| DB | DB Supply | Node Manage | Record Count | Period | Update | Category | URL | Notes |
|---|---|---|---|---|---|---|---|---|
| 3D MR Microscopic Images of Kyoto Collection of Human Embryos | Kyoto univ・Tsukuba univ | 12 | 2005-08-08 | 2010-03-17 | > Development | http://mrlab.frsc.tsukuba.ac.jp/human_embryos/ | This database demonstrates you 3D MR microscope images of 1,204 chemically fixed human embryos acquired with a super-parallel MR microscpe developed in Magnetic Resonance Imaging Laboratory in University of Tsukuba. The 1,204 chemically fixed human embryos were important parts of the Kyoto Collection of Human Embryos, which were collected from 1961 to 1974. | |
| 3DPL | 慶應義塾大学 理工学部 | 174 | 2014-06-03 | > Protein > Function/Localize | http://chordate.bpni.bio.keio.ac.jp/3dpl/top.html | カタユウレイボヤ初期胚におけるタンパク質の局在情報の3次元イメージ（免疫局在、GFP融合タンパクの発現）、および関連情報（細胞局在、染色法、発生ステージ、実験条件など）を搭載したデータベースです。CIPRO（カタユウレイボヤのタンパク質データベース）の一環として開発されました。 | ||
| 3DinSight | Kyushu tech univ | NBDC | 60486 | 1997-2007 | 2010-03-17 | > Protein > Domain/Motif/Structure | http://gibk26.bse.kyutech.ac.jp/jouhou/3dinsight/3DinSight.html | 蛋白質と核酸の複合体構造を集めたデータベースで、認識モチーフや構造型にしたがって分類 |
| AOE[Archive] | NBDC | 0 | 2019-08-20 | > Integrated Database Project > Life Science Database Archive | https://dbarchive.biosciencedbc.jp/en/aoe/desc.html | |||
| AT Atlas(Archive) | Platform for Drug Discovery, Informatics, and Structural Life Science Research Organization of Information and Systems National Institute of Genetics | 322 | 2013-12-10 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/atatlas/desc.html | AT Atlas will make you familiar with the accomplishments by research groups of "Protein Production", "Structural Analysis" and "Chemical Regulation" in the Targeted Proteins Research Program. AT Atlas is composed of graphical abstract (flow chart) , information in text including actual application of the method and link to PRotein Experimental Information Management System (PREIMS). You will be able to find experimental methods used to elucidate the structure and/or functions of proteins that you are interested in. Further, you will be able to reproduce the experimental process to study corresponding entries of PREIMS. (Most of the graphical abstracts have been drawn by use of Cell Illustrator that is a pathway-drawing software developed by Prof. Satoru Miyano and his colleagues at the U. Tokyo) The database provides techniques in protein production (hardly-soluble proteins, membrane proteins, protein complexes etc.), structural analysis of proteins and chemical library for protein regulation technology, which were worked in Targeted Proteins Research Program (TPRP). It is a practical database including graphical abstracts and links to detailed protocols in PREIMS (Protein Experimental Information Management System). | ||
| ATTED-II | Tokyo univ | 1346748 | 2012-03-28 | > Gene Expression/Transcription > Transcription Motif | http://atted.jp/ | シロイヌナズナのアレイデータから遺伝子の共発現関係を計算し、データベースとして公開 | ||
| Aaindex | GenomeNet | 685 | 2008-03-31 | 2010-03-17 | > Protein > Sequence/Family | http://www.genome.ad.jp/aaindex/ | 20種のアミノ酸の物理化学的・生物学的特性値（インデックス）、およびアミノ酸間の類似度のマトリクスを収集したデータベース。 | |
| AcEST(Archive) | Tokyo Metropolitan University Graduate School of Science and Engineering | 34834 | 2012-12-28 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/acest/desc.html | |||
| Arabidopsis Phenome Database[Archive] | NBDC | 0 | 2017-03-14 | > Integrated Database Project > Life Science Database Archive | https://dbarchive.biosciencedbc.jp/en/arabidopsis-phenome/desc.html | |||
| Asian-Pacific Alien Species Database | 農業環境技術研究所 | NIAS | 202 | 2004-2010 | 2010-06-17 | > Environment > Farm > Encyclopedia/Taxonomy > Encyclopedia |
http://apasd-niaes.dc.affrc.go.jp/ | [Background] As the trade of agricultural products increases more and more globally, many of their diseases and pests are traveling with them. There has been a marked increase in the number of accidentally introduced pests of late years. Non indigenous species of all kinds - animals, plants, and microorganisms - are flowing into the Asian and Pacific region at a remarkable rate. Moreover alien species which have been introduced intentionally for pets, cultivation and industrial use have increased too. A lot of them have escaped and colonized in agro-ecosystem. Unchecked by natural enemies, many of these are becoming invasive pests that threaten not only human, animal, and plant health but also ecosystem. The losses caused by invasive alien species to Asian agriculture have been enormous. [Purpose] In order to establish countermeasures to prevent their invasion and spread, and minimize the economic and environmental damages caused by invasive alien species, it is very important to develop a database on invasive alien species for sharing new information with Asia Pacific countries by the Internet. To develop such a database and make up the network of the specialists for invasive alien species, the International Seminar (Tsukuba in 2003) and the International Workshop (Taichung in 2004) with attendants from Asian-Pacific countries were held, which were organized jointly by NIAES of Japan and FFTC of Taiwan. The database named "Asian-Pacific Alien Species Database (APASD)" was opened on the Internet in 2004. The purposes of the APASD are to help regulate the spread and infestation of invasive alien species, and to minimize economic damage and environmental impacts in the Asia-Pacific region caused by such species, by sharing information on invasive alien plants, insects, microorganisms, et cetera. Through the cooperation of contributors in many countries and regions, the data will become more and more useful for the accomplishment of this purpose. |
| AtGenExpress | 独立行政法人理化学研究所 横浜研究所 | 178 | 2014-02-04 | > Gene Expression/Transcription > Microarray | http://atpbsmd.yokohama-cu.ac.jp/ | 理化学研究所植物科学研究センターがMaxPlank研究所などと協力して、植物において初めて大規模なトランスクリプトームデータ（Affymetrixチップ1000枚以上）を収集して公開した「AtGenExpress」国際プロジェクト（2004年）の成果です。材料にはモデル植物シロイヌナズナを用い、生育段階、器官特異性、ストレス応答、ホルモン応答、栄養、光など、植物の成長と環境応答に関する基本データを網羅しています。 | ||
| AtMetExpress LC-MS | RIKEN Center for Sustainable Resource Science | 16658 | 2020 | 2020-05-19 | > Pathway/Interaction/Reaction | http://prime.psc.riken.jp/lcms/AtMetExpress/ | AtMetExpress LC-MS is a phytochemical atlas of Arabidopsis thaliana. Here, following two datasets are available; a dataset for phytochemical accumulation of many developmental stages and organs in Arabidopsis thaliana (AtMetExpress Development LC-MS) and a dataset of the composition of secondary metabolites among 20 Arabidopsis ecotypes (AtMetExpress 20 ecotypes LC-MS). Integrated clustering of transcriptome and metabolome data are also available. | |
| BGDB | Kazusa DNA Research Institute | 8000 | 2020-06-25 | > Term > Genome/Gene/RNA > Genome |
http://buckwheat.kazusa.or.jp | BGDB is a genome database for Buckwheat. It provides a draft assembly sequence of the genome using short reads obtained by NGS, and information of predicted genes with annotation by BLAST analysis of the NCBI NR and/or TAIR 10 databases. The results of a domain search against InterPro are also available. | ||
| BSORF - Bacillus subtilis Genome Database | GenomeNet | 4231 | 2006 | 2010-03-17 | > Genome/Gene/RNA > Genome | http://bacillus.genome.ad.jp/ | Bacillus subtilis genome database at Kyoto U. 枯草菌の全ゲノム配列を公開している。 | |
| Biological Magnetic Resonance Data Bank (BMRB) | Osaka univ | 9644 | 2010 | 2014-06-19 | > Protein > Domain/Motif/Structure | http://bmrb.protein.osaka-u.ac.jp/ | 生体分子のNMR分子のデータベース | |
| BodyParts3D | DBCLS | 1523 | 2011-12-28 | 2011-12-28 | > Integrated Database Project > Medical/Drug > Anatomy |
http://lifesciencedb.jp/bp3d/ | Body Parts 3D | |
| BodyParts3D(Archive) | The Database Center for Life Science | 51763 | 2013-07-01 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/bodyparts3d/desc.html | Dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a three-dimensional whole-body model for an adult human male. | ||
| Bombyx Trap DataBase | 独立行政法人農業生物資源研究所 | 1506 | 2013-10-02 | > Genome/Gene/RNA > Gene/Transcription | http://sgp.dna.affrc.go.jp/ETDB/ | エンハンサートラップ法によりカイコの新規突然変異系統を作出し、これらの系統におけるGFPレポーター発現部位情報や画像、ゲノム挿入位置情報などをまとめた新規突然変異系統データベースを構築しました。カイコゲノムデータベース（KAIKObase）との統合を行い、トランスポゾンベクターの挿入位置が染色体地図にマップされるようになりました。 | ||
| Budding yeast cDNA sequencing project(Archive) | Tokyo univ | 82262 | 2011-03-10 | > Integrated Database Project > Life Science Database Archive | http://itolab.cb.k.u-tokyo.ac.jp/GCap/ | |||
| CAGE | Riken | 3191 | 2004 | 2010-03-17 | > Gene Expression/Transcription > SAGE/CAGE/ATAC-PCR/iAFLP | http://fantom31p.gsc.riken.jp/cage/mm5/ | CAGE法によって集められたRNAライブラリやCAGEライブラリなどのデータを検索・閲覧するシステム | |
| CELLPEDIA (Repository database for current knowledge about human cells) | 独立行政法人産業技術総合研究所 | NBDC | 3984 | 2013-11-07 | > Cell/Organ | http://cellpedia.cbrc.jp/cgi-bin/index.cgi?page=1 | ヒト正常細胞に関する情報を統合的に整備したデータベースです。ヒト成人細胞、幹細胞と成熟前の先駆細胞約2300種類について、独自に開発したノイズ画像に強い細胞形態測定ツールを用いて測定した染色画像データ等による形態情報、物理的位置や機能、遺伝子発現、細胞オントロジー等、細胞に関する情報を網羅的に集めて、細胞情報の系統的検索や可視化が可能な辞書を作成しました。将来的には、細胞分化や再生医療等の細胞医療をサポートする情報を提供することを目的としています。 | |
| CGED - Cancer Gene Expression Database | NAIST・Osaka univ | 6546 | - | 2010-03-17 | > Gene Expression/Transcription > SAGE/CAGE/ATAC-PCR/iAFLP > Medical/Drug > Medical |
http://lifesciencedb.jp/cged/ | 遺伝子発現データ及び臨床情報の統合データベース | |
| CHEMTHEATRE[Archive] | NBDC | 78284 | 2019-03-25 | > Integrated Database Project > Life Science Database Archive | https://dbarchive.biosciencedbc.jp/en/chemtheatre/desc.html | |||
| CIBEX | DDBJ | 203 | 2009 | 2010-03-17 | > Gene Expression/Transcription > Microarray | http://cibex.nig.ac.jp | マイクロアレイデータを中心とする遺伝子発現データベース | |
| CITRES | 筑波大学 下田臨海実験センター | 125 | 2014-06-03 | > Cell/Organ | http://marinebio.nbrp.jp/ciona/ | カタユウレイボヤの系統、GFP導入ベクターによる蛍光発現画像や関連文献が掲載されています。各系統種やベクターの分与申し込みも可能になっています。 | ||
| COXPRESdb | HGC | 59154 | 2010 | 2010-03-17 | > Gene Expression/Transcription > Microarray > Pathway/Interaction/Reaction |
http://coxpresdb.hgc.jp/ | ヒト・マウス遺伝子の共発現データベース | |
| ChemTHEATRE | Ehime University | 4492 | 2018-04-17 | > Environment > Environment | http://chem-theatre.com/ | ChemTHEATRE is a database to deposit and visualize monitoring data of environmental contaminants, especially chemicals in organisms. The data were collected from published articles and reports by public institutions. Each dataset comprises measurement data, experimental methods (Instrument information, Extraction method, Clean-up method, etc.), and biological specimens (Instrument group, Name of instrument, Extraction method, Clean-up method, etc.). | ||
| CiAID | 千葉大学 大学院融合科学研究科 ナノサイエンス専攻 | 60395 | 2014-06-03 | > Genome/Gene/RNA > Gene/Transcription | http://bioinfo.s.chiba-u.jp/ciaid/ | カタユウレイボヤ幼若体/成体の遺伝子発現プロファイルデータベースです。WISHデータ（約1,700）を各種関連データ(組織別ESTグラフ、ステージ別ESTグラフ、ステージ別マイクロアレイグラフ、ghost KH-ID、ghost clone-ID、ghost gene collection-ID、ghost CLSTR-ID、CIPRO-ID)と統合しています。また、CiAID (約1,700)およびCiona Ghost データベース(約28,386)に対する ２通りの検索（基本検索、組み合わせ検索）が可能であり、さらに幼若体の形態、発生関連の各種情報（360度回転観察データ、3D-CGモデル、連続切片、連続切片からの立体構築モデル）を備えています。 | ||
| ClEST(Archive) | Symbiotic Evolution and Biological Functions Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology | 10550 | 2012-12-14 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/jp/clest/desc.html | |||
| CyanoBase | Kazusa | 0 | - | 2014-05-25 | > Genome/Gene/RNA > Genome | http://www.kazusa.or.jp/cyano/index.html | ラン藻 Synechocystis sp. strain PCC 6803, Anabaena sp. PCC 7120, Thermosynechococcus elongatus BP-1 ならびに光合成細菌 Chlorobium tepidum TLS のゲノムデータベース | |
| D-HaploDB(Archive) | Kyushu University | 1216952 | 2012-12-28 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/dhaplodb/desc.html | |||
| DB-SPIRE | AIST | 60004 | - | 2010-03-17 | > Protein > Domain/Motif/Structure | http://mbs.cbrc.jp/DB-SPIRE/ | PDBエントリに含まれる配列モチーフのデータベース | |
| DBTBS | HGC | 2033 | 2009 | 2010-03-17 | > Gene Expression/Transcription > Transcription Motif | http://dbtbs.hgc.jp/ | 枯草菌の転写制御に関するデータベース | |
| DBTGR | Tokyo univ | 0 | 2008 | 2014-05-13 | > Gene Expression/Transcription > Transcription Motif | http://dbtgr.hgc.jp/v2/ | ホヤ遺伝子の発現位置、制御領域、プロモータ配列、転写因子をまとめたデータベース。 プロモータの種間比較 (C.intestinalis .vs. C.savignyi) を掲載。 | |
| DBTSS | HGC | 31626 | 2009 | 2010-03-17 | > Gene Expression/Transcription > Transcription Motif | http://dbtss.hgc.jp/ | 現在一般に公開されている様々なcDNAデータベースはそのデータベース中のほとんどのcDNAが正確な5'端情報を欠くという意味で不完全なものであるが, DBTSSデータベースはこの欠点を補うものである. mRNA5'端に存在するキャップ構造を特異的に選別するオリゴキャッピング法を用いて完全長cDNA libraryを構築し, ヒト完全長cDNAの大規模収集を行っている. 現在までに収集した284,687クローンの配列解析を行ったところ, 149,950クローンが既知遺伝子8,996種類に対応するものであった. またこれらのcDNA配列とNCBIに存在する代表的参照cDNAデータベースRefSeqの配列を比較した結果, 14,038の全RefSeq登録遺伝子中, 4,802遺伝子(34.2 %)の5'端配列が上流に延長できることが明らかとなった. これらcDNA5'端塩基配列とヒトゲノム配列とを比較する事により, ゲノム上への転写開始点のマッピングを行っている. これら転写開始点の位置情報を用いる事で現在までにその情報蓄積の乏しい転写開始点の詳細な分布様式, 隣接するプロモーター領域の構造がゲノム規模で明らかになりつつある. DBTSS(DataBase of Transcriptional Start Sites)データベースは取得した最新の完全長cDNA配列, その配列から明らかになった転写開始点およびプロモーター領域の情報を公開している. | |
| DOGAN | NITE | 2243 | 2009-10 | 2010-04-23 | > Genome/Gene/RNA > Medals | http://www.bio.nite.go.jp/dogan/Top | DOGANは微生物の塩基配列データやORFなどの遺伝子情報、遺伝子地図、モチーフ情報、推定した遺伝子の根拠となる論文などの情報、プロテオーム解析結果を手に入れることができます。これらの情報は、アノテーターに確認されたものを公開しており、時間の経過に即して再アノテーションも行っている。また、Blastを用いた相同性検索サービスや、DNAクローンの発注サービスも行っています。(出典：MEDALS) | |
| Database for Gene expression and function of Baker's yeast(Archive) | National Food Research Institute, National Agriculture and Food Research Organization(NARO) | 14146 | 2012-12-14 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/dgby/desc.html | |||
| Dicty_cDB(Archive) | Tsukuba univ | 105739 | 2012-12-28 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/dicty-cdb/desc.html | |||
| Dictyostelium cDNA Database | Tsukuba univ | 97464 | 2010-01 | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://dictycdb.biol.tsukuba.ac.jp/cDNA/database.html | Dictyostelium discoideum cDNAクローンの塩基配列・相同性・モチーフ検索・局在性予測等の情報 | |
| Digital Atlas of Actinomycetes | The Society for Actinomycetes Japan | 123 | 2002-11-25 | 2010-03-17 | > Encyclopedia/Taxonomy > Encyclopedia | http://www.nih.go.jp/saj/DigitalAtlas/ | 日本放線菌学会は、1997年に朝倉書店より 『放線菌図鑑、""Atlas of Actinomycetes""』を刊行しました。 本書は、10ヶ国120人の研究者から提供された約400枚の放線菌の顕微鏡写真を日本語と英語の説明付きで収載しており、放線菌の形態上の多様性を網羅した唯一のモノグラフとして国際的に高く評価されています。 今回はこれらの写真の中から著者の了解が得られた約120枚を選び、デジタル放線菌図鑑として編集しました。 | |
| Dynamic Macrophage Pathway CSML Database(Archive) | Tokyo univ | 231 | 2011-03-10 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/dmpd/desc.html | |||
| Extremo Base | JAMSTEC | 0 | - | 2014-05-13 | > Genome/Gene/RNA > Genome | http://www.jamstec.go.jp/gbrowser/cgi-bin/top.cgi | 極限環境微生物の遺伝子情報のDB | |
| EzCatDB | AIST | 869 | 2010 | 2013-07-24 | > Protein > Function/Localize | http://mbs.cbrc.jp/EzCatDB/ | PDBおよびSWISS-PROTに登録されている酵素を、ドメイン構成、EC番号、触媒機構、リガンド構造から分類されている。 情報源は文献とPDBエントリ中の記述である。 | |
| FABA - Ascidian Body Atlas | Keio univ／DDBJ | 5 | 2008 | 2014-05-13 | > Cell/Organ | http://ciona.lab.nig.ac.jp/ascidian/top.html | ホヤの発生過程を通した3次元画像および断面画像 | |
| FAIRsharing.org(databases) | FAIRsharing | NBDC | 0 | - | 2018-02-20 | > Term | https://fairsharing.org | |
| FAIRsharing.org(policies) | FAIRsharing | NBDC | 0 | - | 2018-02-20 | > Term | https://fairsharing.org | |
| FAIRsharing.org(standards) | FAIRsharing | NBDC | 0 | - | 2018-02-20 | > Term | https://fairsharing.org | |
| FANTOM3 | Riken | 18465 | 2005 | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://fantom3.gsc.riken.jp/ | RikenマウスcDNAクローンに関する配列情報とその特徴、そして人手で注釈付けされた機能情報に関するデータベース． | |
| FANTOM4 | Riken | 21402 | 2009 | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://fantom.gsc.riken.jp/4/index.php?lang=jp | FANTOM4では、ゲノム上に同定された要素同士が互いにどのように作用しているかというネットワークの解明に取り組みました。ヒト白血病由来細胞株（THP-1）が単芽球様から単球様に変化する際の、転写開始点（TSS）の動態をdeepCAGE法（deep sequencing with CAGE）により経時的に測定した結果、それぞれの時点において活性なプロモーターと、その発現量をモニタすることができました。これらのデータから転写因子結合部位をコンピューター解析により予測し、THP-1における転写制御ネットワークの一部を明らかにするとともに、この分化において支配的な役割を果たす転写因子を抽出することに成功しました。 転写制御ネットワークの他にも、FANTOM4で取得されたデータを解析することで、転写開始点に関連する短鎖RNAの発見、および、ゲノム配列中に数多く存在する反復配列の役割に関する新たな発見に結びつきました。 | |
| FANTOM5 | 独立行政法人理化学研究所 横浜研究所 | 15703 | 2014-06-03 | > Genome/Gene/RNA > Gene/Transcription | http://fantom.gsc.riken.jp/5/ | FANTOMは、理化学研究所 オミックス基盤研究領域が主催する国際研究コンソーシアムです。 | ||
| FLJ Human cDNA Database | HGC | 240240 | 2009 | 2014-07-23 | > Genome/Gene/RNA > Gene/Transcription | http://flj.hinv.jp/ | 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. And our FLJ cDNAs were covered about 80% of human genes. In these situations we developed efficient human splicing variant cDNA cloning and evaluation systems (Fig. 1-1) in our project. More than one thousand of finished grades of full-length sequenced cDNAs were obtained in this project. Then we constructed the sequence analysis databases focused on mRNA variations using human genome and cDNA sequences, FLJ full-length sequenced cDNAs, 5’-ESTs of FLJ full-length cDNAs and other public cDNA sequences. | |
| FioreDB | National Institute of Advanced Industrial Science and Technology | 127 | 2020-02-25 | > Genome/Gene/RNA > Gene/Transcription | http://www.cres-t.org/fiore/public_db/index.shtml | This database provides information of phenotype in transgenic plants created by CRES-T (Chimeric REpressor gene-Silencing Technology) system which is a novel gene silencing technology for genes encoding transcription factors. Users can search gene-constructs inducing preferable phenotype or browse list of gene-constructs. Almost all the transcription factors of Arabidopsis thaliana are applied to the strategy, and those constructs are used for creating transgenic plants which are not only Arabidopsis thaliana but also other economically important plants. | ||
| Full-Anopheles | 東京大学 医科学研究所附属ヒトゲノム解析センター | 44251 | 2014-04-24 | > Gene Expression/Transcription > EST | http://fullmal.hgc.jp/index_ag_ajax.html | ハマダラカ完全長cDNAデータベースにはBLASTやGenomeBrowserを使用できるようになっています。その中ではゲノム配列のみならず、アミノ酸配列情報も掲載されています。ダウンロードページが機能していません。 | ||
| Full-Babesia | 東京大学 医科学研究所附属ヒトゲノム解析センター | 39543 | 2014-04-24 | > Gene Expression/Transcription > EST | http://fullmal.hgc.jp/index_bb_ajax.html | バベシア完全長cDNAデータベースにはBLASTやGenomeBrowserを使用できるようになっています。その中ではゲノム配列のみならず、アミノ酸配列情報も掲載されています。 | ||
| Full-Cryptosporidium | 東京大学 医科学研究所附属ヒトゲノム解析センター | 69731 | 2014-04-24 | > Gene Expression/Transcription > EST | http://fullmal.hgc.jp/index_cp_ajax.html | クリプトスポリジウム完全長cDNAデータベースにはBLASTやGenomeBrowserを使用できるようになっています。その中ではゲノム配列のみならず、アミノ酸配列情報も掲載されています。ダウンロードページでは配列情報がFASTA形式で取得できます。 | ||
| Full-Echinococcosis | 東京大学 医科学研究所附属ヒトゲノム解析センター | 10590 | 2014-04-24 | > Gene Expression/Transcription > EST | http://fullmal.hgc.jp/index_em_ajax.html | エキノコックス完全長cDNAデータベースには、クローンシーケンス情報がBLASTN(nt),BLASTX(nr),BLASTN(Em EST)と比較した結果と共に掲載されています。また、BLASTSearchも使用することができ、本DBの配列と比較することが可能になっています。 | ||
| G-compass | AIST | 108049 | 2010-03 | 2010-04-23 | > Genome/Gene/RNA > Medals | http://www.h-invitational.jp/g-compass/ | G-compassは比較ゲノム解析研究のためのツールとして開発され、進化的に保存されたゲノム領域とオルソログ遺伝子のデータを提供しています。解析対象はヒト＋12生物種です（チンパンジー、マカクザル、マウス、ラット、イヌ、ウマ、ウシ、オポッサム、ニワトリ、ゼブラフィッシュ、メダカ、ミドリフグ）。ゲノムの極保存領域(UCE)とコピー数多型領域(CNV)の情報を提供するとともに、ウィンドウ解析やドットプロットを表示するツールを備えています。(出典：MEDALS) | |
| GENIUS II | AIST | 7808 | 2005 | 2010-03-17 | > Protein > Domain/Motif/Structure | http://genius.cbrc.jp/ | 多重媒介配列検索法（MISS法）を用いて各生物種ゲノムの全ORFを構造既知の蛋白質の立体構造に帰属したデータベースシステム | |
| GETDB(Archive) | RIKEN Center for Developmental Biology | 4250 | 2011-03-10 | > Integrated Database Project > Life Science Database Archive | http://kyotofly.kit.jp/stocks/GETDB/getdb.html | |||
| GLIDA | Kyoto univ | 23429 | 2009 | 2010-03-17 | > Protein > Interaction > Pathway/Interaction/Reaction |
http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ | G蛋白質共役レセプタ－リガンド相互作用データベース。G蛋白質共役レセプタとリガンドの相互作用が公開データベースより収集され結合されている。 | |
| GRIPDB[Archive] | NBDC | 0 | 2017-07-27 | > Integrated Database Project > Life Science Database Archive | https://dbarchive.biosciencedbc.jp/en/gripdb/desc.html | |||
| Gclust Server(Archive) | Tokyo univ | 204748 | 2011-03-10 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/gclust/desc.html | |||
| GenLibi(Archive) | Japan Science and Technology Agency | 216 | 2014-04-03 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/genlibi/desc.html | GenLibi (Gene Linker to bibliography) provides information on genes and their related diseases and phenotypes that were obtained from the JST bibliographic information JDream II.Users can get bibliographic information by searching with the name of the diseases and the phenotypes.The original site automatically integrated information from EntrezGene, RefSeq, HGNC, KEGG PATHWAY, Reactome, KEGG SSDB and JDream II, and provided together information on genes, proteins, polymorphisms, pathways, phenotypes and ortholog/protein sequences related to human, mouse and rat genes. | ||
| Gene Wiki | Wikimwdia | 10707 | 2010-03-10 | 2013-12-05 | > Term | http://en.wikipedia.org/wiki/Portal:Gene_Wiki | Welcome to the Gene Wiki portal. This portal is dedicated to the goal of applying community intelligence to the annotation of gene and protein function. The Gene Wiki is an informal collection of pages on human genes and proteins, and this effort to develop these pages is tightly coordinated with the Molecular and Cellular Biology Wikiproject. Our specific aims are summarized as follows: * To provide a well written and informative Wikipedia article for every notable human gene * To invite participation by interested lay editors, students, professionals, and academics from around the world * To integrate Gene Wiki articles with existing Wikipedia content through the use of internal wiki links increasing the value of both Please browse around the Gene Wiki, make an edit to your favorite gene page, and feel free to ask questions! | |
| Genome Network Project | DDBJ | 60334 | 2010 | 2010-03-17 | > Pathway/Interaction/Reaction | http://genomenetwork.nig.ac.jp/ | GenomeNetワークプロジェクト参加研究機関より得られたデータに既存のゲノム情報を有機的に統合させることにより、個別生命機能の解析の為の有用なデータの提供を可能にする環境の構築を目指します。 また、個別生命機能の解析の研究から得られたデータのフィードバックを行い、より広範な情報を集積することで今後の学術、産業界に広く貢献できるデータの提供を行って行きます。 | |
| Genome information broker | DDBJ | NBDC | 1050 | 2010 | 2010-03-17 | > Genome/Gene/RNA > Genome | http://gib.genes.nig.ac.jp | 微生物を中心とした比較ゲノムシステム |
| Genomic Object Net Pathway Database (GON) | Yamaguchi univ | 27 | - | 2010-03-17 | > Protein > Interaction > Pathway/Interaction/Reaction |
http://genome.ib.sci.yamaguchi-u.ac.jp/~gon/ | ハイブリッド関数ペトリネットを用いてこれまでに作成した生命パスウエイを掲載している． | |
| Hepatitis Virus Database (HVDB) | Nagoya city univ | 5 | - | 2013-08-28 | > Genome/Gene/RNA > Gene/Transcription | http://s2as02.genes.nig.ac.jp/ | 肝炎ウィルス(B型、C型、E型）の各遺伝子の進化系統解析結果を掲載。INSD(DDBJ)から抜き出した肝炎ウイルス配列の機械的な整理。 | |
| Het-PDB Navi. | Nagahama Inst.Bio-Sci.and Tech | 111928 | 2009 | 2014-05-09 | > Protein > Interaction | http://hetpdbnavi.nagahama-i-bio.ac.jp/index.php | Hetero-atoms in protein structures | |
| Hintdb | Osaka univ・Tokyo univ | 176983 | - | 2013-08-21 | > Protein > Interaction | http://hintdb.hgc.jp/hint/ | 実験的に得られた９生物種間のタンパク質ータンパク質相互作用のデータベース | |
| HitPredict | Osaka univ・Tokyo univ | 154538 | - | 2013-08-21 | > Protein > Interaction | http://hintdb.hgc.jp/htp/ | ハイスループットデータから予測されたタンパク質ータンパク質相互作用のデータベース | |
| InGap | Kazusa | 58 | - | 2010-03-17 | > Protein > Function/Localize | https://webcreate.kazusa.or.jp/create/ | mKIAA抗体及びmKIAA cDNAマイクロアレイ解析情報 データベース | |
| J-CHECK: Japan chemical collaborative knowledge database | NBDC | 59601 | - | 2018-07-19 | > Term | http://www.safe.nite.go.jp/jcheck/top.action?request_locale=ja | ||
| JASPAR | University of Copenhagen | 0 | > Gene Expression/Transcription > Transcription Motif | http://jaspar.genereg.net/ | ||||
| KAIKOGAAS | National Institute of Agrobiological Sciences | 116023 | 2013-09-03 | > Genome/Gene/RNA > Genome | http://kaikogaas.dna.affrc.go.jp | カイコゲノム配列を元にタンパク質をコードする遺伝子構造を自動予測するシステムです。予測処理では複数の解析ツール(GeneScan、FGENESH、HMMER等)の解析結果を統合して行なっています。カイコゲノム配列に対する本システムの予測結果が参照できます。またお手持ちの塩基配列に対しての予測処理もできます。 | ||
| KATANA | Kazusa | 3 | 2007 | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://www.kazusa.or.jp/katana/ | シロイヌナズナ（Arabidopsis thaliana）遺伝情報統合データベース | |
| KEGG BRITE | Kyoto univ | 98 | 2010 | 2014-07-03 | > Encyclopedia/Taxonomy > Classification | http://www.genome.ad.jp/dbget/ | KEGG BRITE is a collection of hierarchical classifications representing our knowledge on various aspects of biological systems. | |
| KEGG COMPOUND | Kyoto univ | 17252 | 2010 | 2014-05-16 | > Pathway/Interaction/Reaction | http://www.genome.jp/kegg/compound/ | KEGG COMPOUND is a chemical structure database for metabolic compounds and other chemical substances that are relevant to biological systems. Each entry is identified by the C number, such as C00047 for L-lysine, and contains various links to other KEGG databases and also to outside databases. | |
| KEGG DISEASE | Kyoto univ | 1368 | 2010 | 2014-05-02 | > Medical/Drug > Medical | http://www.genome.jp/kegg/disease/ | KEGG DISEASE は各疾患について遺伝子と環境のゆらぎに関する知識を蓄積したデータベースです。各疾患エントリーは H 番号で識別され、病因遺伝子、環境因子、診断マーカー、治療薬を含む遺伝子・分子リストで表現されています。遺伝要因既知の疾患と病原体ゲノム既知の感染症疾患をすべてこの形式で表現し蓄積することを目指しています。 The KEGG DISEASE database is a new collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry is identified by the H number and contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. | |
| KEGG DRUG | Kyoto univ | 10090 | 2010 | 2014-06-30 | > Medical/Drug > Pharmaceutical | http://www.genome.ad.jp/kegg/drug/drug_ja.html | KEGG DRUG は日本および米国で承認されたすべての薬の情報を、化学構造をベースに蓄積したデータベースです。各化学構造は D 番号で識別され、一般名、商品名、効能、ターゲットおよび関連パスウェイなどの情報が提供されています。 KEGG DRUG は LIGAND リレーショナルデータベースの一部として構築されています。 KEGG DRUG is a unified drug information resource that contains chemical structures and/or chemical components of all prescription and OTC drugs in Japan, most prescription drugs in the USA, and many prescription drugs in Europe. Thus, all the marketed drugs in Japan are fully represented in KEGG DRUG and linked to the package insert information (labels information). These include crude drugs and TCM (Tradictional Chinese Medicine) drugs, which are very popular in Japan and some of which are specified in the Japanese Pharmacopoeia. | |
| KEGG ENZYME | Kyoto univ | 6312 | 2010 | 2014-05-02 | > Protein > Function/Localize | http://www.genome.ad.jp/dbget/ | KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number) of the IUBMB/IUPAC biochemical nomenclature committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG LIGAND relational datababase. | |
| KEGG GENES | Kyoto univ | 26480 | 2010 | 2013-09-02 | > Genome/Gene/RNA > Gene/Transcription | http://www.genome.ad.jp/dbget/ | KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes generated from publicly available resources, mostly NCBI RefSeq. | |
| KEGG GENOME | Kyoto univ | 3058 | 2010 | 2014-05-02 | > Genome/Gene/RNA > Genome | http://www.genome.ad.jp/dbget/ | KEGG organisms | |
| KEGG GLYCAN | Kyoto univ | 10985 | 2010 | 2014-07-01 | > Glyco/Lipid | http://www.genome.jp/kegg/glycan/ | The KEGG GLYCAN database is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. Each structure is identified by the G number, such as G00197 for CD65. KEGG GLYCAN is maintained in the KEGG LIGAND relational database. | |
| KEGG MEDICUS(Archive) | Kanehisa Laboratory, Institute for Chemical Research, Kyoto University | 12292 | 2014-05-20 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/kegg-medicus/desc.html | KEGG MEDICUS is an integrated information resource of diseases, drugs, and health-related substances, aiming to bring the genomic revolution to society. | ||
| KEGG REACTION | Kyoto univ | 9277 | 2010 | 2010-03-17 | > Pathway/Interaction/Reaction | http://www.genome.jp/kegg/reaction/ | KEGG REACTION contains all reactions taken from KEGG ENZYME and additional reactions taken from the KEGG metabolic pathways. Each reaction is identified by the R number, such as R00259 for the acetylation of L-glutamate. Reactions are linked to ortholog groups of enzymes as defined by the KEGG ORTHOLOGY database, enabling integrated analysis genomic (enzyme genes) and chemical (compound pairs) information. | |
| KEGG RPAIR | Kyoto univ | 14739 | 2010 | 2014-07-29 | > Pathway/Interaction/Reaction | http://www.genome.ad.jp/dbget/ | KEGG RPAIR is a collection of chemical structure transformation patterns for substrate-product pairs (reactant pairs) in KEGG REACTION. In general, a reaction consists of multiple reactant pairs, and the one that appears on the KEGG metabolic pathway is called the main pair, such as A04458 for the above acetylation reaction. | |
| KEGG VGENES | Kyoto univ | 35481 | 2010 | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://www.genome.ad.jp/dbget/ | KEGG Viral gene catalogs | |
| KEGG VGENOME | Kyoto univ | 5273 | 2010 | 2014-07-28 | > Genome/Gene/RNA > Genome | http://www.genome.ad.jp/dbget/ | KEGG Viral genomes | |
| KaFTom | かずさディー・エヌ・エー研究所 | 13227 | 2014-06-03 | > Gene Expression/Transcription > EST | http://www.pgb.kazusa.or.jp/kaftom/ | 矮性トマト品種マイクロトムの完全長cDNAに由来するESTおよび完全長配列のデータベースです。 | ||
| Keio Mutation Databases | Keio univ | 52 | - | 2010-03-17 | > Genome/Gene/RNA > Polymorphism | http://mutview.dmb.med.keio.ac.jp/MutationView/jsp/index.jsp | ヒトの疾患と関連する遺伝子変異・遺伝子多型に関する統合データベース | |
| Knowledge-Oriented Molecular Biological Encyclopedia (KOME) | NIAS | NIAS | 27172 | - | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://cdna01.dna.affrc.go.jp/cDNA/ | イネ完全長cDNA情報データベース |
| Knowledge-based Oryza Molecular biological Encyclopedia(Archive) | National Institute of Agrobiological Sciences | 0 | 2013-09-03 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/kome/desc.html | Information about approximately 38,000 full-length cDNA clones that were completely sequenced in the Rice full-length cDNA project is shown in the database. The full-length cDNA clones were collected from various tissues treated under various stress conditions. The database contains not only information about complete nucleotide sequences and encoded amino acid sequences, but also results of homology searches against public databases, mapping information, information about patterns of alternative splicing, protein domains and transmembrane structures, and information about cellular localizations and gene functions annotated with Gene Ontology.The full-length cDNA libraries were constructed from randomly picked 170,000 clones derived from twenty types of stressed tissues of japonica rice. The clones were grouped into 28,000 independent classes according to their 3' terminal single-pass sequences. All of the representative clones were completely sequenced. | ||
| LIPS | 東京大学 | 36 | 2014-07-01 | > Cell/Organ | http://hasezawa.ib.k.u-tokyo.ac.jp/lips/index.html | |||
| Life Science Database Archive metadata | Japan Science and Technology Agency | 779 | 2020-06-04 | 2024-04-26 | > Integrated Database Project > Life Science Database Archive | https://dbarchive.biosciencedbc.jp/index-e.html | ||
| LipidBank | JCBL | 10486 | 2007 | 2010-03-17 | > Glyco/Lipid | http://lipidbank.jp/index.html | LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. The database contains more than 6000 unique molecular structures (ChemDraw cdx format, MDL MOL format), their lipid names (common name, IUPAC), spectral information (mass, UV, IR, NMR and others), and most importantly, literature information. The database lists natural lipids only, and all molecular information is manually curated and approved by experts in lipid research (see Informant in each record). LipidBank is the official database of the Japanese Conference on the Biochemistry of Lipids (JCBL). | |
| MAGEST | Kyoto univ | 8639 | 2008 | 2010-03-17 | > Gene Expression/Transcription > EST | http://magest.hgc.jp/ | マボヤの遺伝子発現パターンおよびESTに関するデータベース | |
| MBGD - Microbial Genome Database for Comparative Analysis | GenomeNet | 7128670 | -- | 2010-03-17 | > Genome/Gene/RNA > Genome | http://mbgd.genome.ad.jp/ | バクテリアの完全ゲノム配列を比較解析するためのデータベース | |
| MMDBJ | DDBJ | 1387 | 2009 | 2014-07-12 | > Genome/Gene/RNA > Polymorphism | http://www.shigen.nig.ac.jp/mouse/mmdbj/top.jsp | Moue Microsatellite Data Base of Japanの略。マウス系統のマイクロサテライトマーカーの多型情報の統合データベース | |
| MacroArray Analysis Page of Bradyrhizobium japonicum | 大阪大学 大学院理学研究科 | 21 | 2014-02-04 | > Gene Expression/Transcription > Microarray | http://orca10.bio.sci.osaka-u.ac.jp/array02/ | 根粒菌Bradyrhizobium japonicumのゲノムワイドな発現比較およびCGH解析データをまとめています。１）芳香族化合物の分解過程における遺伝子発現解析結果、２）ダイズ種子抽出物と大豆由来フラボノイドGenisteinで誘導された遺伝子発現解析結果、３）バクテロイドと自由生活細胞の遺伝子発現比較結果、４）Bradyrhizobium japonicum株間におけるCGH比較結果が掲載されています。 | ||
| MeKO | RIKEN Center for Sustainable Resource Science | 149 | 2020-02-25 | > Pathway/Interaction/Reaction > Glyco/Lipid |
http://prime.psc.riken.jp/meko/ | MeKO is a database of metabolomic data for Arabidopsis thaliana. It contains profiling data of metabolites in 50 Arabidopsis mutants, using gas chromatography/mass spectrometry (GC-MS). It allows to browse using a mutants list. Non-processed data, including chromatograms, mass spectra, and experimental metadata, follow the guidelines set by Metabolomics Standards Initiative (MSI) and are downloadable freely. | ||
| MedlinePlus | NIH | 951 | 2010 | 2014-08-02 | > Medical/Drug > Medical | http://medlineplus.gov/ | MedlinePlus will direct you to information to help answer health questions. MedlinePlus brings together authoritative information from NLM, the National Institutes of Health (NIH), and other government agencies and health-related organizations. | |
| MedlinePlus Drugs & Supplements | NIH | 1279 | 2010 | 2010-03-17 | > Medical/Drug > Pharmaceutical | http://www.nlm.nih.gov/medlineplus/druginformation.html | Prescription and over-the-counter medication information is from AHFS Consumer Medication Information, a product of the American Society of Health-System Pharmacists (ASHP). Information on herbs and supplements is from Natural Standard. | |
| MiBASE | Kazusa | 16610 | 2007 | 2010-03-17 | > Gene Expression/Transcription > EST | http://www.kazusa.or.jp/jsol/microtom/indexj.html | 矮性トマト品種マイクロトムのEST、Unigene、マーカー、GOなどのデータベース | |
| Mouse Basement Membrane Bodymap | Osaka univ | 41 | 2007 | 2010-03-17 | > Development | http://www.matrixome.com/bm/Home/home/home.asp | MOUSE BASEMENT MEMBRANE BODYMAP, a database of body-wide localizations of basement membrane proteins in developing mouse embryos. The database consists of hundreds of high resolution virtual slides created from gigapixel digital images representing immunohistochemically stained whole mouse sagittal and head frontal sections and hematoxylin/eosin stained adjacent sections. | |
| Mouse DNA Microarray | Kazusa | 5 | 2003 | 2013-06-27 | > Gene Expression/Transcription > Transcription Motif > Gene Expression/Transcription > Microarray |
http://www.kazusa.or.jp/DNA_Microarray/mouse/2003-B6vs129/ | マウスDNAマイクロアレイ 解析情報データベース | |
| Mycoplasma penetrans genome | NIID | 997 | 2009 | 2010-03-17 | > Genome/Gene/RNA > Genome | http://www.nih.go.jp/Mypet/ | Mycoplasma penetrans のゲノムデータベース. | |
| NBDC RDF Portal | 0 | 2018-02-20 | > Integrated Database Project | http://integbio.jp/rdf/ | ||||
| NEDO | Kazusa | 420 | -- | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://www.kazusa.or.jp/NEDO/ | The NEDO database was constructed to make available sequence data of cDNA clones from the Kazusa DNA Research Institute human spleen cDNA library, which was determined by the NEDO human cDNA sequencing project. If you would like to know more about the NEDO human cDNA sequencing project, please visit the NEDO Web site. Although the cDNA clones provided by other groups for the NEDO project were generated by the oligo-capping method, the cDNAs supplied by Kazusa DNA Research Institute were generated by conventional methods and strictly size-selected from a cDNA library of adult human spleen. Consequently, not all of our cDNAs may be full-length, though all possess relatively long cDNA inserts, whose average size is about 4.5 kb. In this project, cDNAs having unknown end sequences and high protein-coding probability at their 5' ends were selected and sequenced. Please remember that the clone selection method is not identical to that of the Kazusa human cDNA sequencing project. This is the reason why we designate cDNA clones obtained through the NEDO project with the prefix FLJ followed by a five-digit number and cDNAs discovered by the Kazusa cDNA sequencing project by the prefix KIAA followed by a four-digit number. | |
| NITE-CHRIP: NITE Chemical Risk Information Platform | NBDC | 81 | - | 2018-07-19 | > Term | http://www.nite.go.jp/chem/chrip/chrip_search/systemTop | ||
| Nocardia farcinica genome | NIID | 5765 | 2010 | 2014-08-03 | > Genome/Gene/RNA > Genome | http://nocardia.nih.go.jp/ | Nocardia farcinica ゲノムの全塩基配列データと解析結果 | |
| O157 genome database | NAIST | 5447 | 2009 | 2010-03-17 | > Genome/Gene/RNA > Genome | http://genome.naist.jp/bacteria/o157/index.html | 病原性大腸菌 O157のゲノム情報データベースであり、種々の情報検索や、関連論文の検索が可能 | |
| OLIGAMI | Osaka univ | 80359 | - | 2010-03-17 | > Protein > Domain/Motif/Structure | http://protein.t.soka.ac.jp/oligami/ | 蛋白質のオリゴマー構造のデータベース | |
| OMIM | NCBI | 0 | 2010 | 2014-04-25 | > Medical/Drug > Medical | http://www.ncbi.nlm.nih.gov/omim/ | ヒト遺伝子変異と遺伝病に関する代表的なデータベース． | |
| Oligonucleic Acid Drug Database[Archive] | NBDC | 0 | 2018-04-24 | > Integrated Database Project > Life Science Database Archive | https://dbarchive.biosciencedbc.jp/en/nucleic-acid-drug/desc.html | |||
| Open TG-GATEs - Pathological images(Archive) | National Institute of Biomedical Innovation, National Institute of Health Sciences, and 15 pharmaceutical companies | 52879 | 2002-2006 | 2014-05-08 | > Integrated Database Project > Life Science Database Archive | http://toxico.nibio.go.jp/ | ||
| Open TG-GATEs(Archive) | National Institute of Biomedical Innovation, National Institute of Health Sciences, and 15 pharmaceutical companies | 269042 | 2002-2006 | 2014-05-08 | > Integrated Database Project > Life Science Database Archive | http://toxico.nibio.go.jp/ | ||
| PCIDB | Kyoto University Institute for Chemical Research Bioinformatics Center | 50409 | 2020-04-24 | > Pathway/Interaction/Reaction | https://www.genome.jp/db/pcidb | PCIDB is a database to elucidate therapeutic effect of plants on human. It provides integrated data from KNApSAcK, ChEMBL, CTD, OMIM and KEGG DISEASE. Users can search data by KNApSAcK Metabolite ID/NAME or KNApSAcK Species. Users can also browse data from KNApSAcK Metabolite Activity, KNApSAcK Natural Activity and 83 phytochemical clusters. | ||
| PEC(Profiling of E. coli Chromosome) | Research Organization of Information and Systems National Institute of Genetics | 8459 | 2014-07-12 | > Genome/Gene/RNA > Genome | http://www.shigen.nig.ac.jp/ecoli/pec/index.jsp | |||
| PGDBj - Ortholog DB(Archive) | Kazusa DNA Research Institute | 0 | 2017-06-01 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/pgdbj-ortholog-db/desc.html | |||
| PHDB(PHML Model Database) | physiome.jp | 240 | 2018-02-06 | > Pathway/Interaction/Reaction | http://www.physiome.jp/phdb/index.html | |||
| PHDB(morphologydb) | physiome.jp | 10 | - | 2018-02-06 | > Term > Medical/Drug > Anatomy |
http://www.bartleby.com/107/ | ||
| PHYSCObase | NIBB | 55 | 2010 | 2010-03-17 | > Gene Expression/Transcription > EST | http://moss.nibb.ac.jp/ | モデル植物ヒメツリガネゴケについてのプロトコール集、完全長cDNAおよびESTクローンの塩基配列解析結果 | |
| PIR | GUMC | 1415174 | - | 2014-05-15 | > Protein > Sequence/Family | http://pir.georgetown.edu/ | ゲノムおよびたんぱく質の研究をサポートする統合公開バイオインフォマティックスリソース | |
| PLACE | NIAS | NIAS | 469 | - | 2010-03-17 | > Gene Expression/Transcription > Transcription Motif | http://www.dna.affrc.go.jp/PLACE/ | 植物の遺伝子発現制御に関わる塩基配列を掲載 |
| PPDB | Nagoya univ | 584 | 2007-2008 | 2014-05-12 | > Gene Expression/Transcription > Transcription Motif | http://ppdb.gene.nagoya-u.ac.jp | 植物のプロモータ配列のデータベース | |
| PepBase | 慶應義塾大学 | 2597 | 2014-07-01 | > Protein > Domain/Motif/Structure | http://pepbase.iab.keio.ac.jp/phospho/msb/ | |||
| PharmGKB | Stanford University | 33507 | 2010 | 2014-07-12 | > Genome/Gene/RNA > Polymorphism > Medical/Drug > Pharmaceutical |
http://www.pharmgkb.org/index.jsp | PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products. Our mission is to catalyze pharmacogenomics research. | |
| Plabrain DB(Archive) | Laboratory for Molecular Developmental Biology Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University | 24 | 2014-04-10 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/plabrain-db/desc.html | |||
| Plant Organelles Database | NIBB | 11 | 2004-2008 | 2010-03-17 | > Cell/Organ | http://podb.nibb.ac.jp/Organellome | 植物のオルガネラの画像データベース | |
| ProNuc | Kyushu tech univ | 565 | 2006 | 2010-03-17 | > Protein > Domain/Motif/Structure > Protein > Interaction |
http://gibk26.bse.kyutech.ac.jp/jouhou/pronuc/pronuc.html | 蛋白質と核酸の複合体構造を集めたデータベースで、認識モチーフや構造型にしたがって分類 | |
| Protein Mutant Database | DDBJ | 45239 | 2007 | 2013-08-28 | > Protein > Function/Localize | http://spock.genes.nig.ac.jp/~pmd/pmd.html | 変異タンパク質データベース(PMD:Protein Mutant Database) は、タンパク質工学への貢献を目的として作られた文献単位のデータベースです。自然変異、人工変異、ランダム変異、部位指定変異などの全ての変異体を含み、グロビン属と免疫グロブリン属以外の全てのタンパク質を対象としています。 | |
| Protein Quaternary Structure | EBI | 89243 | - | 2014-07-18 | > Protein > Domain/Motif/Structure | http://www.ebi.ac.uk/pdbe/pqs/ | 蛋白質の４次構造データベース | |
| Proteopedia | The Weizmann Institute of Science | 102380 | - | 2014-07-31 | > Term | http://www.proteopedia.org/ | 3D encyclopedia of proteins and other molecules | |
| Pt_spiderBASE | 株式会社 生命誌研究館 | 0 | 2018-02-20 | > Genome/Gene/RNA > Genome | http://www.spider-brh.jp/pt_spiderbase/ | |||
| Q-TARO(Archive) | National Institute of Agrobiological Sciences | 1051 | 2014-01-14 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/qtaro/desc.html | This is a database of Rice QTL information extracted from published research papers.From 1214 reports, we selected 5096 QTLs. The positions of these QTLs were estimated from the physical positions of either two flanking markers (the genomic positions of the distal ends of the two markers) or a co-segregated single marker (between the start and end positions on the genome). If the QTLs were isolated by map-based cloning, the position of the BAC/PAC clone or gene locus was used. By screening for redundancy of traits at the same physical positions, as of March 31 of 2008, we selected 1051 QTLs extracted from 463 reports as representative QTLs. To arrange QTL information, we constructed QTL database (QTL Annotation Rice Online database; Q-TARO, http://qtaro.abr.affrc.go.jp/) consists of two web interfaces. One interface is a table containing information on the mapping of each QTL and its genetic parameters. The other interface is a genome viewer for viewing genomic locations of the QTLs. Currently, update of QTL information is not continued.Over the past two decades, genetic dissection of complex phenotypes of economic and biological interest has revealed the chromosomal locations of many quantitative trait loci (QTLs) in rice and their contributions to phenotypic variation. Mapping resolution has varied considerably among QTL studies, owing to differences in population size and number of DNA markers used. Additionally, the same QTLs have often been reported with different locus designations. This situation has made it difficult to determine allelic relationships among QTLs and to compare their positions. To facilitate reliable comparisons of rice QTLs, we extracted QTL information from published research papers and constructed a database of 1051 representative QTLs, which we classified into 21 trait categories. Q-TARO clearly displays the co-localization of QTLs and distribution of QTL clusters on the rice genome. | ||
| REFOLDdb | National Institute of Genetics | 1869 | 2019-12-17 | > Protein > Domain/Motif/Structure | http://pford.info/refolddb/search.cgi?lang=JP | REFOLDdb is a database for the protein refolding methods, which based on published papers written about the refolding of recombinant proteins. A combined search (Article and Protein and Experiment), Blast search and statistics of REFOLDdb are available. All REFOLDdb data is freely downloadable. All data in the other REFOLD database (http ://refold.med.monash.edu.au) managed by Monash University (Australia) have been integrated with this database.. | ||
| REPAIRtoire | International Institute of Molecular and Cell Biology in Warsaw | 4273 | 2020-04-24 | > Pathway/Interaction/Reaction | http://repairtoire.genesilico.pl | REPAIRtoire is a database for DNA damage and repair. The database contains the following types of information: 1) DNA damage linked to environmental mutagenic and cytotoxic agents, 2) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, 3) proteins participating in DNA repair, 4) diseases correlated with mutations in genes encoding DNA repair proteins. REPAIRtoire provides also links to publications and external databases. | ||
| RESOPS | Center for Informational Biology, Ochanomizu University | 165 | 2019-03-04 | > Protein > Domain/Motif/Structure | http://cib.cf.ocha.ac.jp/RNAEDITING/ | |||
| RGP Rice cDNA Sequence Database | NIAS | NIAS | 67 | 2003 | 2010-03-17 | > Gene Expression/Transcription > EST | http://bank.dna.affrc.go.jp/~qxrice/hiho/ | イネESTデータベース |
| RIKEN BRC Arabidopsis activation (T-DNA)-tagged lines | Riken | 17 | 2013-08-07 | > Cell/Organ | http://www.brc.riken.jp/lab/epd/catalog/actic.shtml | シロイヌナズナのアクティベーションタグラインは、理研バイオリソースセンター（BRC）または理研ゲノム科学総合研究センター植物ゲノム機能情報研究グループ植物変異探索研究チームにおいて、Dr. Waldenらが作成したT-DNA ベクター、pPCVICEn4HPTをAgrobacteriumの系を用いて野生株（Col-0）に導入することにより作成されました。本ラインの特徴は、T-DNAの挿入による遺伝子破壊とともにT-DNA中に存在するエンハンサーの効果により近傍遺伝子の過剰発現効果が期待できることにあります。本ラインはスクリーニングに供することを前提として種子プールの形で提供されます。 | ||
| RIKEN BRC Japan Collection of Microorganisms | Riken | 21752 | 2013-09-03 | > Cell/Organ | http://www.jcm.riken.go.jp/JCM/JCM_Home_J.shtml | 理研・微生物材料開発室は、 Japan Collection of Microorganisms（JCM）として発足し、1981年より微生物株の収集・保存・提供を行う微生物系統保存事業を実施してきました。2004年のRIKEN BRCへの統合後、独自のバイオリソース事業を展開することにより、微生物に関連する研究の支援とその発展に貢献することをめざしています。2010年9月現在、約19,900株を保有し、このうち細菌（放線菌を含む）約7,400株、アーキア（古細菌）約300株、真菌（酵母と糸状菌）約4,100株、総計約12,000株を提供対象としています。 | ||
| RMG(Archive) | National Institute of Agrobiological Sciences | 151 | 2013-09-03 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/rmg/desc.html | This database contains information on the rice mitochondrial genome. You can refer entire sequence of rice mitochondrial genome and information on the analysis results.The mitochondrial genome information can be used as standard for analysis of the mitochondria of major cereal crops such as corn and wheat as well as other monocotyledonous plants. | ||
| ROUGE | Kazusa | 2169 | -- | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://www.kazusa.or.jp/rouge/index.html | The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs). Since KIAA genes were characterized as unknown genes at least at the time of being sequenced, little is known about their biological functions. To understand physiological roles of KIAA genes in human, we expect that functional characterization using a model animal makes a great contribution of exploration of physiological functions. In this respect, we selected mouse as the model mammal, and started cloning cDNAs for mouse homologues of KIAA genes. | |
| RPG - Ribosomal Protein Gene database | Miyazaki univ学フロンティア科学実験総合センター | 0 | - | 2014-05-13 | > Genome/Gene/RNA > Gene/Transcription > Protein > Function/Localize |
http://ribosome.miyazaki-med.ac.jp/ | リボソームタンパク質遺伝子のデータベース | |
| RefDIC | 独立行政法人理化学研究所 横浜研究所 | 1908 | 2014-03-05 | > Cell/Organ | http://refdic.rcai.riken.jp/welcome.cgi | 代表的な免疫関連細胞の標準的な状態（無刺激、もしくはごく一般的な刺激後）のmRNAプロファイル、タンパク質定量プロファイルデータを閲覧、ダウンロード、解析できるデータベースです。測定プラットフォームは、Affymetrix GeneChip、Luminex、二次元電気泳動です。 | ||
| RefSeq | NCBI | 69635 | 2012-01-24 | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://www.ncbi.nlm.nih.gov/RefSeq/ | The Reference Sequence (RefSeq)は, 広範囲にわたる統合的なゲノムDNA, transcript(RNA)およびタンパク質生成物の非冗長配列セットを提供する. GenBankはすべての配列の保管倉庫である. それに対してRefSeqデータベースは, 染色体, 完全ゲノム分子(細胞小器官ゲノム, ウィルス, プラスミド), 中間のアセンブルされたゲノムコンティグ, キューレーティッド(正確で完全な)ゲノム領域, mRNA, RNAおよびタンパク質の参照の基準となるの非冗長セットである. | |
| RhizoBase | Kazusa | 68 | - | 2014-05-18 | > Genome/Gene/RNA > Genome | http://www.kazusa.or.jp/rhizobase/index.html | 根粒菌ゲノムデータベース．根粒菌はマメ科植物の根に根粒形成を誘導し、根粒内部で窒素固定をおこなう土壌細菌である． ミヤコグサの根に共生する根粒菌、Mesorhizobium loti MAFF303099のゲノムの全塩基配列解析をおこない、その解析結果を公開している． | |
| Rice Annotation Project Database (RAP-DB) | NIAS | NIAS | 241651 | 2005-2009 | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://rapdb.dna.affrc.go.jp/ | Rice Annotation Project DataBase (RAP-DB) は主にイネの遺伝子と転写産物を対象とした統合データベース、イネを中心にイネ科作物等の転写産物の配列をあらゆる手法で解析 |
| Rice Proteome Database (RiceProDB) | NIAS | 14452 | 2002 | 2013-08-28 | > Protein > Expression | http://gene64.dna.affrc.go.jp/RPD/ | イネの各種組織や細胞内小器官を対象に2次元ゲル電気泳動を行い、そのスポットを収集したデータベース。 プロテオーム解析のプロトコルが掲載されている。 | |
| RiceGAAS: Rice Genome Automated Annotation System | NIAS | NIAS | 8698 | 2008 | 2010-03-17 | > Genome/Gene/RNA > Gene/Transcription | http://RiceGAAS.dna.affrc.go.jp/ | 蛋白質をコードする遺伝子構造を予測し解析するプログラムを統合したイネゲノム自動アノテーションシステム |
| SASSC Quick search | 独立行政法人理化学研究所 筑波研究所 | 1210 | 2014-02-04 | > Cell/Organ | http://sassc.epd.brc.riken.jp/sassc/create_search_panel2.php?mode=general | 仙台シロイヌナズナ種子保存センター（SASSC）より寄託されたシロイヌナズナ野生株・近縁種等の種子に関わるデータベースです。各エントリーには葉の表現系や開花情報、写真が掲載されています。 | ||
| SCMD - Saccharomyces cerevisiae Morphological Database | Tokyo univ | 0 | 2005 | 2014-05-13 | > Cell/Organ | http://yeast.gi.k.u-tokyo.ac.jp/ | 出芽酵母の突然変異体の顕微鏡写真を集めたデータベース | |
| SEVENS(Archive) | 産業技術総合研究所 ゲノム情報研究センター | 0 | 2014-07-01 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/jp/sevens/desc.html | |||
| SPD[Archive] | NBDC | 77711 | 2019-12-05 | > Integrated Database Project > Life Science Database Archive | https://dbarchive.biosciencedbc.jp/en/spd/desc.html | |||
| Signaling Pathway Database (SPAD) | Kyushu univ | 182 | 1998 | 2010-03-17 | > Protein > Interaction > Pathway/Interaction/Reaction |
http://www.grt.kyushu-u.ac.jp/spad/ | シグナル伝達パスウェイを収集し可視化したデータベース。 パスウェイは細胞外シグナル分子に応じて、成長因子、サイトカイン、ホルモン、ストレスに分類されている。 | |
| SilkBase | Tokyo univ | 50002 | 2010-03-31 | 2010-03-17 | > Gene Expression/Transcription > EST | http://silkbase.ab.a.u-tokyo.ac.jp/cgi-bin/index.cgi | カイコ Bombyx mori（鱗翅目カイコガ科の昆虫）のESTデータベース。 | |
| Streptomyces avermitilis genome database | Kitasato univ | 16 | 2009-01-27 | 2010-06-09 | > Genome/Gene/RNA > Genome | http://avermitilis.ls.kitasato-u.ac.jp/ | 駆虫薬エバーメクチンを生産する工業微生物Streptomyces avermitilisのゲノム配列データベース | |
| SuperSweet | Charité - Universitätsmedizin Berlin | 22 | 2019-12-24 | > Glyco/Lipid | http://bioinformatics.charite.de/sweet/ | SuperSweet is a database for existing natural and artificial sweeteners, and also includes a homology modelled sweet taste receptor and docked binders. A graphical user-interface allows similarity searching, visualization of docked sweeteners into the modelled receptor etc. A carbohydrate classification tree and browsing features allow quick requests through the database. | ||
| TADB 2.0 | Shanghai Jiao Tong University | 886 | 2019 | 2020-02-25 | > Genome/Gene/RNA > Gene/Transcription | http://202.120.12.135/TADB2/ | TADB is a database for Type 2 Toxin-antitoxin (TA) loci in Bacteria and Archaea. Sequence information of nucleic acids and amino acids, loci in the genome, and information of the Replicons are provided. | |
| TOMATO (National BioResource Project) | 筑波大学 遺伝子実験センター | 2016 | 2014-02-04 | > Cell/Organ | http://tomato.nbrp.jp/indexJa.html | トマトの野生種に加え、ガンマ線照射、EMS(Ethyl Methanesulfonate)処理による変異体の情報を検索することができ、そのまま分与申し込みが可能です。表現系もまとめられており、変異体の形状にあてはめられています。Plant Ontology情報も付加されています。 | ||
| TP Atlas(Archive) | National Institute of Genetics, Research Organization of Information and Systems (ROIS) | 884 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/tpatlas/desc.html | ||||
| TRIP Database | 28 | 2020-02-06 | > Protein > Sequence/Family | http://www.trpchannel.org | TRIP Database is a manually curated database of protein-protein interactions (PPI) for mammalian transient receptor potential (TRP) channels. It provides 4 categories of PPI data, which are screening, validation, characterization, and functional consequence. There are many links to useful external databases for the purpose of providing information of sequence data, related diseases, etc. | |||
| Taxonomy Icon(Archive) | National Bioscience Database Center | 308 | 2013-07-01 | > Integrated Database Project > Life Science Database Archive | http://biosciencedbc.jp/taxonomy_icon/taxonomy_icon.cgi?lng=en | Taxonomy Icon is a collection of icons (illustrations) of biological species that is free to use and distribute. More than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia are available.You can use the icons to create documents and websites. Also, you can look up the classification or scientific name of species. | ||
| The New England Journal of Medicine（NEJM） | The New England Journal of Medicine（NEJM) | 4176 | - | > Medical/Drug > Medical | http://www.nejm.jp/ | The New England Journal of Medicine（NEJM）は，200年以上にわたる歴史を有し，世界でもっとも権威ある週刊総合医学雑誌の一つです．医学界のトップジャーナルとして，また情報提供の優れた媒体として，国内外の医師・研究者から高い評価を受けています.NEJMには，現在アメリカ，日本，国際版があり，毎週木曜日に世界同時発売されています。NEJM日本国内版は，必要な論文に簡単にアクセスできるよう「主要論文アブストラクト」「目次」「This Week at NEJM.org」を，日本語訳にて提供しています. | ||
| The Plant Organelles Database 2 Organelles Movie Database | 自然科学研究機構 基礎生物学研究所 | 85 | 2014-03-05 | > Cell/Organ | http://podb.nibb.ac.jp/Organellome/bin/findMovie.php?status= | 植物の細胞小器官の動画を提供しているサイトです。系統、小器官名、Accession番号、その他キーワードで検索することが可能です。 | ||
| Togo Picture Gallery[Archive] | NBDC | 0 | 2019-04-16 | > Integrated Database Project > Life Science Database Archive | https://dbarchive.biosciencedbc.jp/en/togo-pic/desc.html | |||
| TraP | AIST | 82 | 2012-03-28 | > Protein > Interaction | http://riodb.ibase.aist.go.jp/trap/ | We compare the metabolic pathway such as glycolysis, the TCA cycle, amino acid biosynthesis, and nucleic acid biosynthesis among 7 archaea. It is possible to highlight the differences between diffrerent archaea. | ||
| Transcriptome analysis of 2 component system in Eschericia coli | Nagoya univ | 622 | 2001 | 2010-03-17 | > Gene Expression/Transcription > Microarray | http://ecoli.aist-nara.ac.jp/xp_analysis/2_components/ | 大腸菌２成分制御系の欠失変異株における遺伝子発現プロファイルのマイクロアレイ解析データ。 | |
| Trypanosomes Database(Archive) | National Institute of Genetics, Research Organization of Information and Systems (ROIS) | 17 | 2014-03-05 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/trypanosome/desc.html | The Trypanosomes database is a database providing the comprehensive information of proteins that is effective targets for drug development that can control trypanosomiasis. Trypanosome is a parasitic protozoan of the genus Trypanosoma that infects a variety of hosts and causes various diseases, including African sleeping sickness and South American chagas disease, that is, trypanosomiasis. Every year more than 100 thousands of people suffer from trypanosomiasis. It also infects livestock, and more than 100 thousands of cattle have died per year. So far, it has been found effective targets for drug development that can control trypanosomiasis. One of such targets is a group of enzymes that control trypanosome DNA/RNA biosynthetic pathway. Another target is a group of enzymes that control trypanosome oxidation/reduction pathway. Actually, in case of trypanosomes, these enzymes are involved in both reaction pathways, and greatly affect lives of trypanosomes. | ||
| Two-Dimensional Electrophoresis Database of HSG cells proteins | Iwate medical univ | 802 | 2003 | 2013-08-21 | > Protein > Expression > Medical/Drug > Dental |
http://hitech-d.iwate-med.ac.jp/biochem/biochem/kamo/index.html | 2次元電気泳動で得られたHSG cells (ヒト顎下腺由来腺癌細胞) のプロテオミクスデータベース。 Two-Dimensional Electrophoresis Database of HSG cells proteins Human salivary intercalated duct cell line (HSG) was established from an iradiated human salivary gland. (Shirasuna K, Sato M, Miyazaki T, Canser Res 48: 745-52 (1981)) | |
| UniProt | UniProt Consortium | 245988 | - | 2014-07-24 | > Protein > Sequence/Family | http://www.uniprot.org/ | 詳細な注釈がついたタンパク質配列のデータベース | |
| VIPERdb | TSRI | 419 | - | 2014-08-04 | > Protein > Domain/Motif/Structure | http://viperdb.scripps.edu/ | database for icosahedral virus capsid structures | |
| VegMarks | 農業・食品産業技術総合研究機構 野菜茶業研究所 | NIAS | 2023 | - | 2010-03-17 | > Genome/Gene/RNA > Polymorphism > Environment > Farm |
http://vegmarks.nivot.affrc.go.jp/VegMarks/jsp/index.jsp | 野菜作物の遺伝マーカーデータベース VegMarks, a database for genetic marker database for vegetable crops, accumulates and releases the up-to-date information on DNA markers developed by National Institute of Vegetable and Tea Science (NIVTS). Marker characteristics such as ID number, map position, nucleotide sequence of the clones/PCR primers and polymorphism data among varieties/accessions are available. |
| Vibrio parahaemolyticus genome database | Tokyo Institute of Technology | 4832 | 2009 | 2010-03-17 | > Genome/Gene/RNA > Genome | http://genome.naist.jp/bacteria/vpara/ | 腸炎ビブリオのゲノム情報データベースであり、種々の検索が可能 | |
| Virus-Host DB | Kyoto University Institute for Chemical Research Bioinformatics Center | 14802 | 2020 | 2020-03-05 | > Encyclopedia/Taxonomy > Classification | http://www.genome.jp/virushostdb | Virus-Host DB is a database about the relationships between viruses and their hosts. It provides information of the relationships represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. This database covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained from literatures. | |
| Wormbase | Ontario Institute For Cancer Research | 0 | 2018-03-23 | > Gene Expression/Transcription > EST | http://www.wormbase.org/ | |||
| XDB | 自然科学研究機構 基礎生物学研究所 | 76392 | 2014-07-01 | > Genome/Gene/RNA > Gene/Transcription | http://xenopus.nibb.ac.jp/ | |||
| Yeast Interacting Proteins Database(Archive) | Tokyo univ | 841 | 2011-03-10 | > Integrated Database Project > Life Science Database Archive | http://dbarchive.biosciencedbc.jp/en/yeast-y2h/desc.html | |||
| e-Foram Stock | Tohoku University museum | 85 | 2018-03-22 | > Encyclopedia/Taxonomy > Encyclopedia | http://webdb2.museum.tohoku.ac.jp/e-foram/indexj.html | |||
| gwas | Tokyo univ | 11 | - | 2010-03-17 | > Genome/Gene/RNA > Polymorphism | https://gwas.lifesciencedb.jp/cgi-bin/gwasdb/gwas_top.cgi | 本GWAS(genome wide association study)データベースは、半永続的なデータの管理とGWASデータの共有を目指して構築されたリポジトリー型のデータベースで、東Kyoto univ学医学部、東Kyoto univ学医学部附属病院、東海大学医学部、日立製作所中央研究所の研究グループによって構築されました。本データベースには、アレル頻度や遺伝子型頻度などの頻度情報と、allelic model, dominant model などの主な遺伝統計の計算結果を蓄積しており、CNV(copy number variation)や遺伝子情報などの他の情報と同時にこれら計算結果をグラフ上に表示することにより、多面的に疾患関連候補SNPを選択し易くしています。 | |
| gwas | Tokyo univ／統合DBPJ | NBDC | 15 | - | 2014-07-26 | > Medical/Drug > Medical | https://gwas.lifesciencedb.jp/cgi-bin/gwasdb/gwas_top.cgi | 本GWAS(genome wide association study)データベースは、半永続的なデータの管理とGWASデータの共有を目指して構築されたリポジトリー型のデータベースで、東Kyoto univ学医学部、東Kyoto univ学医学部附属病院、東海大学医学部、日立製作所中央研究所の研究グループによって構築されました。本データベースには、アレル頻度や遺伝子型頻度などの頻度情報と、allelic model, dominant model などの主な遺伝統計の計算結果を蓄積しており、CNV(copy number variation)や遺伝子情報などの他の情報と同時にこれら計算結果をグラフ上に表示することにより、多面的に疾患関連候補SNPを選択し易くしています。 |
| snoOPY | Miyazaki univ | 13770 | 2008 | 2014-05-08 | > Genome/Gene/RNA > Functional RNA | http://snoopy.med.miyazaki-u.ac.jp/ | 核小体に存在する低分子 non-coding RNA (snoRNA) のデータベース． | |
| tRNADB-CE | N-Bio univ / DBPJ | 172073 | 2009 | 2010-03-17 | > Genome/Gene/RNA > Functional RNA | http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/index.cgi | The tRNA Gene DataBase Curated by Experts “tRNADB-CE” was constructed by analyzing 740 complete and 616 draft genomes of Bacteria and Archaea, 151 complete virus genomes and approximately 17 million DNA sequence entries that originated from environmental metagenomic clones. This exhaustive search for tRNA genes from DDBJ/EMBL/GenBank was performed by running tRNAscan-SE, a computer program widely used for tRNA gene searches, in combination with ARAGORN and tRNAfinder, to enhance completeness and accuracy of the prediction. Discordance of assignment by these three programs was found for approximately 4 % of the total of tRNA gene candidates. These discordant cases were manually checked by experts in the tRNA experimental field. In addition, tRNA genes of Archaea obtained from SPLITSdb were included. The 172,073 tRNA genes in total (42,575, 33,383, 961 and 95,154 genes from complete genomes, draft genomes, virus genomes and metagenomes, respectively) were registered in the present database; and sequence information, clover-leaf structure, and results of similarity search among tRNA genes can be browsed. For each of the completely sequenced genome, the number of anticodon and the codon usage frequency and the positioning of individual tRNA genes in each genome along with those of neighboring tRNA genes can be browsed. In the database, users can conduct various sequence analyses including sequence similarity search and oligonucleotide pattern search. This comprehensive database should contribute to various studies of tRNA gene evolution and diversity and of tRNA molecular biology. In the future, we will add all eukaryotic tRNA genes under the collaboration of experts of various eukaryotic tRNA research fields | |
| tRNADB-CE (tRNA gene database curated manually by experts)(Archive) | Nagahama Institute of Bio-Science and Technology | 458123 | 2012-12-19 | > Integrated Database Project > Life Science Database Archive | http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/index.cgi |