Identification of Candidate Genes and Physiological Pathways Involved in Gonad Deformation in Whitefish (Coregonus spp.) from Lake Thun, Switzerland
Abstract
:1. Introduction
2. Experimental Section
2.1. Sampling
2.2. Experimental Design
2.3. Microarrays
2.4. cRNA Synthesis, Hybridizations, Imaging and Feature Extraction
2.5. Normalization and Data Filtering
2.6. Gene-by-Gene Analysis
2.7. Gene Ontology Analysis
2.8. Hierarchical Clustering
2.9. Real-Time qPCR Analysis
3. Results and Discussion
3.1. Gene-by-Gene Analysis
3.2. GO Analysis
3.3. Deviation in Regulation of Immune System Processes
3.4. Autoimmune Disease?
3.5. Indications of Ictacalcin
4. Conclusions
Supplementary Materials
ijerph-08-02706-s001.docAcknowledgements
References and Notes
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Liver: GEXP = 7,013 | Comparison | 5% | FDR | 1% | FDR | FDR ≤ 5% |
---|---|---|---|---|---|---|
A | 346 (0.049) | 1 | 78 (0.011) | 0.88 | 0 | |
B | 74 (0.011) | 1 | 10 (0.001) | 1 | 0 | |
C | 177 (0.025) | 1 | 33 (0.005) | 1 | 0 | |
D | 3,407 (0.486) | 0.1 | 2,407 (0.343) | 0.03 | 2,764 (0.394) | |
Head kidney: GEXP = 17,834 | Comparison | 5% | FDR | 1% | FDR | FDR ≤ 5% |
A | 1,162 (0.065) | 0.77 | 264 (0.015) | 0.68 | 0 | |
B | 2,548 (0.143) | 0.35 | 528 (0.030) | 0.31 | 0 | |
C | 651 (0.037) | 0.95 | 102 (0.006) | 0.95 | 0 | |
D | 12,416 (0.696) | 0.01 | 10,382 (0.582) | 0.02 | 12,820 (0.719) |
(a) | Liver: Albock normal vs. Albock deformed | ||||
---|---|---|---|---|---|
GO root node | Name | GO ID | Genes | P | |
biological_process | immune response | GO:0006955 | 70 | 0.000 | |
biological_process | humoral immune response | GO:0006959 | 22 | 0.001 | |
biological_process | innate immune response | GO:0045087 | 25 | 0.001 | |
biological_process | activation of immune response | GO:0002253 | 22 | 0.002 | |
biological_process | Proteolysis | GO:0006508 | 160 | 0.004 | |
cellular_component | integral to plasma membrane | GO:0005887 | 60 | 0.009 | |
biological_process | immune effector process | GO:0002252 | 32 | 0.009 | |
(b) | Liver: Brienzlig normal vs. deformed | ||||
GO root node | Name | GO ID | Genes | P | |
cellular_component | extracellular region | GO:0005576 | 197 | 0.002 | |
cellular_component | proteinaceous extracellular matrix | GO:0005578 | 31 | 0.002 | |
biological_process | immune system process | GO:0002376 | 107 | 0.006 | |
biological_process | cell adhesion | GO:0007155 | 85 | 0.009 | |
(c) | Head kidney: Albock normal vs. deformed | ||||
GO root node | Name | GO ID | Genes | P | |
biological_process | regulation of cell proliferation | GO:0042127 | 114 | 0.000 | |
biological_process | positive regulation of cell proliferation | GO:0008284 | 54 | 0.000 | |
biological_process | embryonic development | GO:0009790 | 86 | 0.000 | |
biological_process | protein import into nucleus | GO:0006606 | 23 | 0.001 | |
molecular_function | ATP-dependent helicase activity | GO:0008026 | 20 | 0.001 | |
biological_process | cell migration | GO:0016477 | 52 | 0.001 | |
biological_process | embryonic development ending in birth or egg hatching | GO:0009792 | 58 | 0.002 | |
molecular_function | small GTPase regulator activity | GO:0005083 | 49 | 0.004 | |
biological_process | regulation of Ras protein signal transduction | GO:0046578 | 27 | 0.004 | |
biological_process | cellular protein complex assembly | GO:0043623 | 41 | 0.009 | |
biological_process | regulation of immune system process | GO:0002682 | 45 | 0.009 | |
biological_process | central nervous system development | GO:0007417 | 45 | 0.010 | |
(d) | Head kidney: Brienzlig normal vs. deformed | ||||
GO root node | Name | GO ID | Genes | P | |
molecular_function | GTPase activator activity | GO:0005096 | 36 | 0.003 | |
biological_process | leukocyte differentiation | GO:0002521 | 32 | 0.006 | |
biological_process | gamete generation | GO:0007276 | 40 | 0.006 | |
biological_process | T cell activation | GO:0042110 | 31 | 0.008 | |
cellular_component | soluble fraction | GO:0005625 | 32 | 0.009 | |
biological_process | muscle contraction | GO:0006936 | 28 | 0.010 |
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Bittner, D.; Cossins, A.R.; Segner, H.; Excoffier, L.; Largiadèr, C.R. Identification of Candidate Genes and Physiological Pathways Involved in Gonad Deformation in Whitefish (Coregonus spp.) from Lake Thun, Switzerland. Int. J. Environ. Res. Public Health 2011, 8, 2706-2733. https://doi.org/10.3390/ijerph8072706
Bittner D, Cossins AR, Segner H, Excoffier L, Largiadèr CR. Identification of Candidate Genes and Physiological Pathways Involved in Gonad Deformation in Whitefish (Coregonus spp.) from Lake Thun, Switzerland. International Journal of Environmental Research and Public Health. 2011; 8(7):2706-2733. https://doi.org/10.3390/ijerph8072706
Chicago/Turabian StyleBittner, David, Andrew R. Cossins, Helmut Segner, Laurent Excoffier, and Carlo R. Largiadèr. 2011. "Identification of Candidate Genes and Physiological Pathways Involved in Gonad Deformation in Whitefish (Coregonus spp.) from Lake Thun, Switzerland" International Journal of Environmental Research and Public Health 8, no. 7: 2706-2733. https://doi.org/10.3390/ijerph8072706