Table 3.
Descriptions of genes sets and results of analyses.
| Source | Set description | Size | Description | FLX | VNX | CBZ | MIX |
|---|---|---|---|---|---|---|---|
| a. Development collection, containing 20 sets | |||||||
| GO:0007409 | AXONOGENESIS | 437/281 | Genes assoc. with generation of a long process of a neuron that carries efferent (outgoing) action potentials from cell body towards target cells | NES=1.23 p=0.00 q=0.430 |
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| GO:0007420 | BRAIN DEVELOPMENT | 329/200 | Genes assoc. with process whose specific outcome is the progression of the brain over time, from formation to the mature structure | ||||
| GO:0007417 | CENTRAL NERVOUS SYSTEM DEVELOPMENT | 480/289 | Genes assoc. with process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure; the CNS consists of the brain, spinal cord and spinal nerves | ||||
| GO:0021954 | CENTRAL NERVOUS SYSTEM NEURON DEVELOPMENT | 31/20 | Genes assoc. with process whose specific outcome is the progression of a neuron whose cell body is located in the CNS, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron | ||||
| GO:0021545 | CRANIAL NERVE DEVELOPMENT | 29/14 | Genes assoc. with process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure | ||||
| GO:0016358 | DENDRITE DEVELOPMENT | 63/38 | Genes assoc. with dendrite development | ||||
| GO:0007272 | ENSHEATHMENT OF NEURONS | 51/31 | Genes assoc. with process by which the axon of a neuron is insulated, and that insulation maintained |
NES=1.39 p=0.00 q=0.201 |
NES=1.32 p=0.00 q=0.359 |
||
| GO:0030900 | FOREBRAIN DEVELOPMENT | 182/114 | Genes assoc. with process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure | ||||
| GO:0048699 | GENERATION OF NEURONS | 82/52 | Genes assoc. with process by which nerve cells are generated; includes production of neuroblasts and their differentiation into neurons | ||||
| GO:0030902 | HIND BRAIN DEVELOPMENT | 63/36 | Genes assoc. with process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure | ||||
| GO:0007399 | NERVOUS SYSTEM DEVELOPMENT | 381/229 | Genes assoc. with process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state | NES=1.21 p=0.00 q=0.325 |
|||
| GO:0021915 | NEURAL TUBE DEVELOPMENT | 81/48 | Genes assoc. with process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure |
NES=1.58 p=0.00 q=0.159 |
|||
| GO:0022008 | NEUROGENESIS | 20/12 | Genes assoc. with generation of cells within the nervous system | ||||
| GO:0048666 | NEURON DEVELOPMENT | 27/14 | Genes assoc. with process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell | ||||
| GO:0050767 | REGULATION OF NEUROGENESIS | 230/155 | Genes assoc. with processes that modulates the frequency, rate or extent of neurogenesis | ||||
| GO:0050768 | NEGATIVE REGULATION OF NEUROGENESIS | 57/41 | Genes assoc. with process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis | ||||
| GO:0050769 | POSITIVE REGULATION OF NEUROGENESIS | 74/56 | Genes assoc. with process that activates or increases the frequency, rate or extent of neurogenesis | ||||
| GO:0050772 | POSITIVE REGULATION OF AXONOGENESIS | 30/25 | Genes assoc. with process that activates or increases the frequency, rate or extent of axonogenesis | ||||
| GO:0050808 | SYNAPSE ORGANISATION | 73/41 | Genes assoc. with assembly, arrangement of constituent parts, or disassembly of a synapse |
NES=1.61 p=0.00 q=0.128 |
|||
| GO:0044456 | SYNAPSE PART | 273/159 | Genes assoc. with junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell | NES=1.33 p=0.00 q=0.649 |
NES=1.64 p=0.00 q=0.094 |
||
| b. Regulation collection, containing 22 sets | |||||||
| GO:0043679 | AXON TERMINUS | 37/23 | Genes assoc. with terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters | ||||
| GO:0008066 | GLUTAMATE RECEPTOR ACTIVITY | 28/14 | Genes assoc. with combining with glutamate to initiate a change in cell activity | ||||
| MSigDB C2 CPG | HSA04080 NEUROACTIVE LIGAND RECEPTOR INTERACTION | 67/31 | Genes assoc. with neuro-active ligand–receptor interaction | ||||
| MSigDB C2 CPG | LU AGING BRAIN DN | 260/169 | Genes down-regulated in postmortem brain frontal cortex samples from old subjects relative to young ones | ||||
| MSigDB C2 CPG | LU AGING BRAIN UP | 155/107 | Genes up-regulated in postmortem brain frontal cortex samples from old subjects relative to young ones |
NES=1.33 p=0.00 q=0.234 |
NES=1.44 p=0.00 q=0.161 |
||
| GO:0007270 | NERVE-NERVE SYNAPTIC TRANSMISSION | 58/37 | Genes assoc. with process of communication from one neuron to another across a synapse | ||||
| GO:0042165 | NEUROTRANSMITTER BINDING | 75/31 | Gene products capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell |
NES= −1.51 p=0.00 q=0.235 |
|||
| GO:0042133 | NEUROTRANSMITTER METABOLIC PROCESS | 24/18 | Genes assoc. with chemical reactions and pathways involving neurotransmitters | ||||
| GO:0030594 | NEUROTRANSMITTER RECEPTOR ACTIVITY | 65/24 | Genes assoc. with combining with a neurotransmitter to initiate a change in cell activity | ||||
| GO:0007269 | NEUROTRANSMITTER SECRETION | 79/53 | Genes associated with regulated release of neurotransmitter into the synaptic cleft |
NES=1.58 p=0.00 q=0.081 |
|||
| GO:0006836 | NEUROTRANSMITTER TRANSPORT | 121/75 | Genes associated with the directed movement of a neurotransmitter into, out of, within or between cells | NES=1.36 p=0.00 q=0.302 |
|||
| GO:0019228 | REGULATION OF ACTIONPOTENTIAL IN NEURON | 63/37 | Genes assoc. modulating membrane potential involved in the propagation of a neural signal |
NES=1.53 p=0.00 q=0.073 |
NES=1.32 p=0.00 q=0.284 |
||
| GO:0050433 | REGULATION OF CATECHOLAMINE SECRETION | 25/14 | Genes assoc. with any process modulating frequency, rate or extent of regulated release of catecholamines | NES=−1.32 p=0.00 q=0.790 |
|||
| GO:0048168 | REGULATION OF NEURONAL SYNAPTIC PLASTICITY | 31/21 | Genes assoc. with process that modulates neuronal synaptic plasticity, the ability of neuronal synapses to change as circumstances require | ||||
| GO:0001505 | REGULATION OF NEUROTRANSMITTER LEVELS | 109/73 | Genes assoc. with process modulating neurotransmitter level | ||||
| GO:0051969 | REGULATION OF TRANSMISSION OF NERVE IMPULSE | 136/82 | Genes assoc. with modulating frequency, rate or extent of transmission of a nerve impulse | ||||
| GO:0031644 | REGULATION OF NEUROLOGICAL SYSTEM PROCESS | 146/87 | Genes assoc. with process that modulates frequency, rate or extent of a neurophysiological process, an organ system process carried out by any organ or tissue of neurological system | ||||
| GO:0005484 | SNAP RECEPTOR ACTIVITY | 19/14 | Genes assoc. with acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion | ||||
| GO:0000149 | SNARE BINDING | 30/24 | Genes assoc. with interacting selectively and non-covalently with SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein |
NES=1.47 p=0.00 q=0.109 |
NES=1.70 p=0.00 q=0.053 |
NES=1.82 p=0.00 q=0.044 |
|
| GO:0045202 | SYNAPSE | 370/227 | Genes assoc. with junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell | NES=1.24 p=0.00 q=0.342 |
NES=1.63 p=0.00 q=0.100 |
||
| GO:0007268 | SYNAPTIC TRANSMISSION | 361/200 | Genes assoc. with process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse | ||||
| GO:0019226 | TRANSMISSION OF NERVE IMPULSE | 420/235 | Genes assoc. with sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation | NES=1.31 p=0.00 q=0.379 |
|||
| c. Growth collection, containing 16 sets | |||||||
| MSigDB C2 CPG | APPEL IMATINIB RESPONSE | 32/20 | Genes up-regulated by imatinib during dendritic cell differentiation |
NES=−1.46 p=0.00 q=0.065 |
|||
| GO:0030424 | AXON | 180/127 | Genes assoc. with long process of a neuron that conducts nerve impulses, usually away from the cell body to terminals and varicosities |
NES=1.19 p=0.00 q=0.217 |
|||
| GO:0008366 | AXON ENSHEATHMENT | 51/31 | Genes assoc. with processes in which the axon of a neuron is insulated, and that insulation maintained | NES=1.38 p=0.00 q=0.551 |
NES=1.32 p=0.00 q=0.707 |
||
| GO:0048675 | AXON EXTENSION | 47/32 | Genes assoc. with long distance growth of a single process | ||||
| GO:0007411 | AXON GUIDANCE | 325/208 | Genes assoc. with process by which migration of an axon growth cone is directed to a specific target site in response to a combination of attractive and repulsive cues | ||||
| GO:0033267 | AXON PART | 71/47 | Genes assoc. with part of an axon, a cell projection of a neuron | ||||
| GO:0048667 | CELL MORPHOGENESIS INVOLVED IN NEURON DIFFERENTIATION | 465/297 | Genes assoc. with processes in which structures of a neuron are generated and organized | NES=1.22 p=0.00 q=0.614 |
|||
| GO:0021953 | CENTRAL NERVOUS SYSTEM NEURON DIFFERENTIATION | 80/45 | Genes assoc. with process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the central nervous system | ||||
| GO:0070997 | NEURON DEATH | 105/78 | Genes assoc. with process of neuron cell death | ||||
| GO:0030182 | NEURON DIFFERENTIATION | 74/43 | Genes assoc. with process whereby a relatively unspecialized cell acquires specialized features of a neuron | ||||
| GO:0042551 | NEURON MATURATION | 19/12 | Genes assoc. with process, independent of morphogenetic change, required for a neuron to attain its fully functional state | ||||
| GO:0043005 | NEURON PROJECTION | 384/246 | Genes assoc. with prolongation or process extending from a nerve cell, e.g. an axon or dendrite |
NES=1.41 p=0.00 q=0.240 |
|||
| GO:0048812 | NEURON PROJECTION MORPHOGENESIS | 468/302 | Genes assoc. with process in which anatomical structures of a neuron projection are generated and organized | NES=1.21 p=0.00 q=0.493 |
|||
| GO:0043523 | REGULATION OF NEURON APOPTOSIS | 87/64 | Genes assoc. with process that modulates the occurrence or rate of cell death by apoptosis in neurons |
NES=−1.44 p=0.00 q=0.057 |
|||
| GO:0045664 | REGULATION OF NEURON DIFFERENTIATION | 183/126 | Genes assoc. with process that modulates the frequency, rate or extent of neuron differentiation | ||||
| GO:0007416 | SYNAPSE ASSEMBLY | 46/23 | Genes assoc. with aggregation, arrangement & bonding together of set of components to form synapse | ||||
Source indicates the database from which the gene set was derived, either GO (Gene Ontology) or MSigDB (Molecular Signatures Database). Size indicates the number of genes in the set and the number of those genes that were found on the array. FLX, VNX, CBZ and MIX refer to fluoxetine, venlafaxine, carbamazepine and mixture treatments, respectively. NES, p and q refer to the GSEA Net Enrichment Score, p-value and False Discover Rate q-value, respectively. Positive NES values refer to gene sets up-regulated in the treatment (relative to control) while negative NES values refer to gene sets down-regulated in the treatment. Gene sets with p<0.05 and q<0.25 were considered to be statistically significantly enriched (see Subramanian et al., 2005 for details); enriched sets and corresponding scores are marked in bold to highlight this. Sets with high NES scores but failing the FDR test (p<0.05 and q>0.25) are listed for comparison only.