MEDALS METI Life science integrated database portal site

ASTRA

Summary	ASTRA is a database that classifies alternative splicing patterns and alternative transcriptional initiation patterns of Human, Mouse, D.melanogaster, C.elegans, A.thaliana, O. sativa. (cited from the original site)
Data type	DNA-sequence

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CellMontage

Summary	CellMontage is a system for searching gene expression databases for cells or tissues similar to the query gene expression profile. The similarity of two profiles is computed by comparing the order of genes ranked by expression.
Data type	Gene expression \| Cell \| Tissue

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Database of genomes and transcriptional regulations for filamentous fungi

Summary	The filamentous fungus, Aspergillus oryzae, plays an important role in the Japanese sake and fermentation industry, and many industrial enzymes are produced by this organism. We hope this database will provide you useful information for your research and industrial applications.
Data type	DNA-sequence

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Evola

Summary	Evola (Evolutionary annotation database) is a database providing ortholog information of H-InvDB human genes. Evola contains orthologs among human and 14 vertebrates (chimpanzee, macaque, mouse, rat, dog, horse, cow, opossum, chicken, zebrafish, medaka, Tetraodon, and fugu). Evolutionary bioligical information such as protein multiple alignments, phylogenetic trees, transcript variants, and the degree of natural selection (dN/dS) are implemented.
Data type	Comparative genomics

Summary

Evola (Evolutionary annotation database) is a database providing ortholog information of H-InvDB human genes. Evola contains orthologs among human and 14 vertebrates (chimpanzee, macaque, mouse, rat, dog, horse, cow, opossum, chicken, zebrafish, medaka, Tetraodon, and fugu). Evolutionary bioligical information such as protein multiple alignments, phylogenetic trees, transcript variants, and the degree of natural selection (dN/dS) are implemented.

Data type

Comparative genomics

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FLJ Human cDNA Database

Summary	FLJ human cDNA database was constructed as human cDNA sequence analysis database focused on mRNA varieties caused by variations of transcription start site (TSS) and splicing.Human gene number was estimated to be 20-25 thousand. However number of human mRNA varieties was predicted to be about 100 thousand. The varieties are thought to be caused by variations of TSS and splicing. In our previous human cDNA project, about 30 thousand of FLJ human full-length sequenced cDNAs were deposited to DDBJ/GenBank/EMBL, and we obtained about 1.4 million of 5'-end sequences (5'-EST) of FLJ full-length cDNAs from about 100 kinds of cDNA libraries consist of human tissues and cells constructed by oligo-capping method.(cited from original site)
Data type	DNA-sequence full length cDNA

Summary

FLJ human cDNA database was constructed as human cDNA sequence analysis database focused on mRNA varieties caused by variations of transcription start site (TSS) and splicing.Human gene number was estimated to be 20-25 thousand. However number of human mRNA varieties was predicted to be about 100 thousand. The varieties are thought to be caused by variations of TSS and splicing. In our previous human cDNA project, about 30 thousand of FLJ human full-length sequenced cDNAs were deposited to DDBJ/GenBank/EMBL, and we obtained about 1.4 million of 5'-end sequences (5'-EST) of FLJ full-length cDNAs from about 100 kinds of cDNA libraries consist of human tissues and cells constructed by oligo-capping method.(cited from original site)

Data type

DNA-sequence full length cDNA

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G-compass

Summary	G-compass was designed as a tool for the study of comparative genomics. It provides the data of evolutionarily conserved genomic regions and orthologous genes between human and 12 vertebrates (chimpanzee, rhesus monkey, mouse, rat, dog, cow, horse, opossum, chicken, zebrafish, medaka and Tetraodon). Information of ultraconserved elements (UCE) and copy number variable regions (CNV) are provided. Sliding window analysis and dot plot analysis are also implemented.
Data type	Comparative genomics

Summary

G-compass was designed as a tool for the study of comparative genomics. It provides the data of evolutionarily conserved genomic regions and orthologous genes between human and 12 vertebrates (chimpanzee, rhesus monkey, mouse, rat, dog, cow, horse, opossum, chicken, zebrafish, medaka and Tetraodon). Information of ultraconserved elements (UCE) and copy number variable regions (CNV) are provided. Sliding window analysis and dot plot analysis are also implemented.

Data type

Comparative genomics

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GenoBase

Summary	Scope of database (GenoBase) is to understand comprehensively the living-cell system of Escherichia coli K-12 (W3110). Until now, GenoBase is the public repository for Sequence Information, Proteome, Transcriptome, Bioinformatics, and Knowledge based on literature concerning E.coli. The results of the NEDO project was contained.
Data type	Annotation

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GlycoExplorer

Summary	GlycoExplorer is integrated search system for glyco science. This system provides co-occurrence words and reference information.
Data type	Sugar chain

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GlycoPOD

Summary	GlycoPOD is glyco science protocol online database. This database provides main text (introduction, protocol and references), Q&A and rating.
Data type	glyco science protocol

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H-ANGEL

Summary	H-ANGEL is a resource which provides information on human gene expression. H-ANGEL displays expression patterns of transcriptional products generated by the H-Invitational project in practical tissue categories based on tissue-specific expression data from several experimental platforms. H-ANGEL also displays information for the expression of different genes at their corresponding physical positions in the human genome. This information is linked to the corresponding transcript or locus annotation data stored in H-InvDB.
Data type	Gene expression

Summary

H-ANGEL is a resource which provides information on human gene expression. H-ANGEL displays expression patterns of transcriptional products generated by the H-Invitational project in practical tissue categories based on tissue-specific expression data from several experimental platforms. H-ANGEL also displays information for the expression of different genes at their corresponding physical positions in the human genome. This information is linked to the corresponding transcript or locus annotation data stored in H-InvDB.

Data type

Gene expression

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H-DBAS

Summary	H-DBAS is a database of humanalternative splicing (AS) based on H-InvDB. H-DBAS offers variousannotated informarion of genome-wide human AS variants. The fullness ofAS variants were ensured and the representative AS variants (RASVs) were then selected. H-DBAS includes an interactive viewer constructed byFlash. In the viewer, RASVs affecting protein functions, theconservation of RASVs between human and mouse, rat, chimpanzee, macaqueand dog by comparative genomics and so on can be displayed.
Data type	Human and mouse full-length cDNA \| Human and mouse mRNA \| Rat, chimpanzee, macaque and dog RNA

Summary

H-DBAS is a database of humanalternative splicing (AS) based on H-InvDB. H-DBAS offers variousannotated informarion of genome-wide human AS variants. The fullness ofAS variants were ensured and the representative AS variants (RASVs) were then selected. H-DBAS includes an interactive viewer constructed byFlash. In the viewer, RASVs affecting protein functions, theconservation of RASVs between human and mouse, rat, chimpanzee, macaqueand dog by comparative genomics and so on can be displayed.

Data type

Human and mouse full-length cDNA | Human and mouse mRNA | Rat, chimpanzee, macaque and dog RNA

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H-EPD

Summary	H-Inv Extended Protein Database (H-EPD) provides comprehensive, non-redundant human protein sequences, including both curated and predicted human proteins. It was made by merging H-Inv proteins (predicted from transcriptome) with UniProtKB/Swiss-Prot and RefSeq proteins (curated). H-EPD was designed as a reference database for human proteome research.
Data type	Ptotein-sequence

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H-Exp

Summary	This is a DB of Human Tissue-specific expression profile data and it was integrated and coordinated with H-InvDB. This system enables (1) fast search, sort, and view for gene cluster or isoform, (2) comparison of expression pattern for gene cluster or isoform, (3) display of detailed information for gene expression and related data.* Original site is now closed.
Data type	Gene expression

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H-InvDB

Summary	H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, protein functions, etc.
Data type	RNA human full-length cDNA, mRNA

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HGPD

Summary	HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones. In the full-length human cDNA sequencing project (FLJ project at NEDO), nucleotide sequences of approximately 30000 human cDNA clones have been analyzed.(cited from paper http://nar.oxfordjournals.org/cgi/content/abstract/gkn872?ijkey=zKpNqhZH6jrUuzi&keytype=ref)
Data type	DNA-sequence

Summary

HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones. In the full-length human cDNA sequencing project (FLJ project at NEDO), nucleotide sequences of approximately 30000 human cDNA clones have been analyzed.(cited from paper http://nar.oxfordjournals.org/cgi/content/abstract/gkn872?ijkey=zKpNqhZH6jrUuzi&keytype=ref)

Data type

DNA-sequence

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JSNP DATABASE

Summary	The standard allele frequency of 786 Japanese SNPs has been registered since Release 9. NEDO project detaset is includes in JSNP.
Data type	single nucleotide polymorphism (SNP) allele frequency

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Microorganism database system

Summary	This database allows users to search microorganisms and to see the various biological information. This database is available only in Japanese.
Data type	Journal old species name (if any), philogenetic position, type strain, isolation origin, chemical components as chemical taxonomic index, substrate availability, energy gain type, accession number of 16S rDNA to DDBJ/EMBL/GenBank and so on.

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MiFuP

Summary	MiFuP is a database of functional potentials deduced from microbial genomes. You can easily search for microbes with potential functions of your interest.In the function search, you can search for functional potentials from your microbial genome sequences or cds sequences. Associated MiFuP wiki is an information web site about microbial functions (e.g., detailed description of each function, underlying mechanisms, representative microbes, industrial use). MiFuP wiki is in Japanese only.
Data type	DNA-Sequence\| Amino acid sequence\| Annotation

Summary

MiFuP is a database of functional potentials deduced from microbial genomes. You can easily search for microbes with potential functions of your interest.In the function search, you can search for functional potentials from your microbial genome sequences or cds sequences. Associated MiFuP wiki is an information web site about microbial functions (e.g., detailed description of each function, underlying mechanisms, representative microbes, industrial use). MiFuP wiki is in Japanese only.

Data type

DNA-Sequence| Amino acid sequence| Annotation

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NBRC culture catalogue search

Summary	Microorganisms (15,400 clones) held by NBRC of NITE can be searched. There are four ways to search, the first is NBRC number, the second is keyword, the third is scientific name or numberof other institutions, and last is homology search. The results can provide the scientific name, history, agency numbers, culture conditions and the paper information. In addition, prokaryotic (16SrDNA) and eukaryotic (28rDNA) for the registration of the sequence to confirm the identity resources search from the search sequence information. (Own translation)
Data type	DNA-sequence

Summary

Microorganisms (15,400 clones) held by NBRC of NITE can be searched. There are four ways to search, the first is NBRC number, the second is keyword, the third is scientific name or numberof other institutions, and last is homology search. The results can provide the scientific name, history, agency numbers, culture conditions and the paper information. In addition, prokaryotic (16SrDNA) and eukaryotic (28rDNA) for the registration of the sequence to confirm the identity resources search from the search sequence information. (Own translation)

Data type

DNA-sequence

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PMPj-Blast

Summary	The database of nucleotide sequences of ESTs, cDNAs and oligo DNA microarray probes for Lotus japonicus et al. which were obtained from the PMPj(cited from original site).
Data type	DNA-sequence , EST-sequence

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RAvariome

Summary	RAvariome is a human genetic variant database of autoimmune inflammatory disease Rheumatoid Arthritis (RA). RAvariome provides literature-curated data and "HOT variants", the significant and reproducible variants in different studies. Moreover, based on the confirmed associations, we developed genetic risk prediction tool that provides relative risk for RA to be usable for clinicians, researchers and the general public.
Data type	Genetic/Genomic variants

Summary

RAvariome is a human genetic variant database of autoimmune inflammatory disease Rheumatoid Arthritis (RA). RAvariome provides literature-curated data and "HOT variants", the significant and reproducible variants in different studies. Moreover, based on the confirmed associations, we developed genetic risk prediction tool that provides relative risk for RA to be usable for clinicians, researchers and the general public.

Data type

Genetic/Genomic variants

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Recount DB

Summary	RecountDB is a database for corrected read counts and genome mapping on NCBI's Short Read Archive. The corrected count was done using RECOUNT and the mapping with LAST.
Data type	RNA

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RNAapt3D

Summary	RNAapt3D is a database of RNA aptamer which contains RNA sequences, their secondary/tertiary structural information, target proteins of RNA aptamers and network of RNA-protein interaction. The tertiary structures are predicted by a given RNA sequence considering a wide variety of secondary structures with a modelling tool, RASCAL, and molecular dynamics simulations. This database can be used to provide insights for tertiary structural analysis, motif search with base flip position and a starting point by RNA-protein complex molecular simulations. This database facilitates a study on the design of RNA aptamer for a target molecule and improves the efficiency and the productivity in candidate selection.
Data type	RNA structure

Summary

RNAapt3D is a database of RNA aptamer which contains RNA sequences, their secondary/tertiary structural information, target proteins of RNA aptamers and network of RNA-protein interaction. The tertiary structures are predicted by a given RNA sequence considering a wide variety of secondary structures with a modelling tool, RASCAL, and molecular dynamics simulations. This database can be used to provide insights for tertiary structural analysis, motif search with base flip position and a starting point by RNA-protein complex molecular simulations. This database facilitates a study on the design of RNA aptamer for a target molecule and improves the efficiency and the productivity in candidate selection.

Data type

RNA structure

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SAHG

Summary	SAHG is a comprehensive database, which exhibits protein structures encoded in the human genome. All of the Open Reading Frames encodeing proteins in the human genome are subjected to protein structure prediction. The development of this database is supported by JST(Japan Science and Technology Agency). (cited from original site)
Data type	Protein-structure

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The Functional RNA Sequence Database

Summary	fRNAdb is a sequence database hosting a large collection of non-coding RNA sequence data from public non-coding databases.fRNAdb allows users to search the sequences through keywords associated with them. Various kinds of information are associated with a sequence.fRNAdb also provides sequence homology search using Blastn.
Data type	RNA

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TOT-DB

Summary	TOT-DB (The Theileria orientalis Genome Annotation Database) ia a database of the genome information of parasitic protists Theileria orientalis.Genes annotated by an integration of expression data and gene prediction by several software are displayed on the G-integra genome browser.TOT-DB also offers the BLAST homolgy search service and data downloads of the genome sequences and gene annotation of T. orientalis.
Data type	Comparative genomics

Summary

TOT-DB (The Theileria orientalis Genome Annotation Database) ia a database of the genome information of parasitic protists Theileria orientalis.Genes annotated by an integration of expression data and gene prediction by several software are displayed on the G-integra genome browser.TOT-DB also offers the BLAST homolgy search service and data downloads of the genome sequences and gene annotation of T. orientalis.

Data type

Comparative genomics

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TuMaRdb

Summary	TuMaRdb is tumor markers reference database. This database has two ways(marker name and disease name) to search genes and references, and provides 82 markers and 488 case studies.
Data type	Sugar chain marker

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UCSC GenomeBrowser for Functional RNA

Summary	UCSC GenomeBrowser for Functional RNA is a UCSC Genome Browser mirror with large additional custom tracks specifically associated with non-coding elements. It also includes several functional enhancements such as a presentation of a common secondary structure prediction at any given genomic window <500 bp.
Data type	Comparative genomics

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VarySysDB

Summary	This is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. It provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains.
Data type	-

Summary

This is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. It provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains.

Data type

-

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