************************************************************************** ** ** ** README for "White_Table" directory (folder) ** ** ** ** ** ** CCeP (Cybernetic Caenorhabditis elegans Program), ** ** December 28, 2003. ** ** ** ************************************************************************** ================================= INTRODUCTION ================================= Files in this "White_Table" directory (folder) describe the synaptic connectivity shown in the tables in the paper: White, J. G., Southgate, E., Thomson, J. N. and Brenner, S. (1986). "The structure of the nervous system of the nematode Caenorhabditis elegans", Phil. Trans. R. Soc. London B 314, pp.1-340. In that paper, authors have studied the somatic nervous system except that in the pharynx. ================================= NOTICE ================================= The format of data in this "White_Table" directory (folder) is different from those in the "Albertson_Fig" and the "White_Fig" directories (folders). Furthermore, the data files in this directory (folder) describe the synaptic connectivity between the neuron classes while those in the "White_Fig" directory (folder) describe the synaptic connectivity between the neurons. ================================= FILES AND DIRECTORIES (FOLDERS) ================================= - [White_Table] ---+- README_WT.txt +- synapse_WT.txt | +- [neurons] -+- XXX_WT.txt +- XXX_WT_correct.txt o README_WT.txt: This file. ASCII text file that gives general information on files in this "White_Table" directory (folder). o synapse_WT.txt: ASCII text file in which all of the data files "XXX_WT.txt" in the "neurons" directory (folder) are included. For AVF, AVG, HSN and PVN neurons, however, only "AVF_WT_correct.txt", "AVG_WT_correct.txt", "HSN_WT_correct.txt" and "PVN_WT_correct.txt" (the corrected data) are included to make this file (see below for the reason). o XXX_WT.txt in the "neurons" directory (folder): ASCII text files that describe synaptic connectivity shown in the tables in the original paper for each reference neuron. Here XXX denotes a name of reference neuron. In the original paper, inconsistent data are found in the tables of AVF, AVG, HSN and PVN neurons. Those data are recorded in "AVF_WT.txt", "AVG_WT.txt", "HSN_WT.txt" and "PVN_WT.txt" as it stands. We have corrected the data and the corrected data are found in "AVF_WT_correct.txt", "AVG_WT_correct.txt", "HSN_WT_correct.txt" and "PVN_WT_correct.txt". We have confirmed by a private communication with Dr. J. G. White that the correction is adequate. ================================= FORMAT OF DATA ================================= The synaptic connectivity shown in the tables in the original paper consists of the following eight items in the format shown in Table 1. (1) name of reference neuron class (2) mostly name of partner neuron class (3) the number of gap junctions (4) the number of singly contacted chemical synapses from the partner neuron (class) to the reference neuron (class) (5) the number of multiply contacted chemical synapses from the partner neuron (class) to the reference neuron (class) (6) the number of singly contacted chemical synapses from the reference neuron (class) to the partner neuron (class) (7) the number of multiply contacted chemical synapses from the reference neuron (class) to the partner neuron (class) (8) name of corecipients of the multiply contacted chemical synapses Table 1. Example of the synaptic connectivity table in the original paper. A part of the data of PDE neurons is shown. ------------------------------------------------------------------------- PDE VENTRAL CORD SYNAPSES [partners] [gap junctions] [synapses from] [synapses to and corecipients] AVK - 2+2m 1, 20DVA, HDC HDC - - 2, AVK, VA9 PVC 1 1m 2 ------------------------------------------------------------------------- To exactly list the synaptic connectivity shown in the tables in the original paper, we present the eight items of the original data with eight columns of the table and an additional 9th item for the present data files. (9) comment on a questionable data in the original paper. Table 2 shows the present form of record corresponding to Table 1. Table 2. The corresponding record to Table 1. ------------------------------------------------- column 1 2 3 4 5 6 7 8 9 ------------------------------------------------- PDE AVK - 2 - - - - - PDE AVK - - 2 - - - - PDE AVK - - - 1 - - - PDE AVK - - - - 20 DVA - PDE AVK - - - - 1 HDC - PDE HDC - - - 2 - - - PDE HDC - - - - 1 AVK - PDE HDC - - - - 1 VA9 - PDE PVC 1 - - - - - - PDE PVC - - 1 - - - - PDE PVC - - - 2 - - - ------------------------------------------------- [1st column] Name of reference neuron class [2nd column] Mostly name of partner neuron class: For the case of motorneuron, the name of neuron is denoted in the original paper. Contact with ordinary muscle is represented by NMJ (neuron muscle junction) and that with sex specific muscle cell "vm2" is represented by this name. [3rd column] The number of gap junctions [4th column] The number of singly contacted chemical synapses from the partner neuron (class) to the reference neuron (class) [5th column] The number of multiply contacted chemical synapses from the partner neuron (class) to the reference neuron (class) [6th column] The number of singly contacted chemical synapses from the reference neuron (class) to the partner neuron (class) [7th column] The number of multiply contacted chemical synapses from the reference neuron (class) to the partner neuron (class) [8th column] Name of corecipients of the 7th column [9th column] Comment index: When questionable descriptions are found in the original tables, we have commented in this column. We have classified the comments into three types, and distinguish them by the following indices. "-": Nothing to comment. "wt1": The corecipient neuron is not listed as a partner neuron class in the original paper. The lacking record is added in "synapse_WT.txt" and in the corrected data "XXX_WT_correct.txt" (White, private communication). "wt2": In the table on PVN neurons in the original paper, the number of chemical synapses in the 22nd line is inconsistent with that in the 33rd line. The correct number in the 22nd line is "2" (White, private communication). This is corrected in "synapse_WT.txt" and "PVN_WT_correct.txt". "wt3": In the table on PVN neurons in the original paper, the data on the 77th line duplicates that on the 45th line. Data on the 77th line is deleted in "synapse_WT.txt" and "PVN_WT_correct.txt" (White, private communication).