About RubberDandelionOmics
This portal serves rubber dandelion researchers worldwide with genome search, multi-omics evidence, and natural rubber biosynthesis candidate lookup. Data sources and evidence boundaries are noted on the relevant pages.
Evidence Boundaries
Homology, domains, TF, PPI, coexpression, and pathway candidates are database-derived or computational evidence unless explicitly marked as experimentally validated.
Active Modules and Auxiliary Sources
| Layer | Role | Reference / method | Distinct genes | Records | Scope |
|---|---|---|---|---|---|
| TK1151 TF family candidate catalog | Active module | TK1151 / Pfam family rules | 1667 | 1701 | Family assignments used by the active TF page; records and genes counted separately |
| TK1151 motif homology transfer | Active module | TK1151 / BLAST residue-coordinate coverage | 786 | 1941 | Coverage recomputed from residue endpoints; homology candidates are not direct binding validation |
| TK1151 specific TF-motif candidates | Active module | TK1151 / Motif-specific homology | 951 | 3725 | Active source for specific TF-to-motif associations |
| OH1004 LocPro direct localization predictions | Active module | OH1004 / LocPro | 39092 | 195460 | Multiple locations can occur per protein; gene count differs from record count |
| TK1151 LocPro direct localization predictions | Active module | TK1151 / LocPro | 45209 | 226045 | Multiple locations can occur per protein; gene count differs from record count |
| Active coexpression query cache | Active module | dataset-specific / Pearson correlation | — | 216000 | Top 200 per query per dataset; references and units are dataset-specific; sample-local STRG and ambiguous TK1151 StringTie records are excluded |
| Candidate network · coexpression_predicted | Active module | TK1151 official-ID mapped / coexpression_predicted | 20082 | 257434 | Distinct genes within this layer; layers must not be summed as independent interactions. Pending denotes proposed tasks, not completed structural models. |
| Candidate network · domain_compatibility_predicted | Active module | TK1151 official-ID mapped / domain_compatibility_predicted | 3077 | 660897 | Distinct genes within this layer; layers must not be summed as independent interactions. Pending denotes proposed tasks, not completed structural models. |
| Candidate network · orthology_transferred | Active module | TK1151 official-ID mapped / orthology_transferred | 9905 | 140185 | Distinct genes within this layer; layers must not be summed as independent interactions. Pending denotes proposed tasks, not completed structural models. |
| Candidate network · pathway_co_membership | Active module | TK1151 official-ID mapped / pathway_co_membership | 3961 | 20000 | Distinct genes within this layer; layers must not be summed as independent interactions. Pending denotes proposed tasks, not completed structural models. |
| Candidate network · rubber_biosynthesis_co_membership | Active module | TK1151 official-ID mapped / rubber_biosynthesis_co_membership | 99 | 1666 | Distinct genes within this layer; layers must not be summed as independent interactions. Pending denotes proposed tasks, not completed structural models. |
| Candidate network · structure_prediction | Active module · pending | TK1151 official-ID mapped / structure_prediction | 45 | 50 | Distinct genes within this layer; layers must not be summed as independent interactions. Pending denotes proposed tasks, not completed structural models. |
| Candidate network · subcellular_compatibility | Active module | TK1151 official-ID mapped / subcellular_compatibility | 20643 | 416477 | Distinct genes within this layer; layers must not be summed as independent interactions. Pending denotes proposed tasks, not completed structural models. |
| core_gene | Active module | See scope / See scope | — | 39103 | OSU_TarKok_2.0 core genes and aliases |
| id_alias | Active module | See scope / See scope | — | 78206 | Site-wide ID and alias resolver |
| function_description | Active module | See scope / See scope | — | 39103 | GFF and homology-transfer gene descriptions |
| GO_annotation | Active module | See scope / See scope | — | 335702 | Swiss-Prot transferred GO annotation |
| KEGG_annotation | Active module | See scope / See scope | — | 86325 | Swiss-Prot transferred KEGG/KO annotation |
| rubber_biosynthesis | Active module | See scope / See scope | — | 5523 | Natural rubber, MVA/MEP, isoprenoid and terpene candidates |
| expression_atlas | Active module | See scope / See scope | — | 37578919 | Isolated uniform v4: 109 runs, 98,473 fixed TKU loci, separate TPM/FPKM/Coverage; independent OH1004 and publication layers retained; legacy TK1151 values quarantined with no fallback. |
| expression_sample | Active module | See scope / See scope | — | 578 | Sample metadata catalogue; some records lack expression units or complete study design, so inspect each dataset |
| tissue_expression_FPKM | Active module | See scope / See scope | — | 51844 | Gene FPKM from the in-house bred Zhaosu line across 8 tissues with 3 samples each; collection stage and public archive accession were not supplied |
| PMID30514210_expression | Active module | See scope / See scope | — | 46749 | Published supplement contig-level RPKM matrix |
| proteome | Active module | See scope / See scope | — | 9040 | PXD011773 proteome evidence table |
| homology | Active module | See scope / See scope | — | 121540 | Swiss-Prot DIAMOND/BLASTP homolog hits |
| domain_pfam | Active module | See scope / See scope | — | 71718 | Pfam-A hmmscan significant domains |
| subcellular | Auxiliary / historical source | See scope / Source layer | — | 20082 | Auxiliary/historical source layer, not complete coverage of the active module; Swiss-Prot homology-transferred subcellular candidates |
| tf_prediction | Auxiliary / historical source | See scope / Source layer | — | 313 | Auxiliary/historical source layer, not complete coverage of the active module; Conservative Pfam-domain TF family candidates |
| ppi_association | Auxiliary / historical source | See scope / Source layer | — | 500000 | Auxiliary/historical source layer, not complete coverage of the active module; Arabidopsis STRING homology-transferred protein associations |
| coexpression | Auxiliary / historical source | See scope / Source layer | — | 736025 | Auxiliary/historical source layer, not complete coverage of the active module; Precomputed PRJNA745038 coexpression edges |
| reference_gene_catalog | Active module | See scope / See scope | — | 85281 | TK1151 and OH-1004 GFF gene catalogs |
| id_converter_map | Active module | See scope / See scope | — | 84884 | TK1151-OH1004 gene-level RBH ID-mapping records |
| synteny_block | Active module | See scope / See scope | — | 427 | TK1151-OH1004 coordinate-anchor synteny blocks; counted separately from ID-mapping records |
| resequencing_CRA009020 | Active module | See scope / See scope | — | 129 | Metadata, MD5 values, and official GSA links for 129 paired WGS runs in CRA009020; raw FASTQ files are not mirrored locally |
| gene_variants_CRA009020 | Active module | See scope / See scope | — | — | Gene-body PASS SNP/Indel candidates for OH1004 and TK1151 from 129 CRA009020 samples; query by gene, as a live full-table count is not performed and the two references cannot be summed as distinct loci |
Citing Data
When using results from this portal, report the data layer, queried gene or sample IDs, reference version, access date, and portal URL. Also cite the original dataset accession and publication. Original sources are listed under Downloads / Citation. Downloads / Citation
Contact
Yan Zhang (张龑) · yyd19@xaas.ac.cn
Supplementary Data and Software Sources
Sources, original download links, software references, publications and derived-file checksums are organized by category. Unresolved historical checksums, paper links and revisions are explicitly marked.