G2Cdb - Documentation

Documentation: Plasticity Data

These data are the results of a systematic curation of the literature on synaptic plasticity in mice. We focused on papers studying the effects of mutations on plasticity, particularly Long-Term Potentiation (LTP) and Long-Term Depression (LTD).

Contents

Background

Synaptic plasticity is the ability of neurones to alter their responses to each other, and is widely hypothesised to underpin learning. It is studied principally by electrophysiology.

LTP refers to an enduring enhancement of synaptic transmission between two or more neurones. It is typically elicited by high-frequency electrical stimulation. Following this stimulation, the neurones respond more readily to each other; this effect has been observed to last for a period of hours.

LTD is the 'opposite' effect, an enduring reduction in synaptic transmission between two or more neurones. It is produced by prolonged low-frequency stimulation.

We curated data from 259 papers studying the effects of mutations on synaptic plasticity. We classified the plasticity effects into six categories, which are described below. The brain region in which plasticity was studied was also noted and classified, as illustrated in the 'Tissue' field.

We also categorised the mutations into six types; knockout, conditional knockout, point, truncation, over-expression and other. These are represented in the data by abbreviations, to allow a more precise description of the literature. For example, a gene may have been studied using two different mutation types, both of which produce the same plasticity effect. Our system makes such results apparent, without the need for the reader to cross-reference.

In each plasticity effect column (LTP decrease, etc), one sees numbers followed by a short letter string. The letters are the code used to represent the mutation type. This is illustrated in the table below, which displays the codes used to denote one of each mutation type.

Mutation type	Code
Knockout	1ko
Over-Expression	1ov
Point	1po
Truncation	1tr
Conditional	1co
Other	1ot

So, for example, one might see that for one gene, in one particular brain region, the 'LTP decrease' column reads '2ko, 1po'. This means that there are two reports of knockout mutations producing an LTP decrease in that region, and also one report of a point mutation producing an LTP decrease in that region.

Clicking on a data point opens up a new window which displays the paper referred to and also provides more detailed information on the methods and protocols employed.

Tissue
Name of the brain region in which synaptic plasticity was studied. Brain regions were classified as belonging to one of the following categories:

Hippocampal Regions	Non-Hippocampal Regions
Generic Hippocampal	Cerebellum
CA1-CA3 Schaffer Collateral / Commisural	Striatum
Mossy Fibre	Cortex
Dentate Gyrus	Amygdala
Other

LTP decrease
Number of reports, by mutation type, claiming that a mutation in this gene was associated with an LTP decrease.

LTP increase
Number of reports, by mutation type, claiming that a mutation in this gene was associated with an LTP increase.

LTD decrease
Number of reports, by mutation type, claiming that a mutation in this gene was associated with an LTD decrease.

LTD increase
Number of reports, by mutation type, claiming that a mutation in this gene was associated with an LTD increase.

No Effect
Number of reports, by mutation type, claiming that a mutation in this gene produced no changes in synaptic plasticity.

Other synaptic effects
Number of reports, by mutation type, claiming that a mutation in this gene produced a synaptic effect other than those delineated in the LTP and LTD columns. Examples would include a change in baseline synaptic activity, reduced Paired-Pulse Facilitation, etc.

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