The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.
Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan.
Yamasaki
Chisato
C
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Katsuhiko
K
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Yasuyuki
Y
Sato
Yoshiharu
Y
Harada
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Takeda
Jun-ichi
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Barrero
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RA
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Hong-Woo
HW
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Hideki
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Hayakawa
Yosuke
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Hilton
Phillip B
PB
Kaneko
Yayoi
Y
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M
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Yoshihiro
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Kawamura
Toshiyuki
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Matsuya
Akihiro
A
Nagata
Naoki
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Kensaku
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Noda
Akiko Ogura
AO
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Saichi
Naomi
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Hiroaki
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Sanbonmatsu
Ryoko
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Shiba
Rie
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Takabayashi
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Takahashi
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Masayuki
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Susumu
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Todokoro
Fusano
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Yamaguchi
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Okido
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Jun
J
Hashizume
Aki
A
Jin
Lihua
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Lee
Kyung-Bum
KB
Lin
Yi-Chueh
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Asami
A
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Katsunaga
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Tada
Masahito
M
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Takashi
T
Ohyanagi
Hajime
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Naoki
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N
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Yoshiyuki
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Ikeo
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Naruya
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Sugawara
Hideaki
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O'Donovan
Claire
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Kulikova
Tamara
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Whitfield
Eleanor
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Halligan
Brian
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Shimoyama
Mary
M
Twigger
Simon
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Yura
Kei
K
Kimura
Kouichi
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Yasuda
Tomohiro
T
Nishikawa
Tetsuo
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Akiyama
Yutaka
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Motono
Chie
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Yuri
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Nagasaki
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Makiko
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Horton
Paul
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Kikuno
Reiko
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Ohara
Osamu
O
Lancet
Doron
D
Eveno
Eric
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Graudens
Esther
E
Imbeaud
Sandrine
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Debily
Marie Anne
MA
Hayashizaki
Yoshihide
Y
Amid
Clara
C
Han
Michael
M
Osanger
Andreas
A
Endo
Toshinori
T
Thomas
Michael A
MA
Hirakawa
Mika
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Makalowski
Wojciech
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Nakao
Mitsuteru
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Kim
Nam-Soon
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Yoo
Hyang-Sook
HS
De Souza
Sandro J
SJ
Bonaldo
Maria de Fatima
Mde F
Niimura
Yoshihito
Y
Kuryshev
Vladimir
V
Schupp
Ingo
I
Wiemann
Stefan
S
Bellgard
Matthew
M
Shionyu
Masafumi
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Jia
Libin
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Thierry-Mieg
Danielle
D
Thierry-Mieg
Jean
J
Wagner
Lukas
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Zhang
Qinghua
Q
Go
Mitiko
M
Minoshima
Shinsei
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Ohtsubo
Masafumi
M
Hanada
Kousuke
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Tonellato
Peter
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Isogai
Takao
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Ji
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Lenhard
Boris
B
Kim
Sangsoo
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Chen
Zhu
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Hinz
Ursula
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Nakai
Kenta
K
Makalowska
Izabela
I
Hide
Winston
W
Tiffin
Nicola
N
Wilming
Laurens
L
Chakraborty
Ranajit
R
Soares
Marcelo Bento
MB
Chiusano
Maria Luisa
ML
Suzuki
Yutaka
Y
Auffray
Charles
C
Yamaguchi-Kabata
Yumi
Y
Itoh
Takeshi
T
Hishiki
Teruyoshi
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Satoshi
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K
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Sumio
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Nobuo
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Imanishi
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Takashi
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D000818:Animals; D002874:Chromosome Mapping; D018076:DNA, Complementary / Q000737:chemistry; D030541:Databases, Genetic; D005796:Genes; D006801:Humans; D020407:Internet; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D014584:User-Computer Interface
D018076:DNA, Complementary; D011506:Proteins; D012333:RNA, Messenger