Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28415559", "kind": "science-record", "revision": 7, "content_hash": "sha256:1c6b8db43549de18213012820db9a6592cdd7fc0b6e67ed31d224e4b44497e6e", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T21:20:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa.", "doi": "10.18632/oncotarget.16358", "pmid": "28415559", "authors": ["Lu Feng", "John R Houck", "Pawadee Lohavanichbutr", "Chu Chen"], "journal": "Oncotarget", "year": 2017, "abstract": "Oral cavity and oropharyngeal squamous cell carcinoma (OSCC) is a major cancer type in the head and neck region. To better understand the roles long non-coding RNA (lncRNA) play in OSCC carcinogenesis, we compared the expression levels of 3,054 probe sets for lncRNAs between 167 OSCCs and 45 healthy oral mucosa using an Affymetrix HG U133 plus 2.0 array dataset. We found 658 lncRNA transcripts (790 probe sets) to be significantly differentially expressed using a criteria of FDR < 0.01, with 36 of them (39 probe sets) showing more than a 2-fold change. We further validated the top differentially expressed lncRNAs in three independent datasets from Gene Expression Omnibus (GEO) repository: GSE42743, GSE9844, and GSE6791. Fourteen lncRNAs (15 probe sets) were validated in all three datasets using the criteria FDR < 0.01: LOC441178, C5orf66-AS1, HCG22, FLG-AS1, CCL14/CCL15-CCL14, LOC100506990, TRIP10, PCBP1-AS1, LINC01315, LINC00478, COX10-AS1/LOC100506974, MLLT4-AS1, MIR31HG, and DUXAP10/LINC01296. Three lncRNAs in the validated list which showed the highest fold change (LOC441178, HCG22 and C5orf66-AS1) were verified by quantitative RT-PCR in a subset of 20 OSCCs and 10 control samples. In silico prediction of their functional role has given us directions for further investigation.", "claims": [{"id": "claim-method", "statement": "The statistical analysis of differentially expressed lncRNA (between cases and controls) was performed using linear regression, adjusting for age and sex.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28415559", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "The statistical analysis of differentially expressed lncRNA (between cases and controls) was performed using linear regression, adjusting for age and sex."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data were generated using the Affymetrix Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA, USA) and were deposited in the Gene Expression Omnibus (GEO) Repository under the general accession number GSE30784. The dataset has 212 samples in total, 167 of them are OSCCs and 45 of them are oral mucosa from healthy controls.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28415559", "locator": "sections[8] \"Gene expression array data and identification of lncRNAs\" paragraph 2", "quote": "The microarray data were generated using the Affymetrix Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA, USA) and were deposited in the Gene Expression Omnibus (GEO) Repository under the general accession number GSE30784. The dataset has 212 samples in total, 167 of them are OSCCs and 45 of them are oral mucosa from healthy controls."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 658 significantly differentially expressed lncRNA transcripts between OSCC and healthy oral mucosa using linear regression adjusted for age and sex, with FDR < 0.01 and a 2-fold expression difference as selection criteria; source microarray data were obtained from the OralChip study (167 OSCCs and 45 healthy oral-mucosa samples), normalized with RMA, and accessed through GEO under accession GSE30784.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "We found 658 lncRNA transcripts (790 probe sets) to be significantly differentially expressed using a criteria of FDR < 0.01, with 36 of them (39 probe sets) showing more than a 2-fold change."}, "evidence": [{"asset": "source:pmid:28415559", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found 658 lncRNA transcripts (790 probe sets) to be significantly differentially expressed using a criteria of FDR < 0.01, with 36 of them (39 probe sets) showing more than a 2-fold change."}, {"asset": "source:pmid:28415559", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "The statistical analysis of differentially expressed lncRNA (between cases and controls) was performed using linear regression, adjusting for age and sex."}, {"asset": "source:pmid:28415559", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "The false discovery rate (FDR) of 0.01 and a 2-fold difference in expression between the two groups were used as criteria to select the differentially expressed lncRNA."}, {"asset": "source:pmid:28415559", "locator": "sections[8] \"Gene expression array data and identification of lncRNAs\" paragraph 2", "quote": "The microarray data were generated using the Affymetrix Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA, USA) and were deposited in the Gene Expression Omnibus (GEO) Repository under the general accession number GSE30784."}, {"asset": "source:pmid:28415559", "locator": "sections[8] \"Gene expression array data and identification of lncRNAs\" paragraph 2", "quote": "The dataset has 212 samples in total, 167 of them are OSCCs and 45 of them are oral mucosa from healthy controls."}, {"asset": "source:pmid:28415559", "locator": "sections[8] \"Gene expression array data and identification of lncRNAs\" paragraph 2", "quote": "CEL files were preprocessed and normalized using RMA algorithm in Partek Genomics Suite™ software version 6.6."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 658 significantly differentially expressed lncRNA transcripts between OSCC and healthy oral mucosa using linear regression adjusted for age and sex, with FDR < 0.01 and a 2-fold expression difference as selection criteria; source microarray data were obtained from the OralChip study (167 OSCCs and 45 healthy oral-mucosa samples), normalized with RMA, and accessed through GEO under accession GSE30784.", "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:28415559"], "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. 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"section_index": 3, "section_title": "Differentially expressed lncRNA genes between cases and controls", "row_count": 40, "column_count": 8}, "table": {"label": "Table 2", "caption": "Validation of 39 differentially expressed probe sets between OSCC and control in three independent datasets", "rows": [["Probe sets ID", "Gene Symbol", "Chromosomal Location", "Fold change in FHCRC dataset", "Q-value in FHCRC dataset", "Q-value in GSE42743", "Q-value in GSE9844", "Q-value in GSE6791"], ["1563894_at*", "LOC441178", "chr6q27", "–14.50", "8.83E-49", "1.00E-12", "1.11E-06", "6.09E-13"], ["1561685_a_at*", "LOC441178", "chr6q27", "–14.23", "8.83E-49", "5.22E-13", "1.11E-06", "2.26E-13"], ["1558920_at", "SLC8A1-AS1", "chr2p22.1", "–8.43", "5.85E-45", "6.51E-07", "0.02", "1.83E-03"], ["236444_x_at", "C5orf66-AS1", "chr5q31.1", "–6.60", "1.91E-28", "4.32E-09", "2.29E-03", "9.62E-06"], ["227725_at*", "ST6GALNAC1", "chr17q25.1", "–5.87", "1.44E-15", "1.93E-09", "0.02", "1.18E-04"], ["204919_at*", "PRH1-PRR4/PRR4", "chr12p/chr12p13", "–5.31", "4.18E-06", "5.29E-03", "0.59", "0.03"], ["1560767_at*", "HCG22", "chr6p21.33", "–3.95", "1.91E-28", "5.83E-14", "2.35E-05", "1.50E-05"], ["241014_at", "FLG-AS1", "chr1q21.3", "–3.61", "6.52E-35", "5.22E-13", "6.69E-06", "9.62E-06"], ["244620_at", "SLC8A1-AS1", "chr2p22.1", "–3.29", "1.81E-34", "4.33E-06", "0.04", "2.14E-03"], ["224997_x_at", "H19/MIR675", "chr11p15.5", "–3.23", "6.43E-04", "0.05", "0.10", "0.11"], ["205392_s_at*", "CCL14/CCL15-CCL14", "chr17q11.2/chr17q12", "–2.92", "2.08E-14", "1.29E-08", "7.54E-06", "7.39E-07"], ["227917_at", "LOC100506990", "chr8p23.1", "–2.77", "4.44E-21", "1.93E-09", "1.04E-03", "6.38E-04"], ["242546_at", "DUXAP10/LINC01296", "chr14q11.2", "2.75", "3.56E-09", "1.49E-06", "8.29E-03", "3.18E-04"], ["202734_at*", "TRIP10", "chr19p13.3", "–2.69", "4.82E-33", "3.06E-06", "7.44E-03", "6.29E-06"], ["1557389_at", "SH3PXD2A-AS1", "chr10q24.33", "–2.51", "6.31E-14", "2.99E-03", "0.46", "1.03E-03"], ["1554097_a_at", "MIR31HG", "chr9p21.3", "2.50", "1.92E-09", "1.48E-08", "5.59E-03", "8.48E-03"], ["1562921_at", "EP300-AS1", "chr22q13.2", "–2.44", "3.79E-14", "4.87E-03", "0.04", "3.30E-03"], ["228658_at", "MIAT", "chr22q12.1", "2.37", "9.59E-09", "2.31E-04", "0.59", "0.19"], ["236573_at", "MIR1-2/MIR133A1/MIR133A1HG", "chr18q11.2", "–2.34", "2.46E-08", "5.62E-07", "0.17", "0.12"], ["227969_at", "PCBP1-AS1", "chr2p14", "–2.31", "1.24E-35", "6.61E-08", "5.41E-06", "2.18E-04"], ["208908_s_at*", "CAST", "chr5q15", "–2.26", "2.93E-30", "7.59E-06", "0.02", "1.33E-03"], ["229930_at", "LINC01315", "chr22q13.2", "–2.25", "1.77E-22", "6.81E-09", "2.35E-05", "7.86E-06"], ["239999_at", "LINC00478", "chr21q21.1", "–2.25", "2.34E-11", "1.93E-09", "2.35E-05", "1.96E-06"], ["220918_at", "RUNX1-IT1", "chr21q22.12", "2.23", "4.70E-11", "3.42E-07", "0.10", "0.03"], ["202672_s_at*", "ATF3", "chr1q32.3", "2.23", "9.56E-06", "8.20E-05", "0.31", "0.03"], ["1559361_at", "LOC101927668/MACC1", "chr7p21.1", "–2.21", "1.75E-13", "7.55E-04", "0.23", "0.01"], ["230451_at", "COX10-AS1/LOC100506974", "chr17p12", "–2.20", "2.23E-37", "6.63E-09", "1.11E-06", "5.16E-08"], ["219871_at", "KLF3-AS1", "chr4p14", "–2.20", "7.82E-19", "5.00E-08", "0.06", "0.04"], ["238320_at", "MIR612/NEAT1", "chr11q13.1", "2.15", "2.35E-06", "0.02", "0.29", "0.02"], ["207467_x_at*", "CAST", "chr5q15", "–2.14", "1.22E-30", "3.68E-06", "0.01", "1.33E-03"], ["1557146_a_at", "SSTR5-AS1", "chr16p13.3", "–2.12", "7.86E-07", "0.02", "0.40", "0.19"], ["210409_at*", "MLLT4-AS1", "chr6q27", "–2.12", "1.63E-30", "6.45E-07", "1.92E-04", "2.38E-10"], ["226382_at*", "LOC283070", "chr10p13", "–2.09", "9.82E-14", "8.52E-06", "9.58E-03", "0.03"], ["228370_at", "IPW/LOC101930404/PWARSN/SNORD107/SNORD115-13/SNORD115-26/SNORD115-7/SNORD116-22/SNORD116-28/SNORD116-4", "chr15q11.2", "–2.09", "9.34E-08", "1.55E-06", "0.02", "0.04"], ["232034_at", "LINC00537", "chr9q21.11", "–2.05", "1.33E-11", "0.02", "0.10", "0.10"], ["233565_s_at*", 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