NEXTDB: The Expression Pattern Map Database for

C: elegans
Tadasu Shin-iYuji Koharatshini@genes.nig.ac.jp

ykohara@lab.nig.ac.jp

CREST, JST and Genome Biology Laboratory, National Institute of Genetics
1,111 Yata Mishima 411-8540, Japan

1 Introduction
The nematode Caenorhabditis elegans (C. elegans) is a good model system to study functional genomics
with respect to animal development, nervous system and behavior at the level of single cells. Although
C. elegans has the basic structure of animals, it has only about 1,000 somatic cells. This simplicity hasled to the description of entire cell lineage from embryo to adult, which has allowed us to study genefunctions in individual cells [1]. The genome consists of six chromosomes whose total size is about 100
Mbp and total number of genes is estimated to be about 15,000. All the genome will be sequenced by
the consortium of the Sanger Centre and Washington University by the end of 1998 citews95.
In this laboratory, the systematic analysis of cDNA clones of C. elegans with respect to tagsequences, map positions, pattern of expression during development and gene functions, has been
carried out. To integrate all the information, we have developed a WWW-based database, nameNEXTDB. In this report we describe an overview of the current version of the database NEXTDBand future plans to develop new functions of the database.

2 Materials and methods
2.1

Hardware

For data acquisition, processing and displaying, the following machines are used. ABI377 DNA sequencers connected with Power Mac computers. Zeiss AxioPlan photomicroscopes equipped with
CCD cameras that are connected with Power Mac computers. Sun Ultra30 workstation, in which
NEXTDB is created and operated, equipped currently altogether GB hard drives. All the computers
are connected by the Ethernet.
2.2

Processing of ESTs

Raw data of one-pass sequencing were produced and stored in Macintosh computer connected withABI377 DNA sequencers. The ABI chromatogram les and sequence les were transferred to NEXTDB
in the SUN workstation. NEXTDB automatically removes ambiguous regions which contain larger
rate of \N" (ambiguous base) than the threshold and cloning vector sequences. The processed 3'-tagsequences were classi ed into unique cDNA groups applying a cumulative method using FASTA, sincethe 3'-tags should be unique among the cDNAs derived from the same gene. Both 5'- and 3'-tagsequences were mapped to cosmid sequences by use of BLASTN. Then the results were compared tothe cDNA groups to con rm the positions of the groups on the genome.

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2.3

Processing of expression patterns

Images of whole mount in situ hybridization [2] are taken by CCD cameras equipped on the microscopes. The image data are processed (selection of good images, trimming of the images to reduce
le size, etc.) on Macintosh computers and transferred to NEXTDB. Operators annotate individual
images with respect to developmental stages and expression patterns using a Web browser. Currently, the images for embryogenesis are classi ed in 10 stages. The images for post-embryogenesis
are classi ed in 4 stages. Once annotated, the images are arranged properly along development on
the screen.
2.4

Links to the genome map

In order to link NEXTDB with the genome map, we applied a hierarchical model to arrange all theclones and clusters; 1) chromosome, 2) cosmid clone, 3) CDS, 4) cDNA group, and 5) cDNA clone.
The cosmid map data which connects 1) and 2) were obtained from the C. elegans genome database
AceDB which describes the relationships among cosmid clones, predicted genes or CDS and geneticallyde ned genes. The information about cosmids and their CDS was retrieved from the annotations of
the Sanger Centre sequence data. Sequences and homologies of the probe cDNA and all the in-situ
images were arranged by making links to corresponding cDNA clones. All the data are integrated
based on WWW, and the information of maps and their relations are depicted visually by use of
JAVA applets.

3 Result and discussion
As of early October 1998, tag sequences of about 47,000 cDNA clones have been incorporated into
NEXTDB. The database classi es the clones into about 10,000 unique cDNA groups, which correspondto two thirds of the total gene number. About 5,500 groups hit to the predicted CDSs in the genomic
sequences, and about 3,500 hit to the non CDS region. Comparing some ESTs and the corresponding
genomic sequences has revealed the presence of alternative splicings and di erential termination, andsometimes bridging cosmids at gaps of cosmid contigs. Therefore, close comparison of ESTs and thegenomic sequences is very important to identify genes precisely. NEXTDB incorporates in situ imagesof about 2,500 cDNA groups mainly from chromosome 3 and chromosome X. The latest version isavailable through the URL \http://watson.genes.nig.ac.jp:8080/db/index.html." Visual description ofrelationships among cosmids, predicted genes, and clusters of cDNA clones can be seen, and expression
pattern images which are arranged along the genome map are retrievable.

Acknowledgements
This work has been supported by CREST of JST (Japan Science and Technology Corporation) andby a Grant-in-Aid for Scienti c Research on Priority Areas from the Ministry of Education, Science,Sports and Culture of Japan.

References[1] Sulston, J.E., Schierenberg, E., White, E.J., and Thomson, J.N., The embryonic cell lineage ofthe nematode C. elegans, Dev. Biol., 100:64{119, 1983.
[2] Tabara, H., Motohashi, T., and Kohara, Y., A multi-well version of in situ hybridization on whole
mount embryos of Caenorhabditis elegans, Nucl. Acids Res., 24:2119{2124, 1996.
[3] Waterston, R. and Sulston, J., The genome of Caenorhabditis elegans, Proc. Natl. Acad. Sci.
USA, 92:10836{10840, 1995.
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