct assay
0000209 // protein polyubiquitination // not recorded /// 0000209 // protein polyubiquitination // inferred from sequence or structural similarity /// 0006281 // DNA repair // inferred from electronic annotation /// 0006511 // ubiquitin-dependent protein catabolic process // inferred from direct assay /// 0006513 // protein monoubiquitination // not recorded /// 0006915 // apoptotic process // inferred from electronic annotation /// 0006974 // response to DNA damage stimulus // inferred from electronic annotation /// 0016567 // protein ubiquitination // inferred from direct assay /// 0016567 // protein ubiquitination // not recorded /// 0016567 // protein ubiquitination // inferred from electronic annotation /// 0043161 // proteasomal ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0043161 // proteasomal ubiquitin-dependent protein catabolic process // not recorded /// 0043161 // proteasomal ubiquitin-dependent protein catabolic process // inferred from sequence or structural similarity /// 0070936 // protein K48-linked ubiquitination // not recorded /// 0070936 // protein K48-linked ubiquitination // inferred from sequence or structural similarity /// 0070979 // protein K11-linked ubiquitination // not recorded /// 0070979 // protein K11-linked ubiquitination // inferred from sequence or structural similarity
0005768 // endosome // inferred from electronic annotation /// 0005886 // plasma membrane // inferred from electronic annotation /// 0010008 // endosome membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation
0000166 // nucleotide binding // inferred from electronic annotation /// 0004842 // ubiquitin-protein ligase activity // inferred from direct assay /// 0004842 // ubiquitin-protein ligase activity // not recorded /// 0004842 // ubiquitin-protein ligase activity // inferred from sequence or structural similarity /// 0004842 // ubiquitin-protein ligase activity // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0016874 // ligase activity // inferred from electronic annotation /// 0016881 // acid-amino acid ligase activity // inferred from electronic annotation
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
beclin 1, autophagy related
Becn1
chr10q32.1
full length
ENSRNOG00000020513
114558
Q91XJ1
---
NP_001029289 /// NP_446191
NM_001034117 /// NM_053739
0000045 // autophagic vacuole assembly // inferred from mutant phenotype /// 0000910 // cytokinesis // not recorded /// 0000910 // cytokinesis // inferred from sequence or structural similarity /// 0000910 // cytokinesis // inferred from electronic annotation /// 0001666 // response to hypoxia // inferred from expression pattern /// 0006914 // autophagy // inferred from expression pattern /// 0006914 // autophagy // inferred from mutant phenotype /// 0006914 // autophagy // not recorded /// 0006914 // autophagy // inferred from electronic annotation /// 0007040 // lysosome organization // inferred from electronic annotation /// 0007040 // lysosome organization // not recorded /// 0007049 // cell cycle // inferred from electronic annotation /// 0008285 // negative regulation of cell proliferation // inferred from electronic annotation /// 0008285 // negative regulation of cell proliferation // not recorded /// 0009615 // response to virus // inferred from electronic annotation /// 0016239 // positive regulation of macroautophagy // inferred from electronic annotation /// 0016239 // positive regulation of macroautophagy // not recorded /// 0033197 // response to vitamin E // inferred from expression pattern /// 0042493 // response to drug // inferred from expression pattern /// 0048666 // neuron development // inferred from electronic annotation /// 0048666 // neuron development // not recorded /// 0050435 // beta-amyloid metabolic process // inferred from electronic annotation /// 0050435 // beta-amyloid metabolic process // not recorded /// 0051301 // cell division // inferred from electronic annotation /// 0051707 // response to other organism // not recorded /// 0051707 // response to other organism // inferred from electronic annotation /// 0060548 // negative regulation of cell death // inferred from mutant phenotype /// 0071275 // cellular response to aluminum ion // inferred from expression pattern /// 0071364 // cellular response to epidermal growth factor stimulus // inferred from expression pattern
0005634 // nucleus // inferred from direct assay /// 0005737 // cytoplasm // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005802 // trans-Golgi network // inferred from electronic annotation /// 0005802 // trans-Golgi network // not recorded /// 0016020 // membrane // inferred from electronic annotation /// 0016023 // cytoplasmic membrane-bounded vesicle // inferred from electronic annotation /// 0016023 // cytoplasmic membrane-bounded vesicle // not recorded /// 0030425 // dendrite // inferred from direct assay /// 0043234 // protein complex // inferred from electronic annotation /// 0043234 // protein complex // not recorded
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
ADP-ribosylation factor 1
Arf1
chr10q22
full length
---
64310
P84079
---
NP_071963
NM_022518
0006810 // transport // inferred from electronic annotation /// 0006878 // cellular copper ion homeostasis // inferred from electronic annotation /// 0006878 // cellular copper ion homeostasis // not recorded /// 0007264 // small GTPase mediated signal transduction // inferred from electronic annotation /// 0015031 // protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // not recorded
0005622 // intracellular // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005794 // Golgi apparatus // not recorded /// 0005829 // cytosol // inferred from electronic annotation /// 0005829 // cytosol // not recorded /// 0012505 // endomembrane system // inferred from electronic annotation /// 0012505 // endomembrane system // not recorded /// 0030017 // sarcomere // inferred from electronic annotation /// 0030017 // sarcomere // not recorded /// 0048471 // perinuclear region of cytoplasm // inferred from electronic annotation
0000166 // nucleotide binding // inferred from electronic annotation /// 0005525 // GTP binding // inferred from electronic annotation
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
GDP dissociation inhibitor 2
Gdi2
chr17q12.3
full length
ENSRNOG00000018091
29662
H7C5Y3 /// P50399
---
NP_058972
NM_017276
0007264 // small GTPase mediated signal transduction // not recorded /// 0015031 // protein transport // inferred from electronic annotation /// 0015031 // protein transport // traceable author statement /// 0016192 // vesicle-mediated transport // inferred from expression pattern /// 0043547 // positive regulation of GTPase activity // inferred from electronic annotation
0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // not recorded /// 0005829 // cytosol // traceable author statement /// 0009986 // cell surface // not recorded /// 0016020 // membrane // inferred from electronic annotation
0005093 // Rab GDP-dissociation inhibitor activity // inferred from direct assay /// 0005093 // Rab GDP-dissociation inhibitor activity // inferred from electronic annotation /// 0005096 // GTPase activator activity // inferred from electronic annotation /// 0005097 // Rab GTPase activator activity // not recorded /// 0031267 // small GTPase binding // inferred from direct assay
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
coatomer protein complex, subunit beta 1
Copb1
chr1q34
full length
ENSRNOG00000012000
114023
P23514
---
NP_542959
NM_080781
0006810 // transport // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0006890 // retrograde vesicle-mediated transport, Golgi to ER // traceable author statement /// 0006891 // intra-Golgi vesicle-mediated transport // inferred from direct assay /// 0015031 // protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from electronic annotation
0000139 // Golgi membrane // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005783 // endoplasmic reticulum // inferred from electronic annotation /// 0005792 // microsome // inferred from electronic annotation /// 0005793 // endoplasmic reticulum-Golgi intermediate compartment // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from direct assay /// 0005794 // Golgi apparatus // not recorded /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005798 // Golgi-associated vesicle // inferred from direct assay /// 0005886 // plasma membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0030117 // membrane coat // inferred from electronic annotation /// 0030126 // COPI vesicle coat // inferred from direct assay /// 0030126 // COPI vesicle coat // inferred from electronic annotation /// 0030137 // COPI-coated vesicle // not recorded /// 0030137 // COPI-coated vesicle // inferred from electronic annotation /// 0030663 // COPI coated vesicle membrane // inferred from electronic annotation /// 0031410 // cytoplasmic vesicle // inferred from electronic annotation
0005198 // structural molecule activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
defender against cell death 1
Dad1
chr15p13
full length
ENSRNOG00000009090
192275
P61805
EC:2.4.1.119
NP_620265
NM_138910
0001824 // blastocyst development // inferred from electronic annotation /// 0001824 // blastocyst development // not recorded /// 0006486 // protein glycosylation // inferred from sequence or structural similarity /// 0006915 // apoptotic process // inferred from electronic annotation /// 0006916 // anti-apoptosis // inferred from electronic annotation /// 0006916 // anti-apoptosis // not recorded /// 0007584 // response to nutrient // inferred from expression pattern /// 0042493 // response to drug // inferred from expression pattern
0008250 // oligosaccharyltransferase complex // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation
0004576 // oligosaccharyl transferase activity // inferred from sequence or structural similarity /// 0004579 // dolichyl-diphosphooligosaccharide-protein glycotransferase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation
gb:BG380638 /DB_XREF=gi:13305110 /DB_XREF=UI-R-CT0-btz-f-07-0-UI.s1 /CLONE=UI-R-CT0-btz-f-07-0-UI /FEA=EST /CNT=56 /TID=Rn.121.1 /TIER=Stack /STK=45 /UG=Rn.121 /UG_TITLE=ESTs, Weakly similar to T26931 hypothetical protein Y45F10D.4 - Caenorhabditis elegans (C.elegans)
BG380638
Rn.121
Rn.121
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
iron-sulfur cluster scaffold homolog (E. coli)
Iscu
chr12q16
full length
ENSRNOG00000000701
288740
B2RZ79
---
NP_001099406
NM_001105936
0016226 // iron-sulfur cluster assembly // inferred from electronic annotation
0005737 // cytoplasm // not recorded /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005739 // mitochondrion // inferred from electronic annotation /// 0005739 // mitochondrion // not recorded /// 0005829 // cytosol // inferred from electronic annotation /// 0005829 // cytosol // not recorded
0005506 // iron ion binding // inferred from electronic annotation /// 0032947 // protein complex scaffold // inferred from electronic annotation /// 0032947 // protein complex scaffold // not recorded /// 0051536 // iron-sulfur cluster binding // inferred from electronic annotation
0006412 // translation // not recorded /// 0006413 // translational initiation // not recorded /// 0006446 // regulation of translational initiation // not recorded /// 0016070 // RNA metabolic process // inferred from electronic annotation
0005737 // cytoplasm // not recorded /// 0005737 // cytoplasm // inferred from electronic annotation /// 0016281 // eukaryotic translation initiation factor 4F complex // not recorded
0003677 // DNA binding // inferred from electronic annotation /// 0003723 // RNA binding // inferred from electronic annotation /// 0003743 // translation initiation factor activity // not recorded /// 0008135 // translation factor activity, nucleic acid binding // not recorded
gb:AA851321 /DB_XREF=gi:2938861 /DB_XREF=EST194089 /CLONE=RPLAF21 /FEA=EST /CNT=34 /TID=Rn.15760.1 /TIER=Stack /STK=31 /UG=Rn.15760 /UG_TITLE=ESTs, Weakly similar to ARF6_HUMAN ADP-RIBOSYLATION FACTOR 6 (R.norvegicus)
AA851321
Rn.15760
Rn.15760
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
SAR1 homolog A (S. cerevisiae)
Sar1a
chr20q11
full length
ENSRNOG00000000557
361842
Q6AY18
---
NP_001007740
NM_001007739
0006810 // transport // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0015031 // protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // not recorded
0005622 // intracellular // inferred from electronic annotation /// 0005783 // endoplasmic reticulum // not recorded /// 0005783 // endoplasmic reticulum // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005794 // Golgi apparatus // not recorded /// 0016529 // sarcoplasmic reticulum // inferred from electronic annotation /// 0016529 // sarcoplasmic reticulum // not recorded
0000166 // nucleotide binding // inferred from electronic annotation /// 0005525 // GTP binding // inferred from electronic annotation
gb:BI279090 /DB_XREF=gi:14926572 /DB_XREF=UI-R-DA0-byj-b-03-0-UI.s1 /CLONE=UI-R-DA0-byj-b-03-0-UI /FEA=EST /CNT=38 /TID=Rn.1769.1 /TIER=Stack /STK=30 /UG=Rn.1769 /UG_TITLE=ESTs, Highly similar to RPB5_HUMAN DNA-DIRECTED RNA POLYMERASE II 23 KD POLYPEPTIDE (H.sapiens)
BI279090
Rn.1769
Rn.65038
November 2004 (Baylor College of Medicine HGSC Rnor3.4)
polymerase (RNA) II (DNA directed) polypeptide E
Polr2e
chr7q11
full length
ENSRNOG00000013545
690966
B0BNE2 /// D3ZZV6
EC:2.7.7.6
NP_001103084
NM_001109614
0006351 // transcription, DNA-dependent // inferred from electronic annotation /// 0006366 // transcription from RNA polymerase II promoter // not recorded /// 0006366 // transcription from RNA polymerase II promoter // inferred from sequence or structural similarity /// 0006366 // transcription from RNA polymerase II promoter // inferred from electronic annotation /// 0006468 // protein phosphorylation // not recorded /// 0006468 // protein phosphorylation // inferred from sequence or structural similarity /// 0006468 // protein phosphorylation // inferred from electronic annotation
0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // not recorded /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005665 // DNA-directed RNA polymerase II, core complex // not recorded /// 0005665 // DNA-directed RNA polymerase II, core complex // inferred from sequence or structural similarity /// 0005665 // DNA-directed RNA polymerase II, core complex // inferred from electronic annotation
0003677 // DNA binding // inferred from electronic annotation /// 0003899 // DNA-directed RNA polymerase activity // inferred from electronic annotation /// 0004672 // protein kinase activity // not recorded /// 0004672 // protein kinase activity // inferred from sequence or structural similarity /// 0004672 // protein kinase activity // inferred from electronic annotation
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