H-DBAS: human-transcriptome database for alternative splicing: update 2010.
ABSTRACT H-DBAS (http://h-invitational.jp/h-dbas/) is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. In this update, for better annotations of AS events, we correlated RNA-Seq tag information to the AS exons and splice junctions. We generated a total of 148,376,598 RNA-Seq tags from RNAs extracted from cytoplasmic, nuclear and polysome fractions. Analysis of the RNA-Seq tags allowed us to identify 90,900 exons that are very likely to be used for protein synthesis. On the other hand, 254 AS junctions of human RefSeq transcripts are unique to nuclear RNA and may not have any translational consequences. We also present a new comparative genomics viewer so that users can empirically understand the evolutionary turnover of AS. With the unique experimental data closely connected with intensively curated cDNA information, H-DBAS provides a unique platform for the analysis of complex AS.
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ABSTRACT: Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.The Scientific World Journal 01/2013; 2013:703568. · 1.22 Impact Factor
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ABSTRACT: The burgeoning field of high-throughput sequencing significantly improves our ability to understand the complexity of transcriptomes. Alternative splicing, as one of the most important driving forces for transcriptome diversity, can now be studied at an unprecedent resolution. Efficient and powerful computational and statistical methods are in urgent need to facilitate the characterization and quantification of alternative splicing events. Here we discuss methods in splice junction read mapping, and methods in exon-centric or isoform-centric quantification of alternative splicing. In addition, we discuss HITS-CLIP and splicing QTL analyses which are novel high-throughput sequencing based approaches in the dissection of splicing regulation.Statistics in Biosciences 05/2013; 5(1):138-155.
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ABSTRACT: Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. However, despite many efforts, the repertoire of gene splicing variation is still incompletely characterized, even in humans. Here we describe a new computational system, ASprofile, and its application to RNA-seq data from Illumina's Human Body Map project (>2.5 billion reads). Using the system, we identified putative alternative splicing events in 16 different human tissues, which provide a dynamic picture of splicing variation across the tissues. We detected 26,989 potential exon skipping events representing differences in splicing patterns among the tissues. A large proportion of the events (>60%) were novel, involving new exons (~3000), new introns (~16000), or both. When tracing these events across the sixteen tissues, only a small number (4-7%) appeared to be differentially expressed ('switched') between two tissues, while 30-45% showed little variation, and the remaining 50-65% were not present in one or both tissues compared. Novel exon skipping events appeared to be slightly less variable than known events, but were more tissue-specific. Our study represents the first effort to build a comprehensive catalog of alternative splicing in normal human tissues from RNA-seq data, while providing insights into the role of alternative splicing in shaping tissue transcriptome differences. The catalog of events and the ASprofile software are freely available from the Zenodo repository ( http://zenodo.org/record/7068; doi: 10.5281/zenodo.7068) and from our web site http://ccb.jhu.edu/software/ASprofile.F1000Research. 01/2013; 2:188.
H-DBAS: human-transcriptome database for
alternative splicing: update 2010
Jun-ichi Takeda1,2, Yutaka Suzuki2, Ryuichi Sakate1, Yoshiharu Sato1,
Takashi Gojobori1,3, Tadashi Imanishi1,* and Sumio Sugano2
1Integrated Database and Systems Biology Team, Biomedicinal Information Research Center National
Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research Bldg. Aomi 2-4-7, Koto-ku,
Tokyo 135-0064,2Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the
University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and3Center for Information Biology
and DDBJ, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
Received September 15, 2009; Revised October 13, 2009; Accepted October 15, 2009
H-DBAS (http://h-invitational.jp/h-dbas/) is a spe-
cialized database for human alternative splicing
(AS) based on H-Invitational full-length cDNAs.
In this update, for better annotations of AS events,
we correlated RNA-Seq tag information to the AS
exons and splice junctions. We generated a total
of 148376598 RNA-Seq tags from RNAs extracted
from cytoplasmic, nuclear and polysome fractions.
Analysis of the RNA-Seq tags allowed us to identify
90900 exons that are very likely to be used for
protein synthesis. On the other hand, 254 AS junc-
tions of human RefSeq transcripts are unique to
nuclear RNA and may not have any translational
consequences. We also present a new comparative
genomics viewer so that users can empirically
understand the evolutionary turnover of AS. With
the unique experimental data closely connected
analysis of complex AS.
Alternative splicing (AS) is a phenomenon in which a
single gene produces various functional protein isoforms.
AS is frequently observed especially in higher eukaryotes.
At least 50% of human genes are reported to be subjected
to AS. However, the biological significance of this high
level of AS and its regulation mostly remain elusive
(1,2). For better understanding of AS in humans, we con-
structed a human-transcriptome database for alternative
splicing (H-DBAS) in 2006, which collects information
of human AS variants from the viewpoints of protein
functions affected by AS. H-DBAS is based on the
manually inspected and well-annotated cDNA informa-
tion collected by the H-Invitational cDNA Annotation
Project. By utilizing the annotation information and
cDNA sequence information, it was possible to identify
AS events that invoke changes in protein-coding regions,
thereby influencing protein functions (3–5). Based on the
result of intensive annotations of AS events, H-DBAS
presents thousands of AS events that may increase the
functional diversification of the human genome.
conservation of the identified AS events and found that
a large number of these annotated AS events may not be
evolutionarily conserved between humans and mice.
Similar results were also reported by other groups (6).
Our concern was that they could simply represent intrinsic
noise of transcription inherently occurring in the human
genome without biological relevance. Therefore, further
extensive annotations in which AS events are likely to be
translated into proteins and whether such AS events are
evolutionarily conserved would be essential. Such infor-
mation will be extremely useful to prioritize targets for
future functional characterization of AS events and to
determine the direction of validation experiments.
The latest generation of sequencers have greatly
improved the cost and speed of cDNA sequencing (7).
A recent paper reported the use of a new generation
sequencer for in-depth identification and characterization
of human AS events. They generated dozens of millions of
shotgun RNA sequence tags by the so-called RNA-Seq
analysis and analyzed the collected tags (RNA-Seq tags)
to detect positions and frequencies of the usage of every
splice junction (8,9). In this particular study, polyA+
RNA was used for RNA-Seq analysis. However, several
methodological improvements have been made so that it is
now possible to consider a similar approach for analysis of
RNAs from any population. In a very recent study, we
generated a total of 150-million RNA-Seq tag sequences
*To whom correspondence should be addressed. Tel: +81 3 3599 8800; Fax: +81 3 3599 8801; Email: firstname.lastname@example.org
Nucleic Acids Research, 2010, Vol. 38, Database issuePublished online 7 December 2009
? The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
using RNAs that were separately extracted from cyto-
plasmic, nuclear and polysome (translating ribosome)
subcellular fractions in DLD-1 cells, a colon cancer cell
line. In this update of H-DBAS, we incorporated this
RNA-Seq data enabling a clear representation of which
RNAs and their AS variants are identified in which
subcellular fractions. Observing a particular AS variant
in the polysome fraction should be especially important
because it provides direct evidence for its transla-
tional consequence. Also, to determine whether an AS is
evolutionarily conserved, we used a comparative genomic
viewer. In this viewer, AS events are categorized according
to whether they are transcribed from conserved genomic
regions or whether the corresponding transcripts that are
also identified in mice. The updated H-DBAS including
these two expanded features should provide a unique and
important resource to explore the complex world of
Statistics of the new RNA-Seq datasets
By RNA-Seq analysis using Illumina GA, we generated
46354139, 47120831 and 54901628 single-end-read
36-bp RNA-Seq tags from cytoplasmic, nuclear and
polysome fractions of the RNAs from DLD-1 cells,
respectively. Separation of the respective subcellular
glyceraldehyde-3-phosphate dehydrogenase, a cytoplasmic
protein and lamin A/C, a nuclear protein, as well as
real-time RT-PCR analysis of sno/scaRNAs, nuclear
RNAs (see RNA-Seq analysis page on the top page of
H-DBAS for the related experimental data; details of the
experimental procedures are also described there). The
RNA-Seq tags obtained were mapped to the reference
human genome of UCSC genome browser (hg18) (10).
To identify tags that span splice junctions, we used
Eland RNA and TopHat (version 1.0.9) (11,12) with the
default options of considering only junctions following the
‘GT–AG’ rule and allowing up to two base mismatches.
We further selected the splice junctions that were sup-
ported by two or more RNA-Seq tags. As a result,
201280, 236764 and 319577 junctions were represented
in the RNA-Seq datasets derived from cytoplasmic,
nuclear and polysome subcellular fractions, respectively
The RNA-Seq tag information obtained was further
correlated with transcript information. For analyzing the
subdataset of human AS variants, we used RefSeq
by western blotting of
transcripts (release 23) (13). Among the total of 26814
human RefSeq transcripts, 10923 were annotated to rep-
resent mutual AS variants according to H-InvDB (release
6.0) [see ref. (4) for further details]. In total, 81547, 85923
and 90900 exons were represented by RNA-Seq tags
derived from cytoplasmic, nuclear and polysome fractions,
respectively. In addition, 47615, 47260 and 51041 splice
junctions were represented in the RNA-Seq tags in the
respective fractions. Of these, 1067, 1021 and 1114 junc-
tions corresponded to mutual AS junctions, directly sug-
gesting that these AS events are expressed and located in
the respective subcellular locations. Statistical analysis of
the enrichment of tags also showed that some AS variants
were enriched in a given subcellular location: 260, 254
and 299 AS variants were selectively observed in the
cytoplasmic, nuclear and polysome fractions, respectively.
Especially for 178 AS variant pairs, both of the variants
appeared to be translated to proteins simultaneously in
DLD-1 cells. All of the above extensive annotations on
the biological relevance of each AS are represented as
a graphic interface as described below.
RNA-Seq viewer can be accessed from the RNA-Seq
analysis page at the H-DBAS top page. On the
RNA-Seq analysis page, RNA-Seq and AS annotation
information were described in a table. In the table, the
number of corresponding RNA-Seq tags and presumed
subcellular locations of AS events were shown. By follow-
ing the link from the table, details of the RNA-Seq tag
supports in the junction appear in the RNA-Seq viewer. In
this viewer, RefSeq transcripts and tags located in the
splice junctions are represented. RNA-Seq tag informa-
tion was further categorized so that users can examine
tag distribution in each subcellular location. Figure 1
exemplifies RNA-Seq tag analysis in the case of caspase
4, an apoptosis-related cysteine peptidase gene. In this
gene, the AS junction (indicated by a red line) was
exclusively identified in nuclear fractions. Figure 1 also
represents 35 RNA-Seq tags mapped to the corresponding
splice junctions. These results suggested that the AS
variant using the most upstream exon (using splice junc-
tions marked in red) is retained in the nucleus and is not
used for protein translation in DLD-1 cells.
Comparative genomics viewer
In order to distinguish AS events having a clear biological
significance, it would be informative to consider whether
an AS is evolutionarily conserved, for which we newly
Table 1. Statistics of human RefSeq junctions expressed in each cellular fraction using RNA-Seq
Nucleic Acids Research, 2010,Vol.38, Database issue D87
Figure 1. Screenshot of RNA-Seq viewer. Genomic regions in caspase 4, an apoptosis-related cysteine peptidase (CASP4) and the estimated junc-
tions with the two or more supporting RNA-Seq tags mapped to the corresponding genomic regions. (A) AS variants of RefSeq are represented.
Annotated protein-coding regions and untranslated regions are indicated by green and yellow boxes, respectively. (B) Junctions estimated by the
mapped RNA-Seq tags derived from cytoplasmic, nuclear and polysome cellular fractions are shown in cyan, navy and brown, respectively. If the AS
junction of RefSeq transcript is expressed in unique sub-cellular fraction (nuclear in this figure), it is shown in red. The gray boxes indicate the
assembled exonic regions of RefSeq transcripts. (C) RNA-Seq tags which support the junction are represented. Two or more RNA-Seq tags mapped
on the splice sites are shown by each sub-cellular fraction. The represented colors are the same as (B).
D88 Nucleic Acids Research,2010, Vol.38, Database issue
implemented a comparative genomics viewer to empiri-
cally represent the degree of evolutionary conservation for
any AS. In this viewer, each AS variant can be viewed for
the following points: (i) whether its surrounding genomic
sequence is conserved between humans and mice and
(ii) whether the corresponding AS event is also observed
in mice. Genomic sequences and alignment information
were obtained from UCSC genome browser (hg18 and
mm9 for humans and mice, respectively) (10). For
full-length cDNA information, we used 65158 human
full-length cDNAs and122544
Mammalian Gene Collection (15). In total, 20803 repre-
full-length cDNAs are represented. Among 207 399
exons of the total 20803 human RASVs, 27567 exons
were mapped to the genomic regions that had no aligned
mouse genomic regions. On the other hand, 22396 exons
were mapped to the aligned genomic regions (coverage
(14)(5), FANTOM and
?70% and identity ?60%), but the corresponding tran-
scripts were not identified in mice. The remaining 157436
exons were mapped to the conserved genomic regions
and corresponding transcripts were identified in mouse
full-length cDNAs. Among the 7875 conserved RASVs
thus identified, 5494 were equally spliced variants (ESVs)
with mouse full-length cDNAs, which are conserved
between humans and mice and are likely to have
evolutionarily conserved biological roles (Table 2). For
example, as shown in Figure 2, the phosphoinositide-3-
kinase regulatory subunit gene has several AS variants.
For the two AS variants, their splice patterns are identical
to those of the mouse full-length cDNAs. These AS
variants may contribute to functional diversification of
gene function, playing conserved biological roles both in
humans and mice. Further details of the statistical analysis
of frequencies of conserved AS variants in various gene
groups have been described previously (16). The compar-
ative genomics viewer is embedded in the main AS viewer.
It can also be accessed from the summary annotation table
at the H-DBAS top page and users can search specifically
about the comparative genomics analysis from Advanced
search page at the top page.
We updated our H-DBAS so that AS transcripts having
various types of annotation information can be repre-
sented inan integrative manner.These typesof
Figure 2. Screenshot of comparative genomic viewer. AS variants in the phosphatidylinositol 3-kinase regulatory subunit alpha (PI3-kinase p85
subunit alpha) gene are shown both in humans and mice. The exon structures of the human AS variants and the mouse full-length cDNAs are shown
in the upper and lower panels, respectively, across the human–mouse genome alignment. In this view option (Exon view), constitutively spliced
introns of the transcripts are omitted. Mutually equally spliced variants in humans and mice are indicated by blue and orange arrows, respectively.
Table 2. Statistics of comparative genomics between human and
mouse full-length cDNAs
At least one
RASV: representative AS variant; ESV: equally spliced variant.
Nucleic Acids Research, 2010,Vol.38, Database issue D89
cDNA sequences; RNA-Seq tags derived from RNAs
extracted from nuclear, cytoplasm and polysome frac-
tions; and degree of evolutionary conservation of AS. By
enabling the integrative interpretation of annotation infor-
mation, we believe that H-DBAS can serve as a unique
and useful database for future functional characterization
of AS events. In future, we aim to further enrich the
diverse annotation information connected to each AS.
For this purpose, we aim to expand similar RNA-Seq
analysis to cover the transcriptome information of mice
and other mammals. Also, we aim to continue to collect
RNA-Seq tags from a wider variety of cell types cultured
under different conditions in order to understand which
AS events are transcribed in which cell types and under
what cellular conditions. Results of such extensive
analyses will be fed back to the manual annotations in
H-InvDB. With integrative transcriptome data, we aim
to provide expanded knowledge of the biological signifi-
cance of the functional diversification of human genes
realized by AS, which should add useful molecular back-
ground to the complex human gene network created by a
limited number of genes.
The authors thank Y. Kawahara, A. Matsuya, H.
Nakaoka, T. Habara, F. Todokoro and C. Yamasaki
for their assistance in genome mapping and ORF predic-
tion. We also thank E. Sekimori for the technical support
for RNA-Seq analysis, M. Nitta for constructing the com-
parative genomics viewer, and T. Endo for the technical
support for server usage. Finally, we are grateful to all
those who annotated the full-length human cDNAs at
the H-Invitational and H-Invitational two conferences.
Integrated database project of the Ministry of Economy,
Trade, and Industry of Japan, Ministry of Education,
Culture, Sports, Science and Technology of Japan,
National Institute of Advanced Industrial Science and
Technology (AIST) and Japan Biological Informatics
Consortium (JBIC). Funding for open access charge:
Conflict of interest statement. None declared.
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