SilkDB
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The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently.
Description
More detailed information about this field from each metasource.
The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:40.491505
Webpage:
http://silkworm.genomics.org.cn/Webpage
More detailed information about this field from each metasource.
http://silkworm.genomics.org.cn/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:40.491505
Publications:
Publications
More detailed information about this field from each metasource.
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology
PMID: 19793867
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505
Publications
More detailed information about this field from each metasource.
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology
PMID: 19793867
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505
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SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology
PubMed citations: 129.
129 articles citing: SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology
High-Quality de novo Chromosome-Level Genome Assembly of a Single Bombyx mori With BmNPV Resistance by a Combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. PMID:34603381
Proteomic Identification of Bombyx mori Organelles Using the Engineered Ascorbate Peroxidase APEX and Development of Silkworm Organelle Proteome Database (SilkOrganPDB). PMID:34068790
Identification and Characterization of Aldehyde Oxidase 5 in the Pheromone Gland of the Silkworm (Lepidoptera: Bombycidae). PMID:33295983
Synergisms in Science: Climate Change and Integrated Pest Management Through the Lens of Communication-2019 Student Debates. PMID:33119749
Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line. PMID:33023468
Characterization of an Ecdysteroid-Regulated 16 kDa Protein Gene in Chinese Oak Silkworm, Antheraea pernyi (Lepidoptera: Saturniidae). PMID:32396202
Draft Genome of a Blister Beetle Mylabris aulica. PMID:32010178
Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects. PMID:31965990
SGID: a comprehensive and interactive database of the silkworm. PMID:31836898
BmBlimp-1 gene encoding a C2H2 zinc finger protein is required for wing development in the silkworm Bombyx mori. PMID:31754338
Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis. PMID:31682256
SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm. PMID:31642484
Suppression of Wolbachia-mediated male-killing in the butterfly Hypolimnas bolina involves a single genomic region. PMID:31592190
Characterization of a highly conserved Antheraea pernyi spermidine synthase gene. PMID:31139539
Genome-Wide Analysis and Hormone Regulation of Chitin Deacetylases in Silkworm. PMID:30987273
Genome-Wide Identification and Expression Profiling of Wnt Family Genes in the Silkworm, Bombyx mori. PMID:30862048
Smooth Muscle Transcriptome Browser: offering genome-wide references and expression profiles of transcripts expressed in intestinal SMC, ICC, and PDGFRα+ cells. PMID:30674925
The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera). PMID:30476205
Identification of Genes that Control Silk Yield by RNA Sequencing Analysis of Silkworm (Bombyx mori) Strains of Variable Silk Yield. PMID:30467288
The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots. PMID:30293092
Bombyx mori Dihydroorotate Dehydrogenase: Knockdown Inhibits Cell Growth and Proliferation via Inducing Cell Cycle Arrest. PMID:30200251
Mulberry (Morus spp.) has the features to treat as a potential perennial model system. PMID:30047827
Molecular Cloning and Effects of Tm14-3-3ζ-Silencing on Larval Survivability Against E. coli and C. albicans in Tenebrio molitor. PMID:29966317
Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome. PMID:29892960
Disruption of PTPS Gene Causing Pale Body Color and Lethal Phenotype in the Silkworm, Bombyx mori. PMID:29596327
Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus. PMID:29444297
Intrinsic antimicrobial properties of silk spun by genetically modified silkworm strains. PMID:29435708
Complete Genome of Achalarus lyciades, The First Representative of the Eudaminae Subfamily of Skippers. PMID:29081692
The dynamic landscape of gene regulation during Bombyx mori oogenesis. PMID:28893182
The first complete genomes of Metalmarks and the classification of butterfly families. PMID:28757157
Segmental duplications: evolution and impact among the current Lepidoptera genomes. PMID:28683762
A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana. PMID:28486658
Serine protease Bm-SP142 was differentially expressed in resistant and susceptible Bombyx mori strains, involving in the defence response to viral infection. PMID:28414724
Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs. PMID:28203233
Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins. PMID:28163896
Ultrabithorax and abdominal-A specify the abdominal appendage in a dosage-dependent manner in silkworm, Bombyx mori. PMID:28121309
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. PMID:27899580
LBD1 of Vitellogenin Receptor Specifically Binds to the Female-Specific Storage Protein SP1 via LBR1 and LBR3. PMID:27637099
Genome-wide identification and analysis of JHBP-domain family members in the silkworm Bombyx mori. PMID:27631967
BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori. PMID:27623959
Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands. PMID:27576083
A comprehensive view of the web-resources related to sericulture. PMID:27307138
Comparative analysis of the integument transcriptomes of the black dilute mutant and the wild-type silkworm Bombyx mori. PMID:27193628
Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence. PMID:27120974
Proteins in the Cocoon of Silkworm Inhibit the Growth of Beauveria bassiana. PMID:27032085
The C-terminus of DSX(F5) protein acts as a novel regulatory domain in Bombyx mori. PMID:26975733
Speciation in Cloudless Sulphurs Gleaned from Complete Genomes. PMID:26951782
Reassessing ecdysteroidogenic cells from the cell membrane receptors' perspective. PMID:26847502
Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution. PMID:26772750
Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori. PMID:26771876
Molecular mapping and characterization of the silkworm apodal mutant. PMID:26738847
deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. PMID:26590255
InsectBase: a resource for insect genomes and transcriptomes. PMID:26578584
The evolutionary landscape of intergenic trans-splicing events in insects. PMID:26521696
Skipper genome sheds light on unique phenotypic traits and phylogeny. PMID:26311350
Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis. PMID:26244979
A novel laminin β gene BmLanB1-w regulates wing-specific cell adhesion in silkworm, Bombyx mori. PMID:26212529
Aspartate Decarboxylase is Required for a Normal Pupa Pigmentation Pattern in the Silkworm, Bombyx mori. PMID:26077025
Transcriptome analysis of BmN cells following over-expression of BmSTAT. PMID:25998838
Genome-wide identification and characterization of Fox genes in the silkworm, Bombyx mori. PMID:25893708
Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms. PMID:25887670
Comparative transcriptome analyses on silk glands of six silkmoths imply the genetic basis of silk structure and coloration. PMID:25886738
Developmental Changes for the Hemolymph Metabolome of Silkworm (Bombyx mori L.). PMID:25825269
Digestive organ in the female reproductive tract borrows genes from multiple organ systems to adopt critical functions. PMID:25725432
Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense. PMID:25683714
Repeated horizontal transfers of four DNA transposons in invertebrates and bats. PMID:25606061
Overexpression of host plant urease in transgenic silkworms. PMID:25549597
Molecular characterization and phylogenetic analysis of the eukaryotic translation initiation factor 4A gene in Antheraea pernyi (Lepdoptera: Saturniidae). PMID:25480968
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. PMID:25428351
Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew. PMID:25413576
iPathCons and iPathDB: an improved insect pathway construction tool and the database. PMID:25388589
Crystal structure of Bombyx mori lipoprotein 6: comparative structural analysis of the 30-kDa lipoprotein family. PMID:25379889
A molecular view of autophagy in Lepidoptera. PMID:25143951
Pogo-like transposases have been repeatedly domesticated into CENP-B-related proteins. PMID:25062917
ChiloDB: a genomic and transcriptome database for an important rice insect pest Chilo suppressalis. PMID:24997141
MorusDB: a resource for mulberry genomics and genome biology. PMID:24923822
Antenna-specific glutathione S-transferase in male silkmoth Bombyx mori. PMID:24786099
Molecular Expression of the Scribble Complex Genes, Dlg, Scrib and Lgl, in Silkworm, Bombyx mori. PMID:24705163
Copy number variations among silkworms. PMID:24684762
Crystal structure of Bombyx mori arylphorins reveals a 3:3 heterohexamer with multiple papain cleavage sites. PMID:24639361
in silico identification of protein-protein interactions in Silkworm, Bombyx mori. PMID:24616555
Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands. PMID:24606580
Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. PMID:24489955
Identification and molecular characterization of a chitin deacetylase from Bombyx mori peritrophic membrane. PMID:24473143
Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study. PMID:24324810
New insights into the genomic organization and splicing of the doublesex gene, a terminal regulator of sexual differentiation in the silkworm Bombyx mori. PMID:24244545
Proteomic-based insight into Malpighian tubules of silkworm Bombyx mori. PMID:24098719
BmTEdb: a collective database of transposable elements in the silkworm genome. PMID:23886610
Assessing De Novo transcriptome assembly metrics for consistency and utility. PMID:23837739
KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella. PMID:23837716
Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori. PMID:23821615
Identification and evolution of the silkworm helitrons and their contribution to transcripts. PMID:23771679
The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum. PMID:23761966
Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. PMID:23674305
Antennapedia is involved in the development of thoracic legs and segmentation in the silkworm, Bombyx mori. PMID:23652563
Computational identification of functional introns: high positional conservation of introns that harbor RNA genes. PMID:23605046
Vitellogenin receptor mutation leads to the oogenesis mutant phenotype "scanty vitellin" of the silkworm, Bombyx mori. PMID:23515308
Mechanisms and dynamics of orphan gene emergence in insect genomes. PMID:23348040
A genetic polymorphism evolving in parallel in two cell compartments and in two clades. PMID:23311980
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
MonarchBase: the monarch butterfly genome database. PMID:23143105
Bombyx mori transcription factors: genome-wide identification, expression profiles and response to pathogens by microarray analysis. PMID:22943524
Transcriptome analysis of the silkworm (Bombyx mori) by high-throughput RNA sequencing. PMID:22928022
Resistance to BmNPV via overexpression of an exogenous gene controlled by an inducible promoter and enhancer in transgenic silkworm, Bombyx mori. PMID:22870254
Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. PMID:22862991
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand. PMID:22802635
Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome. PMID:22627775
Retrogenes moved out of the z chromosome in the silkworm. PMID:22535494
Evolutionary genomics of Colias Phosphoglucose Isomerase (PGI) introns. PMID:22388354
Genome-wide identification and immune response analysis of serine protease inhibitor genes in the silkworm, Bombyx mori. PMID:22348050
Molecular cloning and characterization of Ecdysone oxidase and 3-dehydroecdysone-3α-reductase involved in the ecdysone inactivation pathway of silkworm, Bombyx mori. PMID:22215981
Pathogen-origin horizontally transferred genes contribute to the evolution of Lepidopteran insects. PMID:22151541
Identification of Bombyx atonal and functional comparison with the Drosophila atonal proneural factor in the developing fly eye. PMID:21998072
Genome-wide identification and characterization of ATP-binding cassette transporters in the silkworm, Bombyx mori. PMID:21981826
Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects. PMID:21843315
A rearrangement of the Z chromosome topology influences the sex-linked gene display in the European corn borer, Ostrinia nubilalis. PMID:21573787
The phylogenetic origin of oskar coincided with the origin of maternally provisioned germ plasm and pole cells at the base of the Holometabola. PMID:21552321
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. PMID:21515631
Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori. PMID:21508430
Baculovirus VP80 protein and the F-actin cytoskeleton interact and connect the viral replication factory with the nuclear periphery. PMID:21450830
Characterization of the deleted in autism 1 protein family: implications for studying cognitive disorders. PMID:21283809
Diversity in copy number and structure of a silkworm morphogenetic gene as a result of domestication. PMID:21242537
Identification and characterization of Sox genes in the silkworm, Bombyx mori. PMID:21161409
Molecular cloning, expression pattern and phylogenetic analysis of the will die slowly gene from the Chinese oak silkworm, Antheraea pernyi. PMID:21104437
An integrated database for the enhanced identification of silkworm gene resources. PMID:20975904
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
Comparative analysis of proteome maps of silkworm hemolymph during different developmental stages. PMID:20822545
Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. PMID:20478048
Mutations of an arylalkylamine-N-acetyltransferase, Bm-iAANAT, are responsible for silkworm melanism mutant. PMID:20332088
Tags:
Tags
More detailed information about this field from each metasource.
gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505
mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505
sequence assembly
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505
microarray experiment
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505
Tags
More detailed information about this field from each metasource.
gene transcripts
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:40.491505
mapping
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:40.491505
sequence assembly
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:40.491505
microarray experiment
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:40.491505
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:40.491505
gene transcripts mapping sequence assembly microarray experiment gene expression
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