CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris)
Abstract Background The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and trans...
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ftdoajarticles:oai:doaj.org/article:79b86829fd834ed6b7380de75438a87d 2023-11-12T04:15:36+01:00 CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris) In Seok Yang Insu Jang Jin Ok Yang Jinhyuk Choi Min-Seo Kim Ka-Kyung Kim Byung-Joon Seung Jae-Ho Cheong Jung-Hyang Sur Hojung Nam Byungwook Lee Junho Kim Sangwoo Kim 2023-10-01T00:00:00Z https://doi.org/10.1186/s12864-023-09655-0 https://doaj.org/article/79b86829fd834ed6b7380de75438a87d EN eng BMC https://doi.org/10.1186/s12864-023-09655-0 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-023-09655-0 1471-2164 https://doaj.org/article/79b86829fd834ed6b7380de75438a87d BMC Genomics, Vol 24, Iss 1, Pp 1-12 (2023) Domestic dog Canine mammary tumor SNP Transcriptome Transcript isoform Database Biotechnology TP248.13-248.65 Genetics QH426-470 article 2023 ftdoajarticles https://doi.org/10.1186/s12864-023-09655-0 2023-10-22T00:43:19Z Abstract Background The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. Results We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. Conclusions CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ . Article in Journal/Newspaper Canis lupus Directory of Open Access Journals: DOAJ Articles BMC Genomics 24 1 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Domestic dog Canine mammary tumor SNP Transcriptome Transcript isoform Database Biotechnology TP248.13-248.65 Genetics QH426-470 |
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Domestic dog Canine mammary tumor SNP Transcriptome Transcript isoform Database Biotechnology TP248.13-248.65 Genetics QH426-470 In Seok Yang Insu Jang Jin Ok Yang Jinhyuk Choi Min-Seo Kim Ka-Kyung Kim Byung-Joon Seung Jae-Ho Cheong Jung-Hyang Sur Hojung Nam Byungwook Lee Junho Kim Sangwoo Kim CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris) |
topic_facet |
Domestic dog Canine mammary tumor SNP Transcriptome Transcript isoform Database Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. Results We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. Conclusions CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ . |
format |
Article in Journal/Newspaper |
author |
In Seok Yang Insu Jang Jin Ok Yang Jinhyuk Choi Min-Seo Kim Ka-Kyung Kim Byung-Joon Seung Jae-Ho Cheong Jung-Hyang Sur Hojung Nam Byungwook Lee Junho Kim Sangwoo Kim |
author_facet |
In Seok Yang Insu Jang Jin Ok Yang Jinhyuk Choi Min-Seo Kim Ka-Kyung Kim Byung-Joon Seung Jae-Ho Cheong Jung-Hyang Sur Hojung Nam Byungwook Lee Junho Kim Sangwoo Kim |
author_sort |
In Seok Yang |
title |
CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris) |
title_short |
CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris) |
title_full |
CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris) |
title_fullStr |
CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris) |
title_full_unstemmed |
CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris) |
title_sort |
caniso: a database of genomic and transcriptomic variations in domestic dog (canis lupus familiaris) |
publisher |
BMC |
publishDate |
2023 |
url |
https://doi.org/10.1186/s12864-023-09655-0 https://doaj.org/article/79b86829fd834ed6b7380de75438a87d |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
BMC Genomics, Vol 24, Iss 1, Pp 1-12 (2023) |
op_relation |
https://doi.org/10.1186/s12864-023-09655-0 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-023-09655-0 1471-2164 https://doaj.org/article/79b86829fd834ed6b7380de75438a87d |
op_doi |
https://doi.org/10.1186/s12864-023-09655-0 |
container_title |
BMC Genomics |
container_volume |
24 |
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1 |
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1782332885344190464 |