Table 2.
Over-representation analysis for DEGs in whole brain and striatum.
| Brain Region | General category | Classification terma | Resourceb | # genesc | p-valued | Corrected p-valuee |
|---|---|---|---|---|---|---|
| Striatum | Synapse/Signaling | Potassium channel activity | Gene Ontology | 14 | 9.92E-08 | 1.01E-05 |
| G-protein coupled receptor signaling pathway | Gene Ontology | 23 | 3.01E-06 | 5.00E-04 | ||
| Signal transduction | Gene Ontology | 68 | 1.00E-03 | 2.00E-03 | ||
| Neuron development | Gene Ontology | 17 | 7.15E-05 | 2.00E-03 | ||
| Non-odorant G-protein coupled receptors | Wikipathways | 13 | 2.00E-04 | 3.40E-03 | ||
| Calcium signaling pathway | KEGG | 12 | 2.00E-04 | 5.60E-03 | ||
| Dopamine receptor activity | Gene Ontology | 2 | 9.00E-04 | 6.10E-03 | ||
| Beta-adrenergic receptor kinase activity | Gene Ontology | 2 | 9.00E-04 | 6.10E-03 | ||
| Neuroactive ligand-receptor interation | KEGG | 11 | 4.00E-04 | 7.50E-03 | ||
| Negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway | Gene Ontology | 4 | 5.00E-04 | 8.80E-03 | ||
| Synapse | Gene Ontology | 15 | 4.20E-03 | 3.65E-02 | ||
| Opioid peptide activity | Gene Ontology | 2 | 8.40E-03 | 4.18E-02 | ||
| Gap junction | KEGG | 7 | 4.30E-03 | 4.82E-02 | ||
| Behavior | Response to amphetamine | Gene Ontology | 4 | 1.00E-04 | 2.00E-03 | |
| Ribosome | Cytoplasmic ribosomal proteins | Wikipathways | 13 | 1.22E-07 | 4.15E-06 | |
| Ribosome | KEGG | 13 | 2.61E-07 | 1.46E-05 | ||
| Ribosome | Gene Ontology | 13 | 1.10E-03 | 1.41E-02 | ||
| Cell types | Neuron | Cahoy et al | 96 | 1.00E-16 | ||
| Oligodendrocyte | Cahoy et al | 26 | 2.50E-03 | |||
| Lore QTL | Lore4 Chr11:79000000-108000000 | Bennett et al | 13 | 4.10E-02 | ||
|
| ||||||
| Whole Brain | Ribosome | Cytoplasmic ribosomal proteins | Wikipathways | 6 | 1.04E-05 | 7.28E-05 |
| Ribonucleoprotein complex | Gene Ontology | 8 | 4.20E-03 | 2.85E-02 | ||
| Ribosome | KEGG | 7 | 9.19E-07 | 9.19E-06 | ||
| Cell membrane | Extracellular region | Gene Ontology | 13 | 7.00E-04 | 1.86E-02 | |
| Metabolic pathway | Retinol metabolism | Wikipathways | 2 | 1.17E-02 | 4.10E-02 | |
| Immune | MHC protein complex | Gene Ontology | 2 | 3.80E-03 | 2.85E-02 | |
| Cell types | Astrocyte | Cahoy et al | 10 | 2.60E-02 | ||
| Lore QTL | LoreChr3 Chr3:130000000-155000000 | Bennett et al | 2 | 2.70E-02 | ||
a
Term used to classify related genes.
b
Resource used for classification, Gene Ontology, KEGG, NCBI Entrez Gene, Wikipathways, Cahoy et al (2008), or Bennett et al (2006)/personal communication with Dr. Bennett.
c
Number of differentially expressed genes in each category.
d
Uncorrected hypergeometric p-value testing whether number of DEGs in each term more than expected.
e
Benjamini-Hochberg corrected p-values.