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C. elegans connectome gene expression data
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dataset
modified on 2018-10-18, 08:36 Data files required to run analysis of C. elegans connectivity and gene expression analysis:
Arnatkevic̆iūtė, A.*, Fulcher, B. D.*, Pocock, R. & Fornito, A. Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome. PLoS Comp. Biol. 14, e1005989 (2018).
Matlab/python code for processing these data files and reproducing our analyses is in the Github repository (link below).
Note that all data was retrieved from publicly available sources. Please check with each relevant source (described in our paper) for citation/license requirements.
anatomy_association.WS256.txt - gene expression annotations, where genes are assigned to individual neurons (direct assignment) or groups of neurons (indirect assignment). Data were downloaded from ftp://ftp.wormbase.org/pub/wormbase/releases/WS256/ONTOLOGY/anatomy_association.WS256.wb
Neuronal gene expression is measured as a binary indicator on WormBase based on curated data collated from many individual experiments. Expression annotations are made either ‘directly’ to individual neurons (when an experiment indicates expression in an individual neuron), or ‘indirectly’ to broader classes of neurons like ‘interneuron’ or ‘head’ (meaning that some members of that class exhibit expression of that gene). In order to maintain specificity of annotations, we only analyzed `direct' annotations, and excluded annotations labeled as ‘uncertain’ (see manuscript for details).
Celegans_positions.mat - positions for 279 neurons in 2D space accompanied with neuron names. Data were downloaded from http://www.biological-networks.org/?page_id=25. Coordinates for three neurons (AIBL, AIYL, SMDVL) were missing in this dataset, and were reconstructed by assigning identical coordinates to the corresponding contralateral neurons (AIBR, AIYR, SMDVR) according to http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001044).
celegans279_BT.mat - birth times in minutes for 279 neurons accompanied with neuron names. Downloaded from Dynamic Connectome Lab website (https://www.dynamic-connectome.org/?page_id=25)
CelegansEntrezID.txt – a list of genes with corresponding entrezIDs and gene descriptions.
hierarchy.csv – Anatomical hierarchy of neurons as defined in WormBase, which we retrieved using the WormBase API (using RetrieveHierarchy.py in the github repo).
NeuronConnect.xls – neuronal connectivity data from Varshney et al. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001066 obtained from WormAtlas (www.wormatlas.org/neuronalwiring.html#NeuronalconnectivityII). It includes connectivity data for 279 neurons (282 somatic neurons, i.e., excluding CANL/R, and VC6, which do not form synapses with other neurons).
NeuronConnect_corrected.csv – a copy of the NeuronConnect.xls original neuronal connectivity file with headings removed and 1872 line changed to uppercase to match other neuron names. This file is further used in generating the data in Matlab format.
NeuronLineage_Part1.txt and NeuronLineage_Part2.txt – lineage distance for all pairs of neurons from previously published embryonic and post-embryonic lineage trees using data downloaded from WormAtlas (http://www.wormatlas.org/neuronalwiring.html#Lineageanalysis). In this dataset, the closest common ancestor neuron was identified for each pair of neurons, and then the lineage distance was calculated as the number of cell divisions from the closest common progenitor neuron.
NeurotransmitterTypePereira.csv – neurotransmitter systems used by each neuron. Neurons were labeled by matching to Table 2 of Pereira et al., 2015 (https://www.ncbi.nlm.nih.gov/pubmed/26705699).
preComputePositiveMatch.mat – pre-computed values for the positive match measure which is used to determine similarity in gene expression between pairs of neurons focusing only on instances where both neurons express a certain gene and ignoring instances where both neurons do not express it.
Arnatkevic̆iūtė, A.*, Fulcher, B. D.*, Pocock, R. & Fornito, A. Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome. PLoS Comp. Biol. 14, e1005989 (2018).
Matlab/python code for processing these data files and reproducing our analyses is in the Github repository (link below).
Note that all data was retrieved from publicly available sources. Please check with each relevant source (described in our paper) for citation/license requirements.
anatomy_association.WS256.txt - gene expression annotations, where genes are assigned to individual neurons (direct assignment) or groups of neurons (indirect assignment). Data were downloaded from ftp://ftp.wormbase.org/pub/wormbase/releases/WS256/ONTOLOGY/anatomy_association.WS256.wb
Neuronal gene expression is measured as a binary indicator on WormBase based on curated data collated from many individual experiments. Expression annotations are made either ‘directly’ to individual neurons (when an experiment indicates expression in an individual neuron), or ‘indirectly’ to broader classes of neurons like ‘interneuron’ or ‘head’ (meaning that some members of that class exhibit expression of that gene). In order to maintain specificity of annotations, we only analyzed `direct' annotations, and excluded annotations labeled as ‘uncertain’ (see manuscript for details).
Celegans_positions.mat - positions for 279 neurons in 2D space accompanied with neuron names. Data were downloaded from http://www.biological-networks.org/?page_id=25. Coordinates for three neurons (AIBL, AIYL, SMDVL) were missing in this dataset, and were reconstructed by assigning identical coordinates to the corresponding contralateral neurons (AIBR, AIYR, SMDVR) according to http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001044).
celegans279_BT.mat - birth times in minutes for 279 neurons accompanied with neuron names. Downloaded from Dynamic Connectome Lab website (https://www.dynamic-connectome.org/?page_id=25)
CelegansEntrezID.txt – a list of genes with corresponding entrezIDs and gene descriptions.
hierarchy.csv – Anatomical hierarchy of neurons as defined in WormBase, which we retrieved using the WormBase API (using RetrieveHierarchy.py in the github repo).
NeuronConnect.xls – neuronal connectivity data from Varshney et al. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001066 obtained from WormAtlas (www.wormatlas.org/neuronalwiring.html#NeuronalconnectivityII). It includes connectivity data for 279 neurons (282 somatic neurons, i.e., excluding CANL/R, and VC6, which do not form synapses with other neurons).
NeuronConnect_corrected.csv – a copy of the NeuronConnect.xls original neuronal connectivity file with headings removed and 1872 line changed to uppercase to match other neuron names. This file is further used in generating the data in Matlab format.
NeuronLineage_Part1.txt and NeuronLineage_Part2.txt – lineage distance for all pairs of neurons from previously published embryonic and post-embryonic lineage trees using data downloaded from WormAtlas (http://www.wormatlas.org/neuronalwiring.html#Lineageanalysis). In this dataset, the closest common ancestor neuron was identified for each pair of neurons, and then the lineage distance was calculated as the number of cell divisions from the closest common progenitor neuron.
NeurotransmitterTypePereira.csv – neurotransmitter systems used by each neuron. Neurons were labeled by matching to Table 2 of Pereira et al., 2015 (https://www.ncbi.nlm.nih.gov/pubmed/26705699).
preComputePositiveMatch.mat – pre-computed values for the positive match measure which is used to determine similarity in gene expression between pairs of neurons focusing only on instances where both neurons express a certain gene and ignoring instances where both neurons do not express it.
