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. 2019 Dec 14;2019:baz134. doi: 10.1093/database/baz134

Table 1.

A summary of the data in SGID

Item Description Cov. Previous
Genome High-quality assembly of the silkworm genome in chromosome level (7) The same as Kawamoto et al. and Mita et al. (7, 16)
Gene models 16 880 in total, with 12 752 correlated with old gene models (4, 28) The same as Kawamoto et al. and Mita et al. (7, 16)
Gene function annotation 15 594 genes are of function annotations 92.4% 80.3% in Kawamoto et al. and Mita et al. (7, 16)
4937 gene feature annotations 22.0% NA
201 309 annotations from InterproScan 93.9% NA
8730 distinctive GO lists 86.9% 54.2% in Kawamoto et al. and Mita et al. (7, 16)
16 028 correlated KEGG Gene IDs 96.4% NA
138 KEGG pathways 16.5% NA
16  320 correlated Entrez IDs 96.7% NA
Biophysics and chemistry 2487 EC numbers 13.8% NA
329 biophysicochemical properties 0.6% NA
2445 catalytic activity annotations 12.0% NA
1743 cofactor information annotations 7.5% NA
Topology 20 378 subcellular localization annotations 99.9% NA
2878 genes with transmembrane regions 17.0% NA
1960 genes with signal peptides 11.6% NA
Proteomics and protein structure 12 394 real peptides from experiments validated 2999 protein coding genes 17.8% NA
9844 genes significantly correlated PDB protein structures 58.3% NA
1 730 892 correlated EMBL IDs 92.3% NA
17 762 correlated Gene3D IDs 57.2% NA
112 275 correlated Interpro IDs 86.9% NA
6257 CDD annotations 29.0% NA
TFs 704 items 4.2% NA
Repeat elements 571 401 segments, with 28 519 DNA transposons, 190 316 LINE, 13763 LTR and 179 435 SINE In accordance with Osanai-Futahashi et al. (53)
Transcriptomics 306 samples from 41 projects NA
Epigenomics 187 samples from 38 projects NA
Populations genetics Sliding widow analysis results based on 158 silkworm genomes NA

‘Cov.’ denotes the coverage of genes with corresponding annotations in total genes. ‘Previous’ denotes the comparison of SGID and previous work. ‘NA’ denotes that related data is not available in previously built silkworm databases, such as SilkBase, Ensembl Silkworm and SilkDB.