ArticleDatabase : the journal of biological databases and curation2022
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species.
Article in Database : the journal of biological databases and curation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 27 citations in OpenAlex.
- Genome-wide mapping of theiScience · 2026Article
- Identification of an atypical microRNA with sequence variation in the silkworm Bombyx mori.PloS one · 2026Article
- Unraveling developmental gene regulation in holometabolous insects through comparative transcriptomics and proteomics.Communications biology · 2025Article
- The Masc-PSI complex directly induces male-type doublesex splicing in silkworms.Communications biology · 2025Article
- Characterization of Spectrin Family Genes and Their Evolutionary Roles in Domestication and Breeding of the SilkwormInsects · 2025Article
- Integrated Genomic Analysis Reveals the Impact of Avermectin on Chromatin Structure and Gene Expression Regulation inInsects · 2025Article
- Time-course transcriptome data of silk glands in day 0-7 last-instar larvae of Bombyx mori (w1 pnd strain).Scientific data · 2024Article
- The BTB-ZF geneeLife · 2024Article
- SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data.Nucleic acids research · 2024Article
- Article
- High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation.Nature communications · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
We introduce SilkBase as an integrated database for transcriptomic and genomic resources of the domesticated silkworm Bombyx mori and related species. SilkBase is the oldest B. mori database that was originally established as the expressed sequence tag database since 1999. Here, we upgraded the database by including the datasets of the newly assembled B. mori complete genome sequence, predicted gene models, bacterial artificial chromosome (BAC)-end and fosmid-end sequences, complementary DNA (cDNA) reads from 69 libraries, RNA-seq data from 10 libraries, PIWI-interacting RNAs (piRNAs) from 13 libraries, ChIP-seq data of 9 histone modifications and HP1 proteins and transcriptome and/or genome data of four B. mori-related species, i.e. Bombyx mandarina, Trilocha varians, Ernolatia moorei and Samia ricini. Our new integrated genome browser easily provides a snapshot of tissue- and stage-specific gene expression, alternative splicing, production of piRNAs and histone modifications at the gene locus of interest. Moreover, SilkBase is useful for performing comparative studies among five closely related lepidopteran insects. Database URL: https://silkbase.ab.a.u-tokyo.ac.jp.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.