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Gene expression


Aniseed database provides high throughput data (Ciona intestinalis and Halocynthia roretzi) and in situ experiment data from literature (Ciona intestinalis): more than 30 000 in situ hybridization profiles in wild type or mutant conditions. The majority of patterns and images come from the Ghost database, created by Satoh laboratory, while the data from Halocynthia roretzi embryos come from MAGEST consortium. Data from literature are entered by annotators and validated by the database curator (currently, data from 160 articles are hosted in ANISEED).



  • CiAID

CiAID (Ciona intestinalis Adult In situ hybridization Database) is a gene expression database with body atlas of the ascidian Ciona juvenile, supported by Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (JST-BIRD). CiAID has been developed as an aid for biological researches who wants to know the gene expression profiles in Ciona juvenile. CiAID provides useful information such as photographs (localization of the gene expression signals), graphs (existence of ESTs, amount of the transcripts measured by microarray analysis) and text (Cluster ID, annotation of the gene expression). The Cluster ID in CiAID directly links to the corresponding one in the cDNA/EST databases (Ghost) of C. intestinalis. CiAID also provides 3D images of the Ciona juvenile body atlas, and will help you understand the tissues/organs/structures of the Ciona juvenile.




To understand the function of Brachyury-downstream genes in chordate embryos, from a series of survey on differential expression, including subtractive hybridization, dot-blot assays, EST sequences and the expression patterns in whole-mount in situ hybridization at embryonic stages, a database called “CINOBI: Ciona Notochord and Brachyury-downstream gene Index” was developped to create comprehensive catalogues of Brachyury-downstream gene sets in Ciona intestinalis.



  • Ghost

The Ghost database is providing nearly 30,000 in situ hybridization photographs for 4700 genes of Ciona intestinalis. Up-to-date lists of genes for transcription factors, zinc finger proteins and signaling molecules are linked to their expression data. (To access the database, please use the following ID and password, ID: guest, PASSWORD: welcome)




MAGEST is a database dealing with ESTs and gene expression of Halocynthia roretzi.


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