Refining orthologue groups at the transcript level

Jia, Yizhen; Wong, Thomas K. F.; Song, You‐Qiang; Yiu, Siu-Ming; Smith, David K.

doi:10.1186/1471-2164-11-s4-s11

Cited by 5 publications

(3 citation statements)

References 27 publications

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“…It has been suggested that alternative splicing should be considered when defining orthologous genes at the transcript level ( Jia et al , 2010 ; Zambelli et al , 2010 ). In addition to gene sequences, conservation of exon/intron structures should be included when defining orthologous genes.…”

Section: Discussionmentioning

confidence: 99%

Detection of orthologous exons and isoforms using EGIO

Zhu

2022

Bioinformatics

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Motivation Alternative splicing is an important mechanism to generate transcriptomic and phenotypic diversity. Existing methods have limited power to detect orthologous isoforms. Results We develop a new method, EGIO, to detect orthologous exons and orthologous isoforms from two species. EGIO uses unique exonic regions to construct exon groups, in which process dynamic programming strategy is used to do exon alignment. EGIO could cover all the coding exons within orthologous genes. A comparison between EGIO and ExTraMapper shows that EGIO could detect more orthologous isoforms with conserved sequence and exon structures. We apply EGIO to compare human and chimpanzee protein-coding isoforms expressed in the frontal cortex and identify 6912 genes that express human unique isoforms. Unexpectedly, more human unique isoforms are detected than those conserved between humans and chimpanzees. Availability Source code and test data of EGIO are available at https://github.com/wu-lab-egio/EGIO. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Discussionmentioning

confidence: 99%

Detection of orthologous exons and isoforms using EGIO

Zhu

2022

Bioinformatics

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“…At the same time, Jia et al . argue that AS should be taken into account in the refinement of existing orthologous gene groups at the transcript level, resulting in conceptual groups of orthologous isoforms of functional equivalence [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of gene-oriented exon orthology between human and mouse

Lin

2012

BMC Genomics

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BackgroundGene orthology has been well studied in the evolutionary area and is thought to be an important implication to functional genome annotations. As the accumulation of transcriptomic data, alternative splicing is taken into account in the assignments of gene orthologs and the orthology is suggested to be further considered at transcript level. Whether gene or transcript orthology, exons are the basic units that represent the whole gene structure; however, there is no any reported study on how to build exon level orthology in a whole genome scale. Therefore, it is essential to establish a gene-oriented exon orthology dataset.ResultsUsing a customized pipeline, we first build exon orthologous relationships from assigned gene orthologs pairs in two well-annotated genomes: human and mouse. More than 92% of non-overlapping exons have at least one ortholog between human and mouse and only a small portion of them own more than one ortholog. The exons located in the coding region are more conserved in terms of finding their ortholog counterparts. Within the untranslated region, the 5' UTR seems to have more diversity than the 3' UTR according to exon orthology designations. Interestingly, most exons located in the coding region are also conserved in length but this conservation phenomenon dramatically drops down in untranslated regions. In addition, we allowed multiple assignments in exon orthologs and a subset of exons with possible fusion/split events were defined here after a thorough analysis procedure.ConclusionsIdentification of orthologs at the exon level is essential to provide a detailed way to interrogate gene orthology and splicing analysis. It could be used to extend the genome annotation as well. Besides examining the one-to-one orthologous relationship, we manage the one-to-multi exon pairs to represent complicated exon generation behavior. Our results can be further applied in many research fields studying intron-exon structure and alternative/constitutive exons in functional genomic areas.

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“…Rather than cluster homologous sequences alone, Jia et al . [ 23 ] have clustered orthologous sequences at the transcript level while the analysis of Meng et al . [ 24 ] present a first global view of RNA editing in plant nuclear transcripts.…”

Section: Introductionmentioning

confidence: 99%

Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)

et al. 2010

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The 2010 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia’s oldest bioinformatics organisation formed in 1998, was organized as the 9th International Conference on Bioinformatics (InCoB), Sept. 26-28, 2010 in Tokyo, Japan. Initially, APBioNet created InCoB as forum to foster bioinformatics in the Asia Pacific region. Given the growing importance of interdisciplinary research, InCoB2010 included topics targeting scientists in the fields of genomic medicine, immunology and chemoinformatics, supporting translational research. Peer-reviewed manuscripts that were accepted for publication in this supplement, represent key areas of research interests that have emerged in our region. We also highlight some of the current challenges bioinformatics is facing in the Asia Pacific region and conclude our report with the announcement of APBioNet’s 100 BioDatabases (BioDB100) initiative. BioDB100 will comply with the database criteria set out earlier in our proposal for Minimum Information about a Bioinformatics and Investigation (MIABi), setting the standards for biocuration and bioinformatics research, on which we will report at the next InCoB, Nov. 27 – Dec. 2, 2011 at Kuala Lumpur, Malaysia.

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Refining orthologue groups at the transcript level

Cited by 5 publications

References 27 publications

Detection of orthologous exons and isoforms using EGIO

Detection of orthologous exons and isoforms using EGIO

Identification of gene-oriented exon orthology between human and mouse

Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)

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