← All .science files
pmid:31238980
Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma.
Hong-Gang Xiong · Hao Li · Yao Xiao · Qi-Chao Yang · Lei-Lei Yang · Lei Chen · Lin-Lin Bu · Wen-Feng Zhang · Jia-Li Zhang · Zhi-Jun Sun
Journal of experimental & clinical cancer research : CR · 2019 doi:10.1186/s13046-019-1254-4
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 10 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 6 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 12 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 39 items
[0] array · 4 items
[1] array · 2 items
[2] array · 1 item
[3] array · 5 items
[4] array · 5 items
[5] array · 1 item
[6] array · 5 items
[7] array · 5 items
[8] array · 1 item
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 1 item
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 1 item
[19] array · 5 items
[20] array · 5 items
[21] array · 5 items
[22] array · 1 item
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 1 item
[27] array · 5 items
[28] array · 5 items
[29] array · 5 items
[30] array · 1 item
[31] array · 5 items
[32] array · 5 items
[33] array · 5 items
[34] array · 5 items
[35] array · 1 item
[36] array · 5 items
[37] array · 5 items
[38] array · 5 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 15 items
[0] array · 3 items
[1] array · 6 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 23 items
[0] array · 4 items
[1] array · 2 items
[2] array · 1 item
[3] array · 5 items
[4] array · 5 items
[5] array · 1 item
[6] array · 5 items
[7] array · 5 items
[8] array · 1 item
[9] array · 5 items
[10] array · 5 items
[11] array · 1 item
[12] array · 5 items
[13] array · 5 items
[14] array · 1 item
[15] array · 5 items
[16] array · 5 items
[17] array · 1 item
[18] array · 5 items
[19] array · 5 items
[20] array · 1 item
[21] array · 5 items
[22] array · 5 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 10 items
[0] array · 3 items
[1] array · 6 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
gaps array · 2 items
analysis object · 4 fields
methods array · 9 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
evidence object · 3 fields
[1] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[4] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[5] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[6] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[7] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[8] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 6 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 7 items
assays array · 6 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[3] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[4] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[5] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31238980", "kind": "science-record", "revision": 8, "content_hash": "sha256:f621e7b02a4be87d13026ac3be37da801d25725043c986ef56c26038d3bdada3", "created_at": "2026-11-01T15:40:46Z", "updated_at": "2026-11-01T22:44:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma.", "doi": "10.1186/s13046-019-1254-4", "pmid": "31238980", "authors": ["Hong-Gang Xiong", "Hao Li", "Yao Xiao", "Qi-Chao Yang", "Lei-Lei Yang", "Lei Chen", "Lin-Lin Bu", "Wen-Feng Zhang", "Jia-Li Zhang", "Zhi-Jun Sun"], "journal": "Journal of experimental & clinical cancer research : CR", "year": 2019, "abstract": "BACKGROUND: Partial epithelial mesenchymal transition (p-EMT) was found to play a potential role in the initial stage of metastasis in human head and neck squamous cell carcinoma (HNSCC). Some long noncoding RNAs (lncRNAs) have been reported to function as promoters or inhibitors of cancer metastasis. This study aimed to identify p-EMT-related lncRNAs in HNSCC.\nMETHODS: Differentially expressed lncRNAs (DE-lncRNAs) and mRNAs (DEGs) in HNSCC obtained from The Cancer Genome Atlas (TCGA) were screened out by using the \"edgeR\" package. DE-lncRNAs in the Oral squamous cell carcinoma (OSCC) lncRNA microarray dataset GSE84805 were screened out by using the \"limma\" package. Slug-related lncRNAs were determined by Pearson correlation analysis (|Pearson correlation coefficient| ≥ 0.4, p < 0.01) based on TCGA. Survival analysis were performed for the overlapping DE-lncRNAs by using the \"Survival\" package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to predict the potential functions of MYOSLID. RT-qPCR and In Site Hybridization (ISH) were used to explore the MYOSLID expression and its clinical significance in HNSCC specimens. Immunohistochemical staining, siRNA, wound healing assay, transwell assay, and western blot were used to explore the biological function and potential molecular mechanisms.\nRESULTS: MYOSLID was identified as a Slug-related lncRNA and with prognostic value among the 9 overlapping DE-lncRNAs. GO and KEGG analyses revealed that MYOSLID was closely related to important biological processes and pathways that regulate cancer metastasis. The results of univariate and multivariate Cox regression analysis based on TCGA and HNSCC tissue microarray data suggested MYOSLID was an independent prognostic factor. MYOSLID expression in HNSCC was closely correlated with Slug, PDPN and LAMB3. The knockdown of MYOSLID in OSCC cell line significantly inhibited cell migration and invasion compared to those in the control cells. In addition, the knockdown of MYOSLID significantly reduced Slug, PDPN and LAMB3 expression levels. However, the knockdown of MYOSLID had no effect on the expression levels of the EMT biomarkers E-cadherin and Vimentin.\nCONCLUSIONS: Our study revealed that MYOSLID expression was closely related to the p-EMT program in HNSCC, and it might be a new predictive biomarker for aggressive HNSCC.", "claims": [{"id": "claim-method", "statement": "Differentially expressed mRNAs and lncRNAs were identified in HNSCC tissues in comparison with normal tissue with data obtained from the TCGA database using the “edgeR” package in R. Differentially expressed lncRNAs were identified in HNSCC tissues in comparison with normal tissues from data obtained from GEO with the accession number GSE84805 using the “limma” package in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31238980", "locator": "sections[5] \"Identification of DEGs, DE-lncRNAs and the generation of a Venn diagram\" paragraph 2", "quote": "Differentially expressed mRNAs and lncRNAs were identified in HNSCC tissues in comparison with normal tissue with data obtained from the TCGA database using the “edgeR” package in R. Differentially expressed lncRNAs were identified in HNSCC tissues in comparison with normal tissues from data obtained from GEO with the accession number GSE84805 using the “limma” package in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data and materials supporting the conclusions were included in the main paper.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31238980", "locator": "sections[37] \"notes\" paragraph 1", "quote": "All the data and materials supporting the conclusions were included in the main paper."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31238980"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE84805"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE84805"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31238980", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13046-019-1254-4", "sha256": "sha256:c25b9e064034080b0850357bc5253a63550fd96ac77df5662f4dcb83f9107e1c", "bytes": 46531, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13046-019-1254-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6593600", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84805", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84805", "version": null, "note": "All the data and materials supporting the conclusions were included in the main paper.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data and materials supporting the conclusions were included in the main paper.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2251632", "GSM2251633", "GSM2251634", "GSM2251635", "GSM2251636", "GSM2251637", "GSM2251638", "GSM2251639", "GSM2251640", "GSM2251641", "GSM2251642", "GSM2251643"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "16956", "taxon": "Homo sapiens", "title": "Aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31238980:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d5b92b3dae260f270bab34faea9b2599caf8e9821ea85000ff57b9ff0f280f77", "bytes": 1298, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#Tab1", "version": null, "note": "Relationship between MYOSLID expression and clinicopathological Characteristics of HNSCC patients based on TCGA (n = 499)", "structure": {"pmcid": "PMC6593600", "section_index": 21, "section_title": "Survival analysis screening and the assessment of the clinical significance of MYOSLID expression in HNSCC based on the TCGA database", "row_count": 39, "column_count": 5}, "table": {"label": "Table 1", "caption": "Relationship between MYOSLID expression and clinicopathological Characteristics of HNSCC patients based on TCGA (n = 499)", "rows": [["Characteristics", "MYOSLID", "χ2", "p value"], ["Low expression (n = 360)", "High expression (n = 139)"], ["Age(y)"], ["< 60", "149", "72", "4.404", "0.036*"], ["≥ 60", "211", "67", "", ""], ["Gender"], ["Male", "257", "109", "2.534", "0.111"], ["Female", "103", "30", "", ""], ["Race"], ["White", "312", "115", "1.323", "0.724"], ["Black", "31", "16", "", ""], ["Asian", "7", "3", "", ""], ["unknow", "10", "5", "", ""], ["Grade"], ["G1/2", "256", "104", "1.196", "0.754"], ["G3/4", "89", "31", "", ""], ["GX", "13", "3", "", ""], ["unknow", "2", "1", "", ""], ["Stage"], ["Stage I/II", "70", "26", "7.272", "0.026*"], ["Stage III/IV", "232", "103", "", ""], ["unknow", "58", "10", "", ""], ["T"], ["T1 + T2", "166", "49", "8.69", "0.013*"], ["T3 + T4", "175", "87", "", ""], ["unknow", "19", "3", "", ""], ["N"], ["Yes", "167", "69", "1.726", "0.422"], ["No", "173", "66", "", ""], ["unknow", "20", "4", "", ""], ["M"], ["M0", "134", "51", "1.227", "0.747"], ["M1", "1", "0", "", ""], ["Mx", "41", "20", "", ""], ["unknow", "184", "68", "", ""], ["HPV status"], ["Positive", "29", "1", "9.634", "0.002*"], ["Negative", "49", "23", "", ""], ["unknow", "282", "115", "", ""]], "row_count": 39, "column_count": 5, "numeric_cells": 81, "header_rows": 2, "locator": "section[21]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31238980:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c5842a461bb231b8ee2975c16f89edbe4db270b6e4c64d41a96e2c940c26b61f", "bytes": 1216, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[2]#Tab2", "version": null, "note": "Univariate and multivariate Cox regression analysis for OS in HNSCC patient based on TCGA(n = 499)", "structure": {"pmcid": "PMC6593600", "section_index": 21, "section_title": "Survival analysis screening and the assessment of the clinical significance of MYOSLID expression in HNSCC based on the TCGA database", "row_count": 15, "column_count": 7}, "table": {"label": "Table 2", "caption": "Univariate and multivariate Cox regression analysis for OS in HNSCC patient based on TCGA(n = 499)", "rows": [["Variable", "Univariate analysis", "Multivariate analysis"], ["p", "HR", "95% CI", "p", "HR", "95% CI"], ["MYOSLID", "0.041", "1.370", "1.012–1.853", "0.025", "1.429", "1.045–1.953"], ["Age", "0.088", "1.287", "0.963–1.720", "0.118", "1.272", "0.941–1.719"], ["Gender", "0.034", "1.381", "1.024–1.862", "0.048", "1.372", "1.003–1.876"], ["Race", "0.240", "1.218", "0.876–1.694", "0.808", "", ""], ["Race (1)", "", "", "", "0.846", "1.155", "0.271–4.913"], ["Race (2)", "", "", "", "0.892", "1.083", "0.343–3.419"], ["Race (3)", "", "", "", "0.608", "1.381", "0.403–4.734"], ["Grade", "0.872", "0.977", "0.738–1.293", "0.679", "0.941", "0.705–1.255"], ["Stage", "0.127", "1.175", "0.955–1.445", "0.115", "0.760", "0.541–1.069"], ["T", "0.005", "1.454", "1.118–1.891", "0.004", "1.859", "1.224–2.823"], ["N", "0.027", "1.300", "1.030–1.640", "0.001", "1.543", "1.196–1.990"], ["M", "0.039", "1.121", "1.006–1.249", "0.179", "1.080", "0.965–1.209"], ["HPV", "0.024", "1.362", "1.041–1.782", "0.021", "1.374", "1.050–1.798"]], "row_count": 15, "column_count": 7, "numeric_cells": 72, "header_rows": 2, "locator": "section[21]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:31238980:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f45ef80eb77cc6ad4fe1acd2bc0484c15fe9c479f9b65c0b01c5274533d5589d", "bytes": 837, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[1]#Tab3", "version": null, "note": "MYOSLID expression and clinicopathological Characteristics of patients with HNSCC(n = 90)", "structure": {"pmcid": "PMC6593600", "section_index": 24, "section_title": "Evaluation of the clinical significance of MYOSLID expression in a human HNSCC tissue microarray", "row_count": 23, "column_count": 5}, "table": {"label": "Table 3", "caption": "MYOSLID expression and clinicopathological Characteristics of patients with HNSCC(n = 90)", "rows": [["Characteristics", "MYOSLID", "χ2", "p value"], ["Low expression (n = 46)", "High expression (n = 44)"], ["Age(y)"], ["< 60", "23", "26", "0.749", "0.387"], ["≥ 60", "23", "18", "", ""], ["Gender"], ["Male", "41", "34", "2.277", "0.131"], ["Female", "5", "10", "", ""], ["Smoke"], ["Yes", "27", "20", "1.580", "0.209"], ["No", "19", "24", "", ""], ["Drink"], ["Yes", "23", "21", "0.046", "0.829"], ["No", "23", "23", "", ""], ["Stage"], ["Stage I/II", "39", "38", "0.045", "0.831"], ["Stage III/IV", "7", "6", "", ""], ["T"], ["T1 + T2", "27", "28", "2.985", "0.394"], ["T3 + T4", "19", "16", "", ""], ["N"], ["Yes", "30", "25", "0.472", "0.492"], ["No", "16", "18", "", ""]], "row_count": 23, "column_count": 5, "numeric_cells": 47, "header_rows": 2, "locator": "section[24]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:31238980:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e52f7f52a64e68dd80165f1d4faeab56fc2df8273d090c982ccd8d56dcf9b859", "bytes": 918, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[2]#Tab4", "version": null, "note": "Univariate and multivariate Cox regression analysis for OS in HNSCC patients (n = 90)", "structure": {"pmcid": "PMC6593600", "section_index": 24, "section_title": "Evaluation of the clinical significance of MYOSLID expression in a human HNSCC tissue microarray", "row_count": 10, "column_count": 7}, "table": {"label": "Table 4", "caption": "Univariate and multivariate Cox regression analysis for OS in HNSCC patients (n = 90)", "rows": [["Variable", "Univariate analysis", "Multivariate analysis"], ["p", "HR", "95% CI", "p", "HR", "95% CI"], ["MYOSLID", "0.033", "2.096", "1.061–4.140", "0.030", "2.223", "1.079–4.580"], ["Age", "0.128", "1.667", "0.863–3.219", "0.056", "2.029", "0.982–4.195"], ["Gender", "0.130", "1.793", "0.843–3.816", "0.799", "1.146", "0.403–3.252"], ["Smoke", "0.985", "1.006", "0.523–1.936", "0.705", "1.189", "0.486–2.905"], ["Drink", "0.193", "0.641", "0.328–1.253", "0.228", "0.608", "0.271–1.366"], ["Stage", "0.265", "1.601", "0.700–3.659", "0.333", "1.575", "0.628–3.950"], ["T", "0.059", "1.426", "0.987–2.060", "0.101", "1.469", "0.928–2.324"], ["N", "0.002", "2.981", "1.513–5.875", "0.021", "2.353", "1.136–4.877"]], "row_count": 10, "column_count": 7, "numeric_cells": 50, "header_rows": 2, "locator": "section[24]/table-wrap[2]#Tab4"}}], "gaps": ["asset:data:geo:GSE84805 not downloaded", "asset:data:geo:GSE84805 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed mRNAs and lncRNAs were identified in HNSCC tissues in comparison with normal tissue with data obtained from the TCGA database using the “edgeR” package in R. Differentially expressed lncRNAs were identified in HNSCC tissues in comparison with normal tissues from data obtained from GEO with the accession number GSE84805 using the “limma” package in R."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-4", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-5", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-6", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-7", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.7, "band": "medium", "quote": "Pearson correlation"}}, {"id": "method-8", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-9", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: edger."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE84805"], "resolved_accessions": ["GSE84805"], "statements": ["All the data and materials supporting the conclusions were included in the main paper."], "basis": "The paper names GSE84805 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:31238980", "data:geo:GSE84805", "asset:table:pmid:31238980:1", "asset:table:pmid:31238980:2", "asset:table:pmid:31238980:3", "asset:table:pmid:31238980:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE84805"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 39123, "completion_tokens": 1238, "cached_tokens": 13056}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31238980", "type": "paper", "label": "pmid:31238980"}, {"id": "source:pmid:31238980", "type": "manuscript", "label": "PMID 31238980 full text"}, {"id": "data:geo:GSE84805", "type": "dataset", "label": "GEO GSE84805"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31238980", "type": "paper", "label": "pmid:31238980"}, {"id": "source:pmid:31238980", "type": "manuscript", "label": "PMID 31238980 full text"}, {"id": "data:geo:GSE84805", "type": "dataset", "label": "GEO GSE84805"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31238980", "type": "extraction", "used": ["source:pmid:31238980"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE84805", "type": "accession_resolution", "used": ["data:geo:GSE84805"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:31238980", "parent_hash": "sha256:0ab6f58ace1a64466e830928a984d85f68b1c363878f3f6f1bf5b3b8f7c9abbe", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE84805 licence not read", "asset:data:geo:GSE84805 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["predict the potential functions of MYOSLID. RT-qPCR and In Site Hybridization (ISH) were used to", "edict the potential functions of MYOSLID. RT-qPCR and In Site Hybridization (ISH) were used to"], "order_basis": "paper_text_order:1189", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ts clinical significance in HNSCC specimens. Immunohistochemical staining, siRNA, wound healing assay, transw"], "order_basis": "paper_text_order:1322", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ly correlated with Slug, PDPN and LAMB3. The knockdown of MYOSLID in OSCC cell line significantly i", "those in the control cells. In addition, the knockdown of MYOSLID significantly reduced Slug, PDPN", "PN and LAMB3 expression levels. However, the knockdown of MYOSLID had no effect on the expression l", "SCC specimens. Immunohistochemical staining, siRNA, wound healing assay, transwell assay, and w"], "order_basis": "paper_text_order:1352", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["A, wound healing assay, transwell assay, and western blot were used to explore the biological function"], "order_basis": "paper_text_order:1401", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["of Medicine [21]. Cal27, SCC4 and SCC9 were cultured in DMEM/high glucose with 10% fetal bovine seru", "and 1% streptomycin-penicillin. Tca8113 was cultured in RPMI 1640 (Gibco, USA) supplemented with 10%", "1% streptomycin-penicillin. HIOEC cells were cultured in a defined keratinocyte serum-free medium (KS"], "order_basis": "paper_text_order:2946", "id": "assay:5"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed mRNAs and lncRNAs were identified in HNSCC tissues in comparison with normal tissue with data obtained from the TCGA database using the “edgeR” package in R. Differentially expressed lncRNAs were identified in HNSCC tissues in comparison with normal tissues from data obtained from GEO with the accession number GSE84805 using the “limma” package in R."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}