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Do not attach a later paper merely using OSU_TarKok_2.0 (e.g. Gerbera paper dsag002). Year refers to dataset release, not a journal article. 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Direct files are repository-provided; no bulk genome download was required.", "", "", "", "", "", "", "", "", "" ], [ "Transcriptome project", "PRJDB36270", "Developing ovaries RNA-Seq of sexual and apomixis dandelion plants (PRJCA027669)", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJDB36270", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJDB36270", "", "", "No explicitly associated publication identified", "", "", "", "not_found_in_checked_primary_records", "", "NCBI explicitly cross-links NGDC PRJCA027669. NGDC retrieval failed with RemoteDisconnected; NCBI project contains no publication link. No paper assigned.", "PRJDB36270", 9, 9, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJDB36270", "", "", "", "" ], [ "Transcriptome project", "PRJNA1262623", "Taraxacum kok-saghyz Transcriptome or Gene expression", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1262623", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA1262623", "", "REF003", "Geranyl Diphosphate Synthases GDS 1 and GDS7 Facilitate Natural Rubber Biosynthesis in Taraxacum kok-saghyz Roots", 2025, "10.3390/plants14192980", "https://www.mdpi.com/2223-7747/14/19/2980", "verified_article_reuse_accession_origin_not_established", "", "Article section 4.8 explicitly reuses PRJNA1262623 and cites a previous dataset. This establishes article use, not that the article originally generated all runs.", "PRJNA1262623", 15, 15, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA1262623", "", "", "", "" ], [ "Transcriptome project", "PRJNA1490093", "Transcriptome Analysis of Taraxacum kok-saghyz under Salt Stress", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1490093", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA1490093", "", "", "No explicitly associated publication identified", "", "", "", "not_found_in_checked_primary_records", "", "NCBI BioProject record checked on 2026-10-03. No publication assigned by topic alone.", "PRJNA1490093", 15, 15, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA1490093", "", "", "", "" ], [ "Transcriptome project", "PRJNA361575", "Taraxacum kok-saghyz Raw sequence reads", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA361575", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361575", "", "REF004", "Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs", 2017, "10.1038/s41598-017-09034-2", "https://pmc.ncbi.nlm.nih.gov/articles/PMC5577190/", "verified_article_run_accession_to_bioproject", "", "Article explicitly lists SRR5181661-SRR5181665 and SRR5181667. NCBI SRA SRR5181661 belongs to PRJNA361575; linkage is run-level, not a title-only match.", "PRJNA361575", 6, 6, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA361575", "", "", "", "" ], [ "Transcriptome project", "PRJNA413689", "Identification of gene functions in different accessions.", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA413689", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413689", "", "REF005", "Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants", 2018, "10.1186/s12864-018-5287-4", "https://pmc.ncbi.nlm.nih.gov/articles/PMC6280347/", "verified_bioproject_publication_and_article_accession", "", "NCBI BioProject lists this publication; article Data Availability explicitly states PRJNA413689.", "PRJNA413689", 3, 3, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA413689", "", "", "", "" ], [ "Transcriptome project", "PRJNA539838", "Transcriptome of Taraxacum kok-saghyz Rodin roots from different developmental stages", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA539838", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA539838", "", "REF006", "Genome-Wide Identification and Characterization of the HMGR Gene Family in Taraxacum kok-saghyz Provide Insights into Its Regulation in Response to Ethylene and Methyl Jsamonate Treatments", 2024, "10.3390/plants13182646", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11435204/", "verified_article_reuse_accession_origin_not_established", "", "Article section 4.6 explicitly reuses PRJNA539838. Original developmental-root RNA-seq publication remains unresolved; candidate original study recorded separately.", "PRJNA539838", 16, 16, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA539838", "", "", "", "" ], [ "Transcriptome project", "PRJNA681093", "Chrysanthemum lavandulifolium cultivar:G1 Nanopore sequencing data", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA681093", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA681093", "", "REF007", "The\n Chrysanthemum lavandulifolium\n genome and the molecular mechanism underlying diverse capitulum types", 2022, "10.1093/hr/uhab022", "https://academic.oup.com/hr/article/doi/10.1093/hr/uhab022/6510191", "verified_bioproject_publication_and_article_accession", "", "Project primary organism is Chrysanthemum lavandulifolium; website-used run SRR15099898 is explicitly Taraxacum kok-saghyz and belongs to PRJNA681093, confirmed by NCBI SRA. Project includes Asteraceae comparative RNA-seq. Do not label all project runs as T. kok-saghyz.", "PRJNA681093", 12, 0, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA681093", "", "", "", "" ], [ "Transcriptome project", "PRJNA745038", "Taraxacum kok-saghyz Raw sequence reads", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA745038", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA745038", "", "REF008", "Transcriptome analysis of Taraxacum kok-saghyz reveals the role of exogenous methyl jasmonate in regulating rubber biosynthesis and drought tolerance", 2023, "10.1016/j.gene.2023.147346", "https://pubmed.ncbi.nlm.nih.gov/36898514/", "candidate_article_metadata_verified_accession_link_not_verified", "", "Historical website manifest assigns this DOI, and NCBI project/abstract match MeJA laticifer study, but checked primary records do not expose an explicit accession-paper linkage. Publisher full text is access-limited. Do not present linkage as confirmed.", "PRJNA745038", 9, 9, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA745038", "", "", "", "" ], [ "Transcriptome project", "PRJNA827459", "Taraxacum kok-saghyz Transcriptome or Gene expression", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA827459", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA827459", "", "REF009", "Metabolic and Transcriptomic Analyses Reveal the Effects of Ethephon on Taraxacum kok-saghyz Rodin", 2022, "10.3390/molecules27113548", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9182187/", "verified_article_accession", "", "Article Data Availability explicitly links PRJNA827459; PMID checked in downloaded actual article.", "PRJNA827459", 15, 15, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA827459", "", "", "", "" ], [ "Transcriptome project", "PRJNA918839", "Taraxacum kok-saghyz latex RNA-seq by foliar application of lysophosphatidylethanolamine", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA918839", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA918839", "", "REF010", "Enhanced natural rubber production in rubber dandelion Taraxacum kok-saghyz roots by foliar application of a natural lipid", 2024, "10.1016/j.indcrop.2023.117714", "https://www.sciencedirect.com/science/article/pii/S0926669023014796", "candidate_article_metadata_verified_accession_link_not_verified", "", "Publisher abstract and NCBI project both concern lysophosphatidylethanolamine-treated TKS latex; explicit PRJNA918839 linkage not found in accessible records. Title/DOI metadata verified; project-paper association remains candidate.", "PRJNA918839", 6, 6, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA918839", "", "", "", "" ], [ "Transcriptome project", "PRJNA931633", "Taraxacum kok-saghyz Raw sequence reads", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA931633", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA931633", "", "", "No explicitly associated publication identified", "", "", "", "not_found_in_checked_primary_records", "", "NCBI BioProject record checked on 2026-10-03. No publication assigned by topic alone.", "PRJNA931633", 9, 9, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA931633", "", "", "", "" ], [ "Transcriptome project", "PRJNA985648", "RNA-Seq of Taraxacum koksagyhz PEL-like overexpression line vs. near-isogenic line", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA985648", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA985648", "", "REF011", "Overexpression of a pseudo-etiolated-in-light-like protein in Taraxacum koksaghyz leads to a pale green phenotype and enables transcriptome-based network analysis of photomorphogenesis and isoprenoid biosynthesis", 2023, "10.3389/fpls.2023.1228961", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10569127/", "verified_article_accession", "", "Article Data Availability explicitly links PRJNA985648.", "PRJNA985648", 2, 2, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJNA985648", "", "", "", "" ], [ "Transcriptome project", "PRJDB37370", "The effects of MeOH on TKS growth and rubber production (KAP241469)", "", "", "", "", "https://www.ncbi.nlm.nih.gov/bioproject/PRJDB37370", "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJDB37370", "", "", "No explicitly associated publication identified", "", "", "", "not_found_in_checked_primary_records", "", "Original local RunInfo BioProject field was blank. All four actual DRR records now explicitly link PRJDB37370/DRP016186. No invented BioProject. Sample labels must use verified MeOH/control records rather than previously inferred control labels.", "DRA_unassigned_DRR", 4, 4, "Included runs verified as Taraxacum kok-saghyz; the umbrella PRJNA681093 project is Chrysanthemum, requiring run-level verification", "https://www.ebi.ac.uk/ena/browser/view/PRJDB37370", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_TRANSCRIPTOME_PRJNA413689", "Public RNA-seq project", "", "PRJNA413689", "", "publisher_supplement_xlsx", "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA413689", "https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-018-5287-4/MediaObjects/12864_2018_5287_MOESM1_ESM.xlsx", "Author-reported public resource, separate from website-computed results", "REF005", "Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants", 2018, "10.1186/s12864-018-5287-4", "https://doi.org/10.1186/s12864-018-5287-4", "Original data or author-supplied supplementary material publication", "", "Publisher Data Availability explicitly names PRJNA413689; TSA GFZW00000000 and TksCPT3 MG209739 are distinct related accessions.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_TRANSCRIPTOME_S7", "Author-reported contig-level HR/LR/Y11 RPKM matrix, original article Table S7", "", "PMID30514210:Table S7", "", "publisher_supplement_xlsx", "https://link.springer.com/article/10.1186/s12864-018-5287-4#MOESM1", "https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-018-5287-4/MediaObjects/12864_2018_5287_MOESM1_ESM.xlsx", "Import of author-supplied supplementary matrices with the original contig namespace retained; not formal gene-level quantification", "REF005", "Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants", 2018, "10.1186/s12864-018-5287-4", "https://doi.org/10.1186/s12864-018-5287-4", "Original data or author-supplied supplementary material publication", "", "Table S7 contains expression levels of assembled contigs; supplement workbook is publisher source; does not itself establish TK1151/OH-1004 gene ID correspondence.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_TRANSCRIPTOME_S8", "Author-reported differential expression results, original article Table S8", "", "PMID30514210:Table S8", "", "publisher_supplement_xlsx", "https://link.springer.com/article/10.1186/s12864-018-5287-4#MOESM1", "https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-018-5287-4/MediaObjects/12864_2018_5287_MOESM1_ESM.xlsx", "Import of author-supplied supplementary matrices with the original contig namespace retained; not formal gene-level quantification", "REF005", "Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants", 2018, "10.1186/s12864-018-5287-4", "https://doi.org/10.1186/s12864-018-5287-4", "Original data or author-supplied supplementary material publication", "", "Table S8 contains differential expression genes in original paper; original study results, not website rerun statistics.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_PROTEOME_PXD011773", "Author-processed MaxQuant outputs imported as proteomic evidence", "", "PXD011773", "", "original_ftp", "https://www.ebi.ac.uk/pride/archive/projects/PXD011773", "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/05/PXD011773", "Import of author-processed results; MaxQuant was not rerun by the website", "REF012", "Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology", 2020, "10.1093/jxb/erz512", "https://doi.org/10.1093/jxb/erz512", "Original data or author-supplied supplementary material publication", "", "PRIDE API references DOI erz512 and PubMed 31740929 explicitly. Repository title differs from paper title. PRIDE processing protocol explicitly used MaxQuant 1.5.2.8 with Andromeda and dandelion Lin 2017 sequence database; this is the original study pipeline, not proof that website reran MaxQuant. Official FTP path recorded by ProteomeXchange; HTTPS archive directory HEAD access check returned 200.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_PROTEOME_PXD011773", "Author-processed MaxQuant outputs imported as proteomic evidence", "", "PXD011773", "", "pride_repository", "https://www.ebi.ac.uk/pride/archive/projects/PXD011773", "https://www.ebi.ac.uk/pride/archive/projects/PXD011773", "Import of author-processed results; MaxQuant was not rerun by the website", "REF012", "Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology", 2020, "10.1093/jxb/erz512", "https://doi.org/10.1093/jxb/erz512", "Original data or author-supplied supplementary material publication", "", "PRIDE API references DOI erz512 and PubMed 31740929 explicitly. Repository title differs from paper title. PRIDE processing protocol explicitly used MaxQuant 1.5.2.8 with Andromeda and dandelion Lin 2017 sequence database; this is the original study pipeline, not proof that website reran MaxQuant. Official FTP path recorded by ProteomeXchange; HTTPS archive directory HEAD access check returned 200.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_WGR_CRA009020", "Whole-genome resequencing raw reads from 129 samples", "", "CRA009020", "", "publisher_supplement_xlsx", "https://ngdc.cncb.ac.cn/gsa/browse/CRA009020", "https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-022-09105-3/MediaObjects/12864_2022_9105_MOESM2_ESM.xlsx", "GSA raw reads realigned to two references for variant calling", "REF013", "Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin", 2023, "10.1186/s12864-022-09105-3", "https://doi.org/10.1186/s12864-022-09105-3", "Original data or author-supplied supplementary material publication", "", "Publisher data availability explicitly names CRA009020 for WGR raw reads. Population: 127 F1 offspring and two parents (166 and X51). GSA page fetch failed due transient proxy interruption; raw-run download links not invented.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_VARIANTS_GVM000440", "Author-deposited variants, separate from website realignment and variant calling", "", "GVM000440", "", "publisher_supplement_xlsx", "https://ngdc.cncb.ac.cn/gvm/getProjectDetail?project=GVM000440", "https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-022-09105-3/MediaObjects/12864_2022_9105_MOESM2_ESM.xlsx", "Author-reported public resource, separate from website-computed results", "REF013", "Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin", 2023, "10.1186/s12864-022-09105-3", "https://doi.org/10.1186/s12864-022-09105-3", "Original data or author-supplied supplementary material publication", "", "Publisher Data Availability names GVM000440; current GVM repository supplies genotype CSV and diff_parent_SNP_info.xlsx links. Not an unrelated association panel.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_VARIANTS_GVM000440", "Author-deposited variants, separate from website realignment and variant calling", "", "GVM000440", "", "SNP_matrix_final.genotype.csv", "https://ngdc.cncb.ac.cn/gvm/getProjectDetail?project=GVM000440", "http://download.big.ac.cn/GVM/Taraxacum_kok-saghyz/GVM000440/SNP_matrix_final.genotype.csv", "Author-reported public resource, separate from website-computed results", "REF013", "Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin", 2023, "10.1186/s12864-022-09105-3", "https://doi.org/10.1186/s12864-022-09105-3", "Original data or author-supplied supplementary material publication", "", "Publisher Data Availability names GVM000440; current GVM repository supplies genotype CSV and diff_parent_SNP_info.xlsx links. Not an unrelated association panel.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_VARIANTS_GVM000440", "Author-deposited variants, separate from website realignment and variant calling", "", "GVM000440", "", "diff_parent_SNP_info.xlsx", "https://ngdc.cncb.ac.cn/gvm/getProjectDetail?project=GVM000440", "http://download.big.ac.cn/GVM/Taraxacum_kok-saghyz/GVM000440/diff_parent_SNP_info.xlsx", "Author-reported public resource, separate from website-computed results", "REF013", "Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin", 2023, "10.1186/s12864-022-09105-3", "https://doi.org/10.1186/s12864-022-09105-3", "Original data or author-supplied supplementary material publication", "", "Publisher Data Availability names GVM000440; current GVM repository supplies genotype CSV and diff_parent_SNP_info.xlsx links. Not an unrelated association panel.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "PUB_QTL_PHENOTYPE_SUPPLEMENT", "Author-supplied phenotype and QTL supplementary tables", "", "10.1186/s12864-022-09105-3:Additional file 2", "", "publisher_supplement_xlsx", "https://link.springer.com/article/10.1186/s12864-022-09105-3#MOESM2", "https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12864-022-09105-3/MediaObjects/12864_2022_9105_MOESM2_ESM.xlsx", "Author-reported public resource, separate from website-computed results", "REF013", "Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin", 2023, "10.1186/s12864-022-09105-3", "https://doi.org/10.1186/s12864-022-09105-3", "Original data or author-supplied supplementary material publication", "", "Supplement publisher metadata describes resequencing, bin-marker coordinates, genotypes, QTL gene regions, QTL genetic effects and QTL genotypes. Per-individual phenotype availability has not been checked inside workbook; do not label this entire file a complete raw phenotype matrix.", "", "", "", "", "", "", "", "", "" ], [ "Other omics or author-supplied data", "OWN_TKS_TISSUE_FPKM_202609", "In-house bred Zhaosu line: FPKM for 24 samples from eight tissues", "", "Not deposited in a public repository", "", "tissue_fpkm_original.xlsx (user-supplied original workbook)", "User-provided research data", "http://47.95.224.165/rubber/tissue-expression/files/matrix", "Import of the user-provided matrix with TK1151 ID checks; no public raw-read deposition claimed", "", "No explicitly associated publication identified", "", "", "", "Unpublished or no associated publication supplied", "", "The website provides the user-supplied workbook. No public upstream raw-read accession, associated publication, or processing-software version has been supplied", "", "", "", "", "", "", "", "", "" ], [ "Cross-species literature evidence", "HB_HRT1_ELIFE_2016", "", "", "BAB71776.2;AB061234.3;LC057267", "", "", "https://doi.org/10.7554/eLife.19022", "", "", "REF041", "Identification and reconstitution of the rubber biosynthetic machinery on rubber particles from Hevea brasiliensis", 2016, "10.7554/eLife.19022", "https://doi.org/10.7554/eLife.19022", "Evidence in the original species; not experimental validation in Taraxacum kok-saghyz", "", "DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion", "", "", "", "", "", "HB", "direct functional experiment", "Rubber particles", "" ], [ "Cross-species literature evidence", "HB_CPT_2003", "", "", "AB061234.3;AB064661.2", "", "", "https://doi.org/10.1046/j.1432-1033.2003.03863.x", "", "", "REF042", "Molecular cloning, expression and characterization of cDNA encoding\n cis\n \u2010prenyltransferases from\n Hevea brasiliensis", 2003, "10.1046/j.1432-1033.2003.03863.x", "https://doi.org/10.1046/j.1432-1033.2003.03863.x", "Evidence in the original species; not experimental validation in Taraxacum kok-saghyz", "", "DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion", "", "", "", "", "", "HB", "enzyme experiment", "Latex and recombinant enzyme", "" ], [ "Cross-species literature evidence", "HB_GEO_LATEX_2018", "", "", "GSE101568;PRJNA394848;SRP112717", "", "", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101568", "", "", "", "No explicitly associated publication identified", "", "", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101568", "Evidence in the original species; not experimental validation in Taraxacum kok-saghyz", "", "DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion", "", "", "", "", "", "HB", "RNA-seq processed-result source", "21 latex samples healthy and tapping panel dryness or ethephon conditions", "" ], [ "Cross-species literature evidence", "PA_CPT_CBP_2019", "", "", "MF688933;MF688934;MF688936;MF688938;SRP107961", "", "", "https://pmc.ncbi.nlm.nih.gov/articles/PMC6397875/", "", "", "REF043", "Molecular Studies of the Protein Complexes Involving Cis-Prenyltransferase in Guayule (Parthenium argentatum), an Alternative Rubber-Producing Plant", 2019, "10.3389/fpls.2019.00165", "https://doi.org/10.3389/fpls.2019.00165", "Evidence in the original species; not experimental validation in Taraxacum kok-saghyz", "", "DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion", "", "", "", "", "", "PA", "direct functional experiment", "PI478663 and heterologous systems", "" ], [ "Cross-species literature evidence", "PA_CPT_CBP_2022", "", "", "MF688933;MF688934;MF688936;MF688938", "", "", "https://pmc.ncbi.nlm.nih.gov/articles/PMC8904820/", "", "", "REF044", "Reconstitution of prenyltransferase activity on nanodiscs by components of the rubber synthesis machinery of the Para rubber tree and guayule", 2022, "10.1038/s41598-022-07564-y", "https://doi.org/10.1038/s41598-022-07564-y", "Evidence in the original species; not experimental validation in Taraxacum kok-saghyz", "", "DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion", "", "", "", "", "", "PA", "direct functional experiment", "Cell-free nanodisc reconstruction", "" ], [ "Cross-species literature evidence", "PA_AOS_2019", "", "", "X78166.2", "", "", "https://pmc.ncbi.nlm.nih.gov/articles/PMC6607968/", "", "", "REF045", "Downregulation of a CYP74 Rubber Particle Protein Increases Natural Rubber Production in Parthenium argentatum", 2019, "10.3389/fpls.2019.00760", "https://doi.org/10.3389/fpls.2019.00760", "Evidence in the original species; not experimental validation in Taraxacum kok-saghyz", "", "DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion", "", "", "", "", "", "PA", "direct genetic experiment", "AOS RNAi and overexpression plants", "" ], [ "Cross-species literature evidence", "PA_DROUGHT_2021", "", "", "PRJNA400611", "", "", "https://pmc.ncbi.nlm.nih.gov/articles/PMC8566568/", "", "", "REF046", "RNASeq analysis of drought-stressed guayule reveals the role of gene transcription for modulating rubber, resin, and carbohydrate synthesis", 2021, "10.1038/s41598-021-01026-7", "https://doi.org/10.1038/s41598-021-01026-7", "Evidence in the original species; not experimental validation in Taraxacum kok-saghyz", "", "DOI metadata verified; gene relationships retained from existing manual curation, without independently rechecking every experimental conclusion", "", "", "", "", "", "PA", "RNA-seq processed-result source", "AZ-3 field bark under well-watered and drought conditions", "" ], [ "Cross-species literature evidence", "PA_COLD_2019", "", "", "PRJNA387289;GFTW000000000.1", "", "", "https://pmc.ncbi.nlm.nih.gov/articles/PMC6373111/", "", "", "REF047", "Transcriptome analysis of rubber biosynthesis in guayule (Parthenium argentatum gray)", 2019, "10.1186/s12870-019-1669-2", "https://doi.org/10.1186/s12870-019-1669-2", "Evidence in the original species; 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"CRX553528", "Illumina NovaSeq 6000", "WGS", "PAIRED", "CRR618610_f1.fq.gz", "CRR618610_r2.fq.gz" ], [ "Whole-genome resequencing", "CRR618611", "PRJCA013324", "F1-43", "leaf", "", "", "", "Taraxacum kok-saghyz", "", "https://ngdc.cncb.ac.cn/gsa/browse/CRA009020/CRR618611", "", "", "https://download.cncb.ac.cn/gsa2/CRA009020/CRR618611/CRR618611_f1.fq.gz", "320db3d52a98f68c2600ae7c6a239ba5", 2475704404, "https://download.cncb.ac.cn/gsa2/CRA009020/CRR618611/CRR618611_r2.fq.gz", "63002b24521c6e652c9100ca8048e21a", 2567077039, "REF013", "", "129 runs represent 129 biological samples; alignment to two references does not increase the biological sample count", "SAMC997372", "CRX553529", "Illumina NovaSeq 6000", "WGS", "PAIRED", "CRR618611_f1.fq.gz", "CRR618611_r2.fq.gz" ] ] }, { "name": "S3_Software_and_Databases", "headers": [ "Category", "Resource ID", "Resource name", "Used version or status", "Website application", "Use relationship", "Official URL", "Source-code URL", "Software download URL", "Model download URL", "Reference ID", "Paper title", "Publication year", "DOI", "Paper URL", "Paper relationship", "Limitations" ], "rows": [ [ "Software or website algorithm", "LocPro", "LocPro", "Offline bundle; upstream semantic version not recorded", "Direct localization predictions for representative OH-1004 and TK1151 proteins using ESM2 and PROFEAT features", "Used by the website or supplied as a component", "https://idrblab.org/LocPro/", "https://github.com/idrblab/LocPro", "https://drive.google.com/drive/folders/1twlsmrQRBF7gFMG97tnH0HxzjvExyfsA", "https://drive.google.com/drive/folders/1twlsmrQRBF7gFMG97tnH0HxzjvExyfsA", "REF014", "LocPro: A deep learning-based prediction of protein subcellular localization for promoting multi-directional pharmaceutical research", 2025, "10.1016/j.jpha.2025.101255", "https://doi.org/10.1016/j.jpha.2025.101255", "Software methods publication", "Computational prediction; no microscopy or experimental localization claimed" ], [ "Software or website algorithm", "ESM2", "ESM2", "LocPro-bundled model; checkpoint revision not recorded", "Protein language-model features for LocPro", "Used by the website or supplied as a component", "https://github.com/facebookresearch/esm", "https://github.com/facebookresearch/esm", "https://github.com/facebookresearch/esm", "", "REF015", "Evolutionary-scale prediction of atomic-level protein structure with a language model", 2023, "10.1126/science.ade2574", "https://doi.org/10.1126/science.ade2574", "Software methods publication", "LocPro component, rather than a standalone localization predictor" ], [ "Software or website algorithm", "PROFEAT (sequence features; LocPro reference)", "PROFEAT (sequence features; LocPro reference)", "Feature implementation in the LocPro offline bundle; standalone version not recorded", "Sequence physicochemical features for LocPro", "Used by the website or supplied as a component", "https://doi.org/10.1093/nar/gkr284", "", "", "", "REF016", "Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence", 2011, "10.1093/nar/gkr284", "https://doi.org/10.1093/nar/gkr284", "Software methods publication", "Publication and official software source verified; distinct from similarly named network-feature tools" ], [ "Software or website algorithm", "HISAT2", "HISAT2", "2.2.1", "RNA-seq alignment to the TK1151 reference", "Used by the website or supplied as a component", "https://daehwankimlab.github.io/hisat2/", "https://github.com/DaehwanKimLab/hisat2/releases", "https://github.com/DaehwanKimLab/hisat2/releases", "", "REF017", "Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype", 2019, "10.1038/s41587-019-0201-4", "https://doi.org/10.1038/s41587-019-0201-4", "Software methods publication", "Installed executable version verified; parameters based on retained scripts" ], [ "Software or website algorithm", "StringTie", "StringTie", "3.0.3", "Fixed-model re-quantification of 109 samples using -e -G; coverage, FPKM and TPM", "Used by the website or supplied as a component", "https://ccb.jhu.edu/software/stringtie/", "https://github.com/gpertea/stringtie/releases", "https://github.com/gpertea/stringtie/releases", "", "REF018", "StringTie enables improved reconstruction of a transcriptome from RNA-seq reads", 2015, "10.1038/nbt.3122", "https://doi.org/10.1038/nbt.3122", "Software methods publication", "Not featureCounts integer counts; 98,473 TKU-model genes" ], [ "Software or website algorithm", "SAMtools", "SAMtools", "RNA pipeline: 1.13; variant pipeline: 1.20", "BAM/CRAM processing, sorting and indexing", "Used by the website or supplied as a component", "https://www.htslib.org/", "https://github.com/samtools/samtools/releases", "https://github.com/samtools/samtools/releases", "", "REF019", "Twelve years of SAMtools and BCFtools", 2021, "10.1093/gigascience/giab008", "https://doi.org/10.1093/gigascience/giab008", "Software methods publication", "The two execution environments are recorded separately" ], [ "Software or website algorithm", "SRA Toolkit", "SRA Toolkit", "3.4.1", "Retrieval of public SRA reads with fasterq-dump", "Used by the website or supplied as a component", "https://github.com/ncbi/sra-tools", "https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit", "https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit", "", "", "No explicitly associated publication identified", "", "", "", "Official technical documentation; no specific methods paper", "Actual retained archive-download paths preserved" ], [ "Software or website algorithm", "BLAST+", "BLAST+", "2.12.0+", "Public BLAST searches, historical-ID sequence mapping and homology alignment", "Used by the website or supplied as a component", "https://blast.ncbi.nlm.nih.gov/", "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/", "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/", "", "REF020", "BLAST+: architecture and applications", 2009, "10.1186/1471-2105-10-421", "https://doi.org/10.1186/1471-2105-10-421", "Software methods publication", "Short-sequence alignment parameters controlled by the website" ], [ "Software or website algorithm", "HMMER", "HMMER", "3.3.2", "Pfam-A protein-domain scanning", "Used by the website or supplied as a component", "https://hmmer.org/", "https://hmmer.org/download.html", "https://hmmer.org/download.html", "", "REF021", "Accelerated Profile HMM Searches", 2011, "10.1371/journal.pcbi.1002195", "https://doi.org/10.1371/journal.pcbi.1002195", "Software methods publication", "Domain hits constitute computational evidence" ], [ "Software or website algorithm", "FIMO", "FIMO", "5.4.1", "Retained PlantTFDB/JASPAR motif scans of promoters", "Used by the website or supplied as a component", "https://meme-suite.org/meme/doc/fimo.html", "https://meme-suite.org/meme/doc/download.html", "https://meme-suite.org/meme/doc/download.html", "", "REF022", "FIMO: scanning for occurrences of a given motif", 2011, "10.1093/bioinformatics/btr064", "https://doi.org/10.1093/bioinformatics/btr064", "Software methods publication", "Cached scans use 2500-bp promoters; current on-demand 4000-bp scans use the site-developed implementation" ], [ "Software or website algorithm", "DIAMOND", "DIAMOND", "2.2.4", "Protein homology, reference-version mapping and Swiss-Prot annotation transfer", "Used by the website or supplied as a component", "https://github.com/bbuchfink/diamond", "https://github.com/bbuchfink/diamond/releases", "https://github.com/bbuchfink/diamond/releases", "", "REF023", "Sensitive protein alignments at tree-of-life scale using DIAMOND", 2021, "10.1038/s41592-021-01101-x", "https://doi.org/10.1038/s41592-021-01101-x", "Software methods publication", "Homology-based annotation does not establish experimental validation" ], [ "Software or website algorithm", "JCVI", "JCVI", "1.6.6", "Synteny and ortholog blocks between TK1151 and OH-1004", "Used by the website or supplied as a component", "https://github.com/tanghaibao/jcvi", "https://pypi.org/project/jcvi/", "https://pypi.org/project/jcvi/", "", "REF024", "JCVI: A versatile toolkit for comparative genomics analysis", 2024, "10.1002/imt2.211", "https://doi.org/10.1002/imt2.211", "Software methods publication", "Retained methods: -cscore 0.70 and diamond_blastp" ], [ "Software or website algorithm", "minimap2", "minimap2", "2.30-r1287", "Short-read realignment of CRA009020 using -ax sr --secondary=no", "Used by the website or supplied as a component", "https://github.com/lh3/minimap2", "https://github.com/lh3/minimap2/releases", "https://github.com/lh3/minimap2/releases", "", "REF025", "Minimap2: pairwise alignment for nucleotide sequences", 2018, "10.1093/bioinformatics/bty191", "https://doi.org/10.1093/bioinformatics/bty191", "Software methods publication", "Actual use of this tool verified; obsolete BWA preparation directories are not treated as the executed method" ], [ "Software or website algorithm", "bcftools", "bcftools", "1.20", "Variant mpileup, calling and filtering", "Used by the website or supplied as a component", "https://www.htslib.org/", "https://github.com/samtools/bcftools/releases", "https://github.com/samtools/bcftools/releases", "", "REF019", "Twelve years of SAMtools and BCFtools", 2021, "10.1093/gigascience/giab008", "https://doi.org/10.1093/gigascience/giab008", "Software methods publication", "Diploid assumption; QUAL>=30, DP>=10 and MQ/BQ>=20" ], [ "Software or website algorithm", "KMC3", "KMC3", "3.2.1", "Resequencing k-mer counting", "Used by the website or supplied as a component", "https://github.com/refresh-bio/KMC", "https://github.com/refresh-bio/KMC/releases", "https://github.com/refresh-bio/KMC/releases", "", "REF026", "KMC 3: counting and manipulating k-mer statistics", 2017, "10.1093/bioinformatics/btx304", "https://doi.org/10.1093/bioinformatics/btx304", "Software methods publication", "Installed executable version verified" ], [ "Software or website algorithm", "MaxQuant (upstream source analysis)", "MaxQuant (upstream source analysis)", "Author-processed outputs retained by the website; version unconfirmed", "Upstream proteomic processing of PXD011773 by the original authors", "Used by the upstream authors", "https://www.maxquant.org/maxquant/", "https://www.maxquant.org/archive/maxquant", "https://www.maxquant.org/archive/maxquant", "", "REF027", "MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification", 2008, "10.1038/nbt.1511", "https://doi.org/10.1038/nbt.1511", "Software methods publication", "Used by upstream authors; the website imports results and does not claim reanalysis of raw mass-spectrometry data" ], [ "Software or website algorithm", "featureCounts", "featureCounts", "2.0.3", "Retained independent integer-count data from nine MeJA samples and historical coexpression input", "Used by the website or supplied as a component", "https://subread.sourceforge.net/", "https://sourceforge.net/projects/subread/files/", "https://sourceforge.net/projects/subread/files/", "", "REF028", "featureCounts: an efficient general purpose program for assigning sequence reads to genomic features", 2014, "10.1093/bioinformatics/btt656", "https://doi.org/10.1093/bioinformatics/btt656", "Software methods publication", "Does not justify describing uniform-v4 coverage as integer counts" ], [ "Software or website algorithm", "JBrowse 2", "JBrowse 2", "Major version 2; exact installed build not documented", "Genome browser and source-model tracks", "Used by the website or supplied as a component", "https://jbrowse.org/jb2/", "https://github.com/GMOD/jbrowse-components/releases", "https://github.com/GMOD/jbrowse-components/releases", "", "REF029", "JBrowse 2: a modular genome browser with views of synteny and structural variation", 2023, "10.1186/s13059-023-02914-z", "https://doi.org/10.1186/s13059-023-02914-z", "Software methods publication", "Only the major version is confirmed; minor versions are not inferred" ], [ "Software or website algorithm", "Python", "Python", "3.10.12 (retained methods record)", "Database import, website backend and site-developed algorithms", "Used by the website or supplied as a component", "https://www.python.org/", "https://www.python.org/downloads/", "https://www.python.org/downloads/", "", "", "No explicitly associated publication identified", "", "", "", "Official technical documentation; no specific methods paper", "Historical methods record; not a claim that all current environments use the same version" ], [ "Software or website algorithm", "Flask", "Flask", "Not recorded", "Website backend", "Used by the website or supplied as a component", "https://flask.palletsprojects.com/", "https://flask.palletsprojects.com/en/stable/installation/", "https://flask.palletsprojects.com/en/stable/installation/", "", "", "No explicitly associated publication identified", "", "", "", "Official technical documentation; no specific methods paper", "Official documentation; no specific software publication" ], [ "Software or website algorithm", "Jinja2", "Jinja2", "Not recorded", "Page-template rendering", "Used by the website or supplied as a component", "https://jinja.palletsprojects.com/", "https://jinja.palletsprojects.com/en/stable/intro/", "https://jinja.palletsprojects.com/en/stable/intro/", "", "", "No explicitly associated publication identified", "", "", "", "Official technical documentation; no specific methods paper", "Official documentation; no specific software publication" ], [ "Software or website algorithm", "SQLite", "SQLite", "Not recorded", "Relational database storage", "Used by the website or supplied as a component", "https://sqlite.org/", "https://sqlite.org/download.html", "https://sqlite.org/download.html", "", "", "No explicitly associated publication identified", "", "", "", "Official technical documentation; no specific methods paper", "Database engine; no specific software publication" ], [ "Software or website algorithm", "NumPy", "NumPy", "Exact version not recorded", "LocPro feature and array processing", "Used by the website or supplied as a component", "https://numpy.org/", "https://github.com/numpy/numpy", "https://github.com/numpy/numpy/releases", "", "REF030", "Array programming with NumPy", 2020, "10.1038/s41586-020-2649-2", "https://doi.org/10.1038/s41586-020-2649-2", "Software methods publication", "Computational dependency; not a separate localization method" ], [ "Software or website algorithm", "pandas", "pandas", "2.0.3 in the LocPro environment (retained methods record)", "LocPro feature-table and result-table processing", "Used by the website or supplied as a component", "https://pandas.pydata.org/", "https://github.com/pandas-dev/pandas", "https://github.com/pandas-dev/pandas/releases", "", "REF031", "Data Structures for Statistical Computing in Python", 2010, "10.25080/Majora-92bf1922-00a", "https://doi.org/10.25080/Majora-92bf1922-00a", "Software methods publication", "Data-processing dependency" ], [ "Software or website algorithm", "PyTorch", "PyTorch", "2.4.1+cpu in the LocPro environment (retained methods record)", "LocPro/ESM2 inference", "Used by the website or supplied as a component", "https://pytorch.org/", "https://github.com/pytorch/pytorch", "https://pytorch.org/get-started/locally/", "", "REF032", "PyTorch: An Imperative Style, High-Performance Deep Learning Library", 2019, "", "https://proceedings.neurips.cc/paper/2019/hash/bdbca288fee7f92f2bfa9f7012727740-Abstract.html", "Official technical documentation; no specific methods paper", "No DOI confirmed for the framework paper; official NeurIPS publication URL retained" ], [ "Software or website algorithm", "Gunicorn", "Gunicorn", "Current system service; exact version not recorded", "Python web-service worker processes", "Used by the website or supplied as a component", "https://gunicorn.org/", "https://github.com/benoitc/gunicorn", "https://github.com/benoitc/gunicorn", "", "", "No explicitly associated publication identified", "", "", "", "Official technical documentation; no specific methods paper", "Does not provide independent biological evidence for algorithmic results" ], [ "Software or website algorithm", "nginx", "nginx", "Software confirmed by the public HTTP response; exact build not recorded", "Public reverse proxy and static-resource serving", "Used by the website or supplied as a component", "https://nginx.org/", "https://nginx.org/en/download.html", "https://nginx.org/en/download.html", "", "", "No explicitly associated publication identified", "", "", "", "Official technical documentation; no specific methods paper", "Website infrastructure; official documentation, with no specific software publication" ], [ "Software or website algorithm", "SITE_QPCR", "Website qPCR primer design", "Website application source SHA256 4fa08ff3adc7b29f8f6c71b018b4d5757ef5ff83031e4067c490cc1ed68bf00a", "rubber_qpcr.py: sequence enumeration, melting-temperature and GC filtering, and transcript/genome specificity checks", "Site-developed algorithm", "http://47.95.224.165/rubber/tools", "Site-developed; no independent public source-code repository released", "No standalone download package released", "", "", "No explicitly associated publication identified", "", "", "", "No independent software publication", "Computational design suggestions; no use of Primer3 or CRISPOR, or experimental validation, claimed" ], [ "Software or website algorithm", "SITE_CRISPR", "Website CRISPR guide design", "Website application source SHA256 4fa08ff3adc7b29f8f6c71b018b4d5757ef5ff83031e4067c490cc1ed68bf00a", "rubber_crispr.py: candidate SpCas9 NGG sites and reference-sequence off-target scanning", "Site-developed algorithm", "http://47.95.224.165/rubber/tools", "Site-developed; no independent public source-code repository released", "No standalone download package released", "", "", "No explicitly associated publication identified", "", "", "", "No independent software publication", "Computational design suggestions; no use of Primer3 or CRISPOR, or experimental validation, claimed" ], [ "Software or website algorithm", "SITE_TFBS_SCAN", "Website on-demand TFBS scanning", "Website application source SHA256 4fa08ff3adc7b29f8f6c71b018b4d5757ef5ff83031e4067c490cc1ed68bf00a", "rubber_app.py: motif probability-matrix scanning of 4000-bp upstream regions or user-submitted sequences", "Site-developed algorithm", "http://47.95.224.165/rubber/tools", "Site-developed; no independent public source-code repository released", "No standalone download package released", "", "", "No explicitly associated publication identified", "", "", "", "No independent software publication", "Computational design suggestions; no use of Primer3 or CRISPOR, or experimental validation, claimed" ], [ "Software or website algorithm", "SITE_SEQUENCE_TOOLS", "Website sequence and homologous-arm tools", "Website application source SHA256 4fa08ff3adc7b29f8f6c71b018b4d5757ef5ff83031e4067c490cc1ed68bf00a", "rubber_sequence.py and website tools: translation, sequence processing and homologous-arm assistance", "Site-developed algorithm", "http://47.95.224.165/rubber/tools", "Site-developed; no independent public source-code repository released", "No standalone download package released", "", "", "No explicitly associated publication identified", "", "", "", "No independent software publication", "Computational design suggestions; no use of Primer3 or CRISPOR, or experimental validation, claimed" ], [ "Reference database", "UniProtKB / Swiss-Prot", "UniProtKB / Swiss-Prot", "Reviewed Swiss-Prot; exact historical download release not recorded", "Homology-based transfer of functional annotations, GO terms and KEGG gene cross-references", "", "https://www.uniprot.org/", "", "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz", "", "REF033", "UniProt: the Universal Protein Knowledgebase in 2025", 2025, "10.1093/nar/gkae1010", "https://doi.org/10.1093/nar/gkae1010", "Database resource publication", "Homology-based transfer; original GO evidence codes retained, without implying experiments on the target gene" ], [ "Reference database", "Pfam (2021 publication)", "Pfam (2021 publication)", "Pfam-A; exact historical database release not recorded", "HMMER domains and candidate transcription-factor families", "", "https://www.ebi.ac.uk/interpro/entry/pfam/", "", "https://www.ebi.ac.uk/interpro/download/Pfam/", "", "REF034", "Pfam: The protein families database in 2021", 2021, "10.1093/nar/gkaa913", "https://doi.org/10.1093/nar/gkaa913", "Database resource publication", "Actual Pfam input cited; no InterProScan execution claimed" ], [ "Reference database", "STRING v12.0", "STRING v12.0", "12.0 (actual source manifest)", "Homology-based transfer of Arabidopsis associations", "", "https://version-12-0.string-db.org/", "", "https://stringdb-static.org/download/protein.links.v12.0/3702.protein.links.v12.0.txt.gz", "", "REF035", "The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest", 2023, "10.1093/nar/gkac1000", "https://doi.org/10.1093/nar/gkac1000", "Database resource publication", "Cross-species functional associations; not physical interactions demonstrated in Taraxacum kok-saghyz" ], [ "Reference database", "JASPAR 2024 (conditional on actual release)", "JASPAR 2024 (conditional on actual release)", "JASPAR2024 CORE plants non-redundant (retained source record)", "Plant motifs and candidate transcription-factor binding sites", "", "https://jaspar.elixir.no/", "", "https://jaspar.genereg.net/downloads/", "", "REF036", "JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles", 2024, "10.1093/nar/gkad1059", "https://doi.org/10.1093/nar/gkad1059", "Database resource publication", "Candidate sites; no direct binding demonstrated" ], [ "Reference database", "PlantTFDB", "PlantTFDB", "5.0 (download endpoint in retained motif-transfer scripts)", "Experimental donor motifs transferred to TK1151 through homology/reciprocal best hits", "", "https://planttfdb.gao-lab.org/", "", "https://planttfdb.gao-lab.org/download/motif/PlantTFDB_TF_binding_motifs_from_experiments.gz", "", "REF037", "PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants", 2017, "10.1093/nar/gkw982", "https://doi.org/10.1093/nar/gkw982", "Database resource publication", "Experimental motifs from donor species are not experimental evidence for the target transcription factor" ], [ "Reference database", "3did", "3did", "3did_flat.gz; historical release date not recorded", "Pfam-domain contact compatibility support", "", "https://3did.irbbarcelona.org/", "", "https://3did.irbbarcelona.org/", "", "REF038", "3did: a catalog of domain-based interactions of known three-dimensional structure", 2014, "10.1093/nar/gkt887", "https://doi.org/10.1093/nar/gkt887", "Database resource publication", "Domain-contact support; no website AlphaFold or molecular-docking result claimed" ], [ "Reference database", "Gene Ontology (original)", "Gene Ontology (original)", "GO identifiers, namespaces and taxon constraints retained; historical ontology revision not recorded", "GO terms and taxonomic-incompatibility screening", "", "https://geneontology.org/docs/go-citation-policy/", "", "https://geneontology.org/docs/download-ontology/", "", "REF039", "Gene Ontology: tool for the unification of biology", 2000, "10.1038/75556", "https://doi.org/10.1038/75556", "Database resource publication", "Annotation summaries provided; enrichment significance testing is not provided" ], [ "Reference database", "KEGG", "KEGG", "Swiss-Prot DAT KEGG gene cross-references; no native KO annotation generated", "KEGG gene cross-references and candidate-pathway support", "", "https://www.kegg.jp/", "", "https://www.kegg.jp/kegg/rest/keggapi.html", "", "REF040", "KEGG: biological systems database as a model of the real world", 2025, "10.1093/nar/gkae909", "https://doi.org/10.1093/nar/gkae909", "Database resource publication", "Gene cross-references are not complete KO annotations or pathway enrichment; the actual upstream source is UniProt DAT" ] ] }, { "name": "S4_Website_Data_Provenance", "headers": [ "Category", "Record ID", "Filename", "Description", "Upstream sources", "Method or definition", "Public page URL", "File bytes", "Evidence layer", "Verification date", "Limitations", "Historical initial checksum", "Retained input SHA256", "Published output SHA256", "Checksum algorithm", "Hash record date", "Source URL", "Checksum scope", "Status", "Data type", "Metadata source", "Expression value rows", "Related tables" ], 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