Nucleic Acids Research
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
Genome Information Integration Project And H-Invitational 2
Nucleic Acids Res. 36:793-799, 2008. First published 18 Dec 2007;
doi:10.1093/nar/gkm999

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Published online 18 December 2007

Nucleic Acids Research, 2008, Vol. 36, Database issue D793–D799
doi:10.1093/nar/gkm999

The H-Invitational Database (H-InvDB),
a comprehensive annotation resource forhuman genes and transcripts
Received September 16, 2007; Revised October 20, 2007; Accepted October 22, 2007

ABSTRACT
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 andtranscripts. H-InvDB, originally developed as anintegrated database of the human transcriptome
based on extensive annotation of large sets of fulllength cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from theInternational Nucleotide Sequence Databases(INSD), in addition to 54 978 human FLcDNAs, in thelatest release H-InvDB_4.6. We mapped those humantranscripts onto the human genome sequences(NCBI build 36.1) and determined 34 699 humangene clusters, which could define 34 057 (98.1%)
protein-coding and 642 (1.9%) non-protein-coding
loci; 858 (2.5%) transcribed loci overlapped withpredicted pseudogenes. For all these transcripts andgenes, 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 ofprotein 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: theDiseaseInfo Viewer, H-ANGEL, the Clustering
Viewer, G-integra, the TOPO Viewer, Evola, the PPIview and the Gene family/group.
INTRODUCTION
Human transcripts represent a biologically and functionally rich format for examining the structure of humangenes and alternative splicing isoforms. In particular,
cloning and sequencing of full-length cDNAs (FLcDNAs)
that cover all exons but no introns can facilitate theprecise determination of human gene structure (1). Studies

on human transcripts have thus been systematically andextensively carried out to draw the outline of the humantranscriptome (2–6). The human transcriptome consistsof protein-coding mRNAs and non-coding functional
RNAs. Analysis of these sequences will provide insights
into how genomic information is transformed into higher
order biological phenomena. By comparative analysis of
the transcriptome with the human genome, we will be able
to determine the transcribed regions of the genome andbetter understand the regulatory machinery of transcription (7, 8). It is therefore of great signiﬁcance to collectinformation about human transcripts as well as theirannotations. We thus held the ﬁrst international workshop
entitled ‘Human Full-length cDNA Annotation
Invitational’ (abbreviated as H-Invitational or H-Inv) in
Tokyo, Japan from 25th August to 3rd September 2002,
and constructed a novel, integrative database of thehuman transcriptome, called H-InvDB (9,10). This consists of the annotation of 42 421 human FLcDNAs,collected from six high-throughput producers of human
FLcDNAs in the world human gene collections.
To cover the increased number of human FLcDNAs
since the initial release of H-InvDB, we held the second
international annotation meeting entitled ‘H-Invitational
2 Functional Annotation Jamboree’ (abbreviated as
H-Invitational 2 or H-Inv2) in Tokyo, Japan from 15th
to 20th November 2003. The second major release of
H-InvDB (release 2.0) was based on the annotation
carried out at the H-Inv2 annotation jamboree. After
H-Inv2, we initiated the Genome Information Integration
Project (GIIP) and held the third and fourth annotation
meetings in October 2005 and October 2006. The productsof those two annotation meetings comprised releases 3.0
and 4.0 of H-InvDB. The increases in the number of
entries in H-InvDB are summarized in Table 1.
THE ANNOTATION IN OUR LATEST UPDATE,
H-InvDB 2007
In our latest release H-InvDB_4.6, we annotated 120 558
human mRNAs extracted from the International
Nucleotide Sequence Databases (INSD) in addition to
54 978 human FLcDNAs that were available on 15th June
2006. We mapped those human transcripts onto the humangenome sequences (NCBI build 36.1) and determined
34 699 human gene clusters, which could deﬁne 34 057*A complete list of authors appears at the end of this article.
ß 2007 The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

D794 Nucleic Acids Research, 2008, Vol. 36, Database issue

Table 1. Statistics of H-InvDB entries
H-InvDB release

Date ofreleaseNumber oftranscripts(HIT)

Numberof geneclusters (HIX)

Number ofproteins (HIP)

Human genome

Date ofsequencedata-ﬁx

1.0
2.0
3.0
4.0
4.6

2004/4/20
2005/8/31
2006/3/31
2007/3/30
2007/9/27

41 11856 419167 992
175 542
175 536

21 03725 58535 00534 70134 699–––116 228
116 142NCBI build 34.1
NCBI build 34.1
NCBI build 35.1
NCBI build 36.1
NCBI build 36.1

2002/7/15
2003/9/1
2005/3/1
2006/6/15
2006/6/15

Table 2. Statistics of manually curated representative H-Inv proteins

genes as non-protein-coding transcript candidates. We
classiﬁed 1216 non-protein-coding transcripts into
‘Identical to known ncRNA’ (124), ‘Similar to known
ncRNA’ (74) and ‘Putative ncRNA’ (1018) by homology
with known ncRNA databases and discrimination
analysis

Category

Deﬁnition

Number of
representative
HITs

%

I

Identical to knowna humanprotein (98% identity, =100%
coverage)
Similar to knowna protein (50%
identity, 50% coverage)
InterPro
domaincontaining
proteinConserved hypothetical protein
Hypothetical protein
Hypothetical short protein (20–79
amino acids)
Pseudogene candidates

12 404

36.42

3165

9.29

3056

8.97

Sequence quality features: nonsense-mediated decay (NMD),
read-through, reverse orientation

4210
5124
5250

12.33
15.05
15.42

A total of 269 transcripts were annotated as candidates ofread-through and 2731 as targets of NMD by the extended
sequence quality annotation.

858
34 057

2.52
100

Category VII: pseudogene candidates

II
III
IV
V
VI
VII
Total
a

‘Known’ proteins are experimentally validated proteins in literatures.

(98.1%) protein-coding and 643 (1.9%) non-proteincoding loci, while 858 (2.5%) transcribed loci overlappedwith predicted pseudogenes. We basically followed themapping technique we described previously (9,10). We
updated annotation for the mitochondrial transcripts since
the previous major release, H-InvDB_4.0, which resulted
in a slightly decreased number for the transcripts andclusters. Then we assigned a standardized functionalannotation to each H-Inv transcript by human curation,
based on the results of similarity searches and InterProScan (11). The numbers of manually curated humanproteins in each category are summarized in Table 2.
For these transcripts and genes, we provide comprehensive annotation including descriptions of their genestructures, alternative splicing isoforms, functional nonprotein-coding RNAs, functional domains of proteins,predicted sub cellular localizations, metabolic pathways,
predictions of protein 3D structure, mapping of SNPs andmicrosatellite repeat motifs, co-localization with orphan
diseases, gene-expression proﬁles, orthologous genes andevolutionary features in model animals, protein–protein
interaction (PPI) and annotation for gene families. We
have also annotated several new features related totranscript quality.
NEW ANNOTATED FEATURES IN H-InvDBClassification of ncRNA
We annotated the transcripts that do not have homology toknown protein-coding genes or InterPro-domain-containing

To annotate transcribed pseudogene candidates, we did
the following: First, we ﬁltered out the functional proteincoding genes by only targeting representative category IItranscripts and those identiﬁed to have frame shifts and/or
nonsense mutations; Second, we predicted transcribed
pseudogene candidates based on a support vector machine(SVM) method. In the current release, we annotated 1112
transcribed pseudogene candidates (Category VII).
Annotation of gene families/groups
We annotated four selected gene families/groups: T-cell
receptor(TCR),
Immunoglobulin
(Ig),
Major
Histocompatibility Complex (MHC) or Human
Leukocyte Antigen (HLA) and Olfactory receptor (OR)using the original pipeline based on sequence analysis
against genome and protein databases complemented by atext-mining approach. In the current release, we identiﬁed
15 TCR, 21 Ig, 72 MHC and 122 OR gene clusters.
All the annotation items and features of H-Inv
transcript sequences are stored and shown in the mainviews or sub-databases in H-InvDB.
COMPREHENSIVE ANNOTATION RESOURCES IN
H-InvDBThe current H-InvDB annotation resources consist of two
main views, Transcript view and Locus view, and eight
sub-databases: the DiseaseInfo Viewer, H-ANGEL, theClustering Viewer, G-integra, the TOPO Viewer, Evola,
the PPI view and the Gene family/group view withthe appropriate cross-links. An overview of the comprehensive annotation resources of the human gene andtranscripts in H-InvDB is shown in Figure 1.

Nucleic Acids Research, 2008, Vol. 36, Database issue D795

Figure 1. H-InvDB: overview of the comprehensive annotation resource for the human genes and transcripts. 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 view. The Transcript view and the Locus view are the mainviewers to display the annotation of each H-Invitational transcript (HIT) and H-Invitational cluster (HIX). The DiseaseInfo Viewer, H-ANGEL, theClustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group view are sub-databases to provide detailed
annotation for each annotation feature. The links to related databases are provided from the appropriate viewers.

Transcript view
The transcript view shows all the annotation of the H-Inv
transcript in 12 section tabs: (i) gene structure, (ii) genefunction, (iii) gene ontology, (iv) predicted CDS,(v) functional motif, (vi) sub cellular localization, (vii)
protein structure information, (viii) gene expression, (ix)disease/pathology, (x) evolutionary information, (xi)polymorphism (SNP, indel and microsatellite) andD796 Nucleic Acids Research, 2008, Vol. 36, Database issue

interspersed repeat information and (xii) transcript andsequence quality information. As seen in the example of atranscript view shown in Figure 1, this view also has links
to many external public databases including DDBJ/
EMBL/GenBank,
RefSeq,UniProtKB,
HGNC,
InterPro, Ensembl, EntrezGene, PubMed, dbSNP, GO
and GTOP and to web sites of the original data producersof the FLcDNA clones and sequences including the
Chinese National Human Genome Center (CHGC),
German cDNA Consortium (DKFZ/MIPS), Helix
Research Institute, Inc. (HRI), the Institute of Medical
Science in the University of Tokyo (IMSUT), the Kazusa
DNA Research Institute (KDRI), the Mammalian Gene
Collection (MGC/NCI) and NEDO. This view waspreviously known as the cDNA view (mRNA view).
Locus view
The Locus view shows all the annotation of a locus in six
section tabs: (i) gene structure and location in the humangenome, (ii) gene function, (iii) alternative splicing pattern,(iv) gene expression, (v) disease/pathology and (vi) cluster
member information. As seen in the example of a Locus
view shown in Figure 1, it shows links to external public
databases including DDBJ/EMBL/GenBank, RefSeq,
EntrezGene, GeneCards, HGNC and OMIM.

Clustering Viewer
The Clustering Viewer facilitates the comparisons ofdiﬀerent clustering. It allows users to see whether H-Inv
transcripts are consistently clustered by diﬀerent clustering
methods. It also displays multiple alignments of transcripts by using CLUSTALW (13). The Clustering Viewer
shows all the member transcripts of an H-Inv cluster towhich a query sequence belongs.
G-integra
G-integra is an integrated genome browser, in which we
can examine the genomic structures of the transcripts. As
seen in an example view in Figure 1, the location in thehuman genome and gene structure of H-Inv transcript(green), and the corresponding RefSeq and Ensembl
entries are shown. The structures of the genes andtranscripts for 11 non-human species, Pan troglodytes(chimpanzee), Macaca sp. (macaque), Mus musculus(mouse), Rattus norvegicus (rat), Canis familiaris (dog),
Bos taurus (cow), Monodelphis domestica (opossum),
Gallus gallus (chicken), Danio rerio (zebraﬁsh),
Tetraodon nigroviridis (tetraodon) and Takifugu rubripes(fugu) can be optionally displayed for comparison. Other
options allow the, the results of gene prediction programs
such as GenScan (14), HMMgene (15), FGENESH (16)and JIGSAW (17) to be displayed.

DiseaseInfo Viewer

TOPO Viewer

The DiseaseInfo Viewer is a database of known andorphan genetic diseases and their relation to H-Inv
clusters with EntrezGene and OMIM cross-links. The
DiseaseInfo Viewer provides two kinds of disease information related to H-Inv clusters: known disease-related
genes and co-localized orphan diseases. An orphan diseaseis deﬁned as a disease mapped on a chromosomal region,but for which the responsible gene has not been identiﬁedyet. Co-localization does not necessarily mean a direct
relationship between gene and disease; however, genesthat are cytogenetically co-localized with a disease
could be possible candidate genes for that disease. The
co-localized H-Inv clusters are chosen by computing thephysical range of each cytogenetic band with a 1 Mbp
margin.

The TOPO Viewer is a tool for viewing subcellulartargeting signals predicted by TargetP (18) and thepresence of transmembrane helices predicted by SOSUI(19) and TMHMM(20). The probabilities that a protein
may be delivered to up to nine distinct sub cellularlocations are predicted by WoLF PSORT (21). TargetP
predicts whether a protein contains a signal peptide, amitochondrial targeting signal or any other type of signal.
The TOPO Viewer consists of four tab pages: TABLE,
MAP, FILE and GFP. The TABLE tab page displays theprediction results for all the programs used.

Human anatomic gene expression library (H-ANGEL)
H-ANGEL is a database of expression patterns that weconstructed to obtain a broad outline of such patterns forhuman genes (12). We collected gene-expression datain normal and adult human tissues that were generated bythree types of methods and in seven diﬀerent platforms,
including: iAFLP, a PCR-based quantitative expression
proﬁling method; DNA arrays (long oligomers, shortoligomers and cDNA microarrays); and cDNA sequencetags (SAGE, EST, BodyMap and MPSS). The H-ANGEL
database comprises the largest and most comprehensive
collection of gene expression patterns so far, which also
provides a classiﬁcation of human genes in terms of theirexpression.

Evola
Evola is a database of evolutionary annotation of humangenes (22). It provides sequence alignments and phylogenetic trees of manually curated orthologous genes among
human and 11 model organisms, Pan troglodytes (chimpanzee), Macaca sp. (macaque), Mus musculus (mouse),
Rattus norvegicus (rat), Canis familiaris (dog), Bos taurus(cow), Monodelphis domestica (opossum), Gallus gallus(chicken), Danio rerio (zebra ﬁsh), Tetraodon nigroviridis(tetraodon) and Takifugu rubripes (fugu). Sequencealignments and phylogenetic trees of the orthologous
genes and homologous genes are shown in Evola.
PPI view
The PPI view displays H-InvDB human PPI information
at http://www.jbirc.aist.go.jp/hinv/ppi/. We collected PPI
data from ﬁve databases; BIND, DIP, MINT, HPRD and
IntAct, removed redundancies of the PPI data among theNucleic Acids Research, 2008, Vol. 36, Database issue D797

databases based on their sequence similarities andintegrated them with the H-Invitational proteins.
Gene family/Group view
The Gene family/Group view provides human-curated
annotation datasets for the selected gene families/groupsathttp://www.jbirc.aist.go.jp/hinv/ahg-db/geneFamily
Index.jsp. For H-InvDB release 4.0, we provided detailed
annotations for four selected gene families/groups: TCR,
Ig, MHC and OR. Each page provides the list of genes,
gene names, deﬁnitions and links for the appropriate
H-InvDB views.
H-InvDB New Identifier
We deﬁned and assigned a unique identiﬁer for eachannotation unit, transcript, protein or cluster (7,8). The
identiﬁer for H-Invitational transcript is ‘HIT’, preﬁx HITplus nine digit numbers (e.g. HIT000000001) and for
H-Invitational cluster is ‘HIX’, preﬁx HIX plus seven digit
numbers (e.g. HIX0000001). In order to identify themodiﬁcation in sequence or annotation of an H-Inv entry,
a version is assigned to each ID and always stated with the
ID. Additionally, we now provide a new identiﬁer for each
H-Invitational protein, ‘HIP’, preﬁx HIP with nine digit
numbers (e.g. HIP000000001).
H-InvDB Data Availability
H-InvDB is freely available for both academic andcommercial use and can be accessed online at http://
www.h-invitational.jp/(or hinv.jp). Annotated data canalso be downloaded in FASTA sequence ﬁles, the originalformat ﬂat ﬁles or XML ﬁles at HTTP and FTP servers.
The mirror database is also available at http://
hinvdb.ddbj.nig.ac.jp/. Minor updates are released every
three months and major updates are released once a year.
ACKNOWLEDGEMENTS
We acknowledge all the members of the H-Invitational 2
consortium and Genome Information Integration Project(GIIP), especially the staﬀs of JBIRC for construction of
H-InvDB, Ryo Aono, Tomohiro Endo, Yukie Makita,
Hiromi Kubooka, Yuji Shinso, Harutoshi Maekawa,
Yasuhiro Fukunaga, Hajime Nakaoka, Yoshito Ueki,
Yoshihide Mimiura, Ryuzou Matsumoto, Seigo Hosoda,
Yo Takahashi, Taichirou Sugisaki, Hiroki Hokari,Hiroaki Kawashima, Yasuhiro Imamizu, Makoto Ogawa
for their technical assistance. This research is ﬁnancially
supported by the Ministry of Economy, Trade andIndustry of Japan (METI), the Ministry of Education,
Culture, Sports, Science and Technology of Japan(MEXT) and the Japan Biological Informatics
Consortium (JBIC). Also, this work is partly supportedby the Research Grant for the RIKEN Genome
Exploration Research Project from MEXT to Y.H. and
the Grant for the RIKEN Frontier Research System,
Functional RNA research program. Funding to pay theOpen Access publication charges for this article wasprovided by JBIC.
Conﬂict of interest statement. None declared.

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D798 Nucleic Acids Research, 2008, Vol. 36, Database issue

LIST OF AUTHORS FOR THE GENOME
INFORMATION INTEGRATION PROJECT AND
H-INVITATIONAL 2 CONSORTIUM
Chisato Yamasaki1,2, Katsuhiko Murakami1,2,
Yasuyuki Fujii3, Yoshiharu Sato1,2, Erimi Harada1,2,
Jun-ichi Takeda1,2, Takayuki Taniya1,2,
Ryuichi Sakate1,2, Shingo Kikugawa1,2,
Makoto Shimada1,2, Motohiko Tanino4,
Kanako O. Koyanagi5, Roberto A. Barrero6,
Craig Gough1,2, Hong-Woo Chun1,2,
Takuya Habara1, Hideki Hanaoka7,
Yosuke Hayakawa1,8, Phillip B. Hilton1,2,
Yayoi Kaneko9, Masako Kanno1,2,
Yoshihiro Kawahara1,2, Toshiyuki Kawamura10,
Akihiro Matsuya1,11, Naoki Nagata12,
Kensaku Nishikata1,13, Akiko Ogura Noda1,2,
Shin Nurimoto14, Naomi Saichi1,2,
Hiroaki Sakai15, Ryoko Sanbonmatsu1,2,
Rie Shiba1,2, Mami Suzuki1,2,
Kazuhiko Takabayashi8, Aiko Takahashi1,2,
Takuro Tamura16, Masayuki Tanaka1,2,
Susumu Tanaka17, Fusano Todokoro1,18,
Kaori Yamaguchi1, Naoyuki Yamamoto1,19,
Toshihisa Okido20, Jun Mashima20,
Aki Hashizume20, Lihua Jin20, Kyung-Bum Lee20,
Yi-Chueh Lin20, Asami Nozaki20,
Katsunaga Sakai20, Masahito Tada20,
Satoru Miyazaki21, Takashi Makino22,
Hajime Ohyanagi20,23, Naoki Osato20,
Nobuhiko Tanaka20, Yoshiyuki Suzuki20,
Kazuho Ikeo20, Naruya Saitou24,
Hideaki Sugawara20, Claire O’Donovan25,
Tamara Kulikova25, Eleanor Whitﬁeld25,
Brian Halligan26, Mary Shimoyama26,
Simon Twigger26, Kei Yura27,
Kouichi Kimura28, Tomohiro Yasuda28,
Tetsuo Nishikawa28,29, Yutaka Akiyama30,
Chie Motono30, Yuri Mukai30,
Hideki Nagasaki15,30, Makiko Suwa30,
Paul Horton30, Reiko Kikuno31, Osamu Ohara31,
Doron Lancet32, Eric Eveno33,34,
Esther Graudens33,34, Sandrine Imbeaud33,34,35,
Marie Anne Debily33,34,36,
Yoshihide Hayashizaki37,38, Clara Amid39,
Michael Han39, Andreas Osanger39,
Toshinori Endo5, Michael A. Thomas40,
Mika Hirakawa41, Wojciech Makalowski42,
Mitsuteru Nakao43, Nam-Soon Kim44,
Hyang-Sook Yoo44, Sandro J. De Souza45,
Maria de Fatima Bonaldo46,
Yoshihito Niimura47, Vladimir Kuryshev48,
Ingo Schupp48, Stefan Wiemann48,
Matthew Bellgard6, Masafumi Shionyu49,
Libin Jia50, Danielle Thierry-Mieg51,
Jean Thierry-Mieg51, Lukas Wagner51,
Qinghua Zhang34,52, Mitiko Go53,
Shinsei Minoshima54, Masafumi Ohtsubo54,
Kousuke Hanada55, Peter Tonellato56, Takao Isogai29,
Ji Zhang34,57, Boris Lenhard58, Sangsoo Kim59,
Zhu Chen34,60,61, Ursula Hinz62, Anne Estreicher62,

Kenta Nakai63, Izabela Makalowska64,
Winston Hide65, Nicola Tiﬃn65,
Laurens Wilming66, Ranajit Chakraborty67,
Marcelo Bento Soares68, Maria Luisa Chiusano69,
Yutaka Suzuki70, Charles Auﬀray33,34,
Yumi Yamaguchi-Kabata2, Takeshi Itoh2,15,
Teruyoshi Hishiki2, Satoshi Fukuchi20,
Ken Nishikawa20, Sumio Sugano2,70, Nobuo Nomura2,
Yoshio Tateno20, Tadashi Imanishi2,5,y and
Takashi Gojobori2,20
1Japan Biological Information Research Center, Japan
Biological Informatics Consortium, 2Biological
Information Research Center, National Institute ofAdvanced Industrial Science and Technology, Tokyo,
3
Graduate School Medicine, Dentistry andPharmaceutical Sciences, Okayama University, Okayama,
4
DNA Chip Research Inc., Kanagawa, 5Hokkaido
University, Hokkaido, Japan, 6Centre for Comparative
Genomics, Murdoch University, WA, Australia,
7
Biotechnology Research Center, The University ofTokyo, 8Hitachi Software Engineering Co., Ltd.,
9
Mitsubishi Kagaku Institute of Life Sciences, 10Fujitsu
Limited, Tokyo, 11Hitachi, Co., Ltd., Saitama, 12Japan
Science and Technology Agency, 13NEC Soft, Ltd.,
14
Mitsui Knowledge Industry Co., Ltd, Tokyo, 15National
Institute of Agrobiological Sciences, Ibaraki, 16BITS Co.,
Ltd., Shizuoka, 17Tokyo Institute of Psychiatry, Tokyo,
18
DYNACOM Co., Ltd., Chiba, 19C’s Lab Co., Ltd.,
Hokkaido, 20Center for Information Biology and DNA
Data Bank of Japan, National Institute of Genetics,
Shizuoka, 21Tokyo University of Science, Chiba, Japan,
22
University of Dublin, Trinity College, Dublin, Ireland,
23
Mitsubishi Space Software Co., Ltd., Ibaraki, 24Divisionof Population Genetics, National Institute of Genetics,
Shizuoka, Japan, 25EMBL Outstation-Hinxton, European
Bioinformatics Institute, Cambridge, UK,26
Bioinformatics Research Center, Medical College of
Wisconsin, WI, USA, 27Center for Computational Scienceand Engineering, Japan Atomic Energy Agency, Kyoto,
28
Central Research Laboratory, Hitachi Ltd., 29Reverse
Proteomics Research Institute, CO., Ltd.,
30
Computational Biology Research Center, National
Institute of Advanced Industrial Science and Technology,
Tokyo, 31Department of Human Gene, Kazusa DNA
Research Institute, Chiba, Japan, 32Department of
Molecular Genetics, Weizmann Institute of Science,
Rehovot, Israel, 33Genexpres, Functional Genomics andSystems Biology for Health (CNRS and Pierre & Marie
Curie University - Paris VI), Villejuif, France,
34
Sino-French Laboratory in Life Sciences and Genomics,
Shanghai, China, 35Centre de Génétique Moléculaire,
CNRS and Gif/Orsay DNA Microarray Platform, Gifs/
Yvette, 36Laboratory of Genomes Functional
Exploration, CEA, DSV, IRCM, Evry, France,
37
Genomic Sciences Center, RIKEN Yokohama Institute,
Kanagawa, 38Genome Science Laboratory, Discovery andResearch Institute, RIKEN Wako Institute, Saitama,
Japan, 39GSF - National Research Center for
Environment and Health, Institute for Bioinformatics,

Nucleic Acids Research, 2008, Vol. 36, Database issue D799
Neuherberg, Germany, 40Idaho State University, ID, USA,41
Institute for Chemical Research, Kyoto University,
Kyoto, Japan, 42Institute of Bioinformatics, University ofMuenster, Muenster, Germany, 43Kazusa DNA ResearchInstitute, Chiba, Japan, 44Korea Research Institute of
Bioscience & Biotechnology, Taejeon, Korea, 45Ludwig
Institute for Cancer Research, Sao Paulo, Brazil,
46
Medical Education and Biomedical Research Facility,
University of Iowa, IA, USA, 47Medical ResearchInstitute, Tokyo Medical and Dental University, Tokyo,
Japan, 48Molecular Genome Analysis, German Cancer
Research Center, Heidelberg, Germany, 49Nagahama
Institute of Bio-Science and Technology, Shiga, Japan,
50
National Cancer Institute, National Institutes of Health,MD, 51National Center for Biotechnology Information,
National Library of Medicine, National Institutes of
Health, MD, USA, 52National Engineering Center for
Biochips at Shanghai, Shanghai, China, 53Ochanomizu
University, Tokyo, 54Photon Medical Research Center,
Hamamatsu University School of Medicine, Shizuoka,
55
Plant Science Center, RIKEN Yokohama Institute,
Kanagawa, 56Harvard Medical School, MA, USA,57
Shanghai Institutes for Biological Sciences, Chinese
Academy of Sciences, Shanghai, China, 58Center for
Genomics and Bioinformatics, Karolinska Institute,

Stockholm, Sweden, 59Soongsil University, Seoul, Korea,
60
State Key Laboratory of Medical Genomics, Shanghai
Institute of Hematology, Rui Jin Hospital, Shanghai Jiao
Tong University School of Medicine, 61Chinese National
Human Genome Center at Shanghai, Shanghai, China,
62
Swiss Institute of Bioinformatics, Geneva, Switzerland,
63
The Institute of Medical Science, The University ofTokyo, Tokyo, Japan, 64The Pennsylvania State
University, PA, USA, 65The South African National
Bioinformatics Institute, University of Western Cape,
Cape Town, South Africa, 66The Wellcome Trust Sanger
Institute, Wellcome Trust Genome Campus, Cambridge,
UK, 67University of Cincinnati, OH, 68Children’sMemorial Research Center, Northwestern University,
Feinberg School of Medicine, USA, 69University of
Naples ‘‘Federico II’’, Naples, Italy and 70Department ofMedical Genome Sciences, Graduate School of Frontier
Sciences, The University of Tokyo, Tokyo, Japany
To whom correspondence should be addressed. Tel: +81-3-3599-8800;
Fax: +81-3-3599-8801; E-mail: t.imanishi@aist.go.jp
Correspondence may also be addressed to Takashi Gojobori. Tel: +8155-981-6847; Fax: +81-55-981-6848; Email: tgojobor@genes.nig.ac.jp