neuroelectro.org a window to the world’s neurophysiology data shreejoy tripathy university of...
TRANSCRIPT
![Page 1: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/1.jpg)
NeuroElectro.orgA window to the world’s neurophysiology data
Shreejoy TripathyUniversity of British Columbia, Canada
Email: [email protected]: @neuronJoy
![Page 2: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/2.jpg)
Main Idea• Given that there is an extensive neuron
electrophysiology literature, what can we learn by compiling it?
PubMed search: neuron AND (electrophysiology OR biophysical OR neurophysiology)
>45K articles
![Page 3: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/3.jpg)
Electrophysiology literature is notoriously heterogeneous
![Page 4: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/4.jpg)
Electrophysiology literature is notoriously heterogeneous
Input resistancemeasurement differences
![Page 5: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/5.jpg)
NeuroElectro overall methodology
![Page 6: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/6.jpg)
6
Semi-automated text-mining overview
• Identify within data tables:– Neuron types (from
NeuroLex.org)– Biophysical properties (in
normotypic conditions)– Biophysical data values
• Experimental conditions defined within methods sections
• Text-mined data is then checked by experts
Tripathy et al, 2014
“Experiments were conducted in acutely prepared brain slices of 24- to 28-day-old (65–120 g) male Wistar rats.”
![Page 7: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/7.jpg)
NeuroElectro.org web interface
Code at github.com/neuroelectroData at neuroelectro.org/api
![Page 8: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/8.jpg)
Database statistics
• Currently 100 neuron types, >300 articles
![Page 9: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/9.jpg)
9
Resting membrane potential
mV
Extensive variability among NeuroElectro data
Netzebrand et al, 1999
Tripathy et al, in revision
Input resistance
MΩ
![Page 10: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/10.jpg)
Accounting for differences in experimental conditions
• Explain variability in electrophysiological data through influence of experimental conditions:– species/strain – electrode type– animal age,– recording temperature– in vitro/in vivo/cell culture– junction potential
10
Electrode type
Tripathy et al, in revision
![Page 11: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/11.jpg)
11
Neu
ron
clus
terin
g on
bas
is o
f el
ectr
ophy
siol
ogy
Tripathy et al, in revision
![Page 12: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/12.jpg)
12
Whole-genome correlation of gene expression and electro-diversity
20,000 genes
Patterns of gene expression
Electrophysiologicalphenotypes
Tripathy et al, in revision/in progress
Systematic variation among
neuron types
![Page 13: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/13.jpg)
Making hypotheses on electrophysiology - gene expression relationships
• Explaining electrophysiological phenotypes in terms of underlying gene expression (and vice versa)
![Page 14: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/14.jpg)
Future directions
• Continuing to expand NeuroElectro– More neuron types– More domains• Synaptic plasticity
• Continuing to demonstrate the value of data integration– How can we move to a situation where
experimentalists are willingly sharing their data?
![Page 15: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/15.jpg)
15
Acknowledgements• Pavlidis Lab @ UBC• Urban Lab @ CMU• Gerkin Lab @ ASU
Shreejoy TripathyEmail: [email protected]
Twitter: @neuronJoyURL: neuroelectro.org
Code: github.com/neuroelectro
![Page 16: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/16.jpg)
16
Mapping neuron electrophysiology to gene expression
Neuron typeresolution
Cell layerresolution
Neuron type to cell layer mapping is approximate. Will be improved in future iterations with high resolution data.
Neocortex L5/6pyramidal cell
Neocortex layer 5/6
Neocortex basket cell
Neocortex
20,000 genes
![Page 17: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/17.jpg)
Finding genes most correlated with electrophysiological diversity
![Page 18: NeuroElectro.org A window to the world’s neurophysiology data Shreejoy Tripathy University of British Columbia, Canada Email: stripathy@chibi.ubc.ca Twitter:](https://reader030.vdocuments.net/reader030/viewer/2022032517/56649cc15503460f94988b1d/html5/thumbnails/18.jpg)
Assessing predictive power between gene expression and electrophysiology