Microarray‑based analysis of COL11A1 and TWIST1 as important differentially‑expressed pathogenic genes between left and right‑sided colon cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31545476", "kind": "science-record", "revision": 8, "content_hash": "sha256:4549a003f1cabd025789cbafebac466b0a3a050d41cad31b4b22fabf683231c2", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T22:44:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microarray‑based analysis of COL11A1 and TWIST1 as important differentially‑expressed pathogenic genes between left and right‑sided colon cancer.", "doi": "10.3892/mmr.2019.10667", "pmid": "31545476", "authors": ["Chen Su", "Jiabao Zhao", "Xinya Hong", "Sijiu Yang", "Ying Jiang", "Jingjing Hou"], "journal": "Molecular medicine reports", "year": 2019, "abstract": "Colonic cancer has become a main reason of mortality associated with cancer; however, left and right‑sided colonic cancer have diverse outcomes in terms of epidemiological, histological, clinical parameters and prognosis. We aimed to examine the discrepancies between these two types of colon cancers to identify potential therapeutic targets. In the present study, three gene expression profiles (GSE44076, GSE31595, GSE26906) from Gene Expression Omnibus (GEO) database were downloaded and further analyzed. A PPI (protein‑protein interaction) network of the differentially‑expressed genes (DEGs) of GSE44076 between tumor and normal was established with the Search Tool for the Retrieval of Interacting Genes database. Then, the DEGs of these two colon cancers (left, right) samples were identified. Subsequently, the intersection of DEGs of left and right‑sided colon cancer samples obtained from three databases, and DEGs of tumor and normal samples were analyzed. Collagen type XI α1 chain (COL11A1), Twist family bHLH transcription factor 1 (TWIST1), insulin‑like 5 and chromogranin A were upregulated proteins, while 3β‑hydroxysteroid dehydrogenase was downregulated protein in right colon cancer than in left‑sided tumor samples. Through further experimental verification, we revealed that COL11A1 and TWIST1 were significantly upregulated at the mRNA and protein levels within right‑sided colon cancer compared with in left‑sided colon cancer samples (P<0.05), consistent with bioinformatical analysis. Furthermore, a positive correlation between COL11A1 and TWIST1 protein expression was observed (P<0.0276). Collectively, our data showed that COL11A1 and TWIST1 may be potential prognostic indicators and molecular targets for the treatment of right‑sided colon cancer.", "claims": [{"id": "claim-method", "statement": "Subsequently, the DEGs between left and right-sided colonic cancer of three separate datasets were conducted by utilizing the limma package (37) in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31545476", "locator": "sections[6] \"Data pre-processing and DEG analysis\" paragraph 2", "quote": "Subsequently, the DEGs between left and right-sided colonic cancer of three separate datasets were conducted by utilizing the limma package (37) in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data of four original microarray datasets GSE44076, GSE31596 and GSE26906 were downloaded from NCBI-Gene Expression Omnibus database (Available online: http://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31545476", "locator": "sections[27] \"Availability of data and materials\" paragraph 2", "quote": "The data of four original microarray datasets GSE44076, GSE31596 and GSE26906 were downloaded from NCBI-Gene Expression Omnibus database (Available online: http://www.ncbi.nlm.nih.gov/geo)."}], "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:31545476"], "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:GSE26906"], "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:GSE26906"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31545476", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/mmr.2019.10667", "sha256": "sha256:8ba82c7a33439242a547eb5475368801f08105a5eda484b4de6816517ec0b412", "bytes": 54826, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/mmr.2019.10667", "version": null, "note": "Full article fetched from PMC; 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"", "", "0.633"], ["Tis +I", "2", "0", ""], ["II", "10", "8", ""], ["III", "4", "4", ""], ["IV", "1", "1", ""], ["Histology grade", "", "", "0.432"], ["Well + moderate", "12", "10", ""], ["Poor", "3", "3", ""], ["Mucinous adenocarcinoma", "2", "0", ""]], "row_count": 18, "column_count": 4, "numeric_cells": 28, "header_rows": 3, "locator": "section[4]/table-wrap[1]#tI-mmr-20-05-4202"}}, {"id": "asset:table:pmid:31545476:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:26ab7f246180e64f081908cdb3566f9fb417a3ea7d60378101c1f7fe3f65c746", "bytes": 1224, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#tV-mmr-20-05-4202", "version": null, "note": "Functional enrichment analysis for differentially-expressed genes between tumor and normal contained TWIST1 or COL11A1 based on GO.", "structure": {"pmcid": "PMC6797952", "section_index": 15, "section_title": "Functional enrichment analysis", "row_count": 8, "column_count": 5}, "table": {"label": "Table V.", "caption": "Functional enrichment analysis for differentially-expressed genes between tumor and normal contained TWIST1 or COL11A1 based on GO.", "rows": [["Category", "Term", "Description", "P-value", "Genes"], ["GOTERM_CC_DIRECT", "GO:0005578", "Proteinaceous extracellular matrix", "0.0022724", "MMP9, COMP, COL11A1, MMP1, COL10A1"], ["GOTERM_BP_DIRECT", "GO:0001649", "Osteoblast differentiation", "0.0028232", "MSX2, COL1A1, TWIST1, SPP1"], ["GOTERM_BP_DIRECT", "GO:0045944", "Positive regulation of transcription from RNA polymerase II promoter", "0.0096635", "CKAP2, FOXA2, ATAD2, BMP7, MYC, ETV4, TWIST1"], ["GOTERM_MF_DIRECT", "GO:0000981", "RNA polymerase II transcription factor activity, sequence-specific DNA binding", "0.0108839", "FOXA2, MYBL2, ETV4, TWIST1"], ["GOTERM_CC_DIRECT", "GO:0005581", "Collagen trimer", "0.0135131", "COL1A1, COL11A1, COL10A1"], ["GOTERM_BP_DIRECT", "GO:0002063", "Chondrocyte development", "0.04367", "MSX2, COL11A1"], ["GOTERM_CC_DIRECT", "GO:0005634", "Nucleus", "0.0498886", "FOXA2, NUF2, TPX2, MND1, ATAD2, UBE2C, MYBL2, CENPH, MSX2, SPC25, CDCA7, CENPA, MYC, ETV4, TWIST1"]], "row_count": 8, "column_count": 5, "numeric_cells": 18, "header_rows": 1, "locator": "section[22]/table-wrap[1]#tV-mmr-20-05-4202"}}, {"id": "asset:table:pmid:31545476:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:78592f6f683cbee7cdd391d4fc865375753e378995ffb12801ff829680f3cd1f", "bytes": 2149, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#tII-mmr-20-05-4202", "version": null, "note": "DEGs were identified from three profile datasets, including up-regulated genes and down-regulated genes in which the colon cancer tissues compared with normal colon tissues and right-sided colon cancer tissues compared to left-sided colon cancer.", "structure": {"pmcid": "PMC6797952", "section_index": 18, "section_title": "Screening of DEGs", "row_count": 5, "column_count": 3}, "table": {"label": "Table II.", "caption": "DEGs were identified from three profile datasets, including up-regulated genes and down-regulated genes in which the colon cancer tissues compared with normal colon tissues and right-sided colon cancer tissues compared to left-sided colon cancer.", "rows": [["DEGs", "Upregulated genes", "Downregulated genes"], ["GSE44076 tumor and normal", "IL8, MYC, MMP9, CCNB1, AGT, BUB1, CENPA, CXCL1, TPX2, CEP55, UBE2C, NUF2, CXCL11, CXCL5, GNG4, TIMP1, SPP1, MMP3, MND1, CXCL2, TRIP13, MMP7, ATAD2, MMP1, CXCL3, COL1A1, ANLN, ERCC6L, CENPH, SKA3, DSCC1, SPC25, SOX9, LGR5, CDCA7, CKAP2, BMP7, RNASEH2A, FOXA2, FAM54A, FCGR3A, MMP10, DIAPH3, COL11A1, TWIST1, ETV4, LCN2, MYBL2, SULT2B1, COMP, COL10A1, FABP6, MTHFD1L, ORC6L, MSX2, FAP", "CXCL12, SST, NPY, PYY, CCL19, GCG, ADRA2A, INSL5, CD36, CA2, CHGA, FABP4, CCL13, HSD3B2, VIP, KLF4, CCL23, PCSK2, PDE6A, FABP1, MUC2, PDE9A, HPGD, OASL, CTSG, RERGL, SGK1, AKR1C1, CFD, SLC4A4, DES, MMP28, HSD17B2, DARC, PCK1, UGT2B15, UGT2B17, ADH1B, MYH11, PTGDR"], ["GSE44076 right and left", "TTPA, TRIM54, PNLIPRP2, ELAVL2, G0S2, RBP2, MSLN, EREG, ZNF43, TNNC1, PRAC, ODAM, QPRT, PCP4, COL9A3, LY6G6D, BEX2, SLC26A3, GAL, CKMT2", "MB, HOXC6, HOXB6, ARX, AIM2, SLC28A3, B3GNT6, L1TD1, DMRTA2, GABRP, GBA3, ART3, CLDN2, FOXA1, CYP4X1, KRT6B, CA9, HEPACAM2, FOXD1, HOXB8, MS4A8B, C4BPA, DMBT1, MT1H, MUC1, IDO1, KLK1, PIGR"], ["GSE31595 right and left", "FGD1, PRAC1, C11orf70, HS3ST3A1, PKIA, PI3, INSL5, HOXB13, PHACTR3, ASB9, SYNE4, RLN2, FLJ41455, TWIST1, CKMT2, SLC35D3, CCDC113, COL11A1, PPBP, EPYC, CPE", "IL10, USP30-AS1, SLC51A, HAR1A, CRTAM, NKG7, NPY6R, NR1H4, TREH, BLNK, MEP1B, GDPD3, PITX2, CYP2C18, AIM2, PP7080, CD69, GBA3, GRAMD1C, CCL8, HSD3B2, CCL5, HMGCS2, RARRES3, SLC20A1"], ["GSE26906 right and left", "PRAC1, CLDN5, SERPINE2, PCDH19, CHGA, PRELP, SERPINA6, PLA1A, SCNN1B, STMN2, MAP7D2, CHRDL1, MUC12, PCP4, HSD17B6, MN1, ARMCX1, CHRDL2, CLDN10, CCL11, AOC3, CLC, BEX2", "PLA2G3, RIBC2, CAPN6, PIWIL1, SLC28A3, GMPR, TMEM171, REG3A, L1TD1, FOXD1, CLDN2"]], "row_count": 5, "column_count": 3, "numeric_cells": 12, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tII-mmr-20-05-4202"}}, {"id": "asset:table:pmid:31545476:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d7adbe18a4297032b751a77e3ca6fb8c4eb2b830fa04f151cdffd39eac758fa3", "bytes": 712, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#tIII-mmr-20-05-4202", "version": null, "note": "Clinicopathological characteristics and COL11A1 mRNA expression in colon cancer samples.", "structure": {"pmcid": "PMC6797952", "section_index": 21, "section_title": "Verification of the DEGs (COL11A1 and TWIST1) between left and right-sided colonic cancer with western blotting analysis and RT-qPCR", "row_count": 13, "column_count": 4}, "table": {"label": "Table III.", "caption": "Clinicopathological characteristics and COL11A1 mRNA expression in colon cancer samples.", "rows": [["Clinicopathological parameters", "No. of cases", "COL11A1 expression (2−ΔCq, mean)", "P-value"], ["Tumor location", "", "", ""], ["Left", "17", "1.1993", "<0.0001"], ["Right", "13", "2.7947", ""], ["TNM stage", "", "", ""], ["Tis + I", "2", "1.1530", "0.7026"], ["II", "18", "1.9950", ""], ["III", "8", "1.9223", ""], ["IV", "2", "1.5617", ""], ["Histology grade", "", "", ""], ["Well + moderate", "22", "1.8974", "0.4455"], ["Poor", "6", "2.1369", ""], ["Mucinous adenocarcinoma", "2", "1.0769", ""]], "row_count": 13, "column_count": 4, "numeric_cells": 22, "header_rows": 1, "locator": "section[21]/table-wrap[1]#tIII-mmr-20-05-4202"}}, {"id": "asset:table:pmid:31545476:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a0b89769ab70681797a960392b2156808b22cd927713a86b93845a6b714eadaa", "bytes": 708, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[2]#tIV-mmr-20-05-4202", "version": null, "note": "Clinicopathological characteristics and TWIST1 mRNA expression in colon cancer samples.", "structure": {"pmcid": "PMC6797952", "section_index": 21, "section_title": "Verification of the DEGs (COL11A1 and TWIST1) between left and right-sided colonic cancer with western blotting analysis and RT-qPCR", "row_count": 13, "column_count": 4}, "table": {"label": "Table IV.", "caption": "Clinicopathological characteristics and TWIST1 mRNA expression in colon cancer samples.", "rows": [["Clinicopathological parameters", "No. of cases", "TWIST1 expression (2−ΔCq, mean)", "P-value"], ["Tumor location", "", "", "<0.0001"], ["Left", "17", "1.1546", ""], ["Right", "13", "2.3867", ""], ["TNM stage", "", "", "0.7767"], ["Tis + I", "2", "1.2984", ""], ["II", "18", "1.7548", ""], ["III", "8", "1.7536", ""], ["IV", "2", "1.2214", ""], ["Histology grade", "", "", "0.3601"], ["Well + moderate", "22", "1.6988", ""], ["Poor", "6", "1.9118", ""], ["Mucinous adenocarcinoma", "2", "0.9055", ""]], "row_count": 13, "column_count": 4, "numeric_cells": 22, "header_rows": 1, "locator": "section[21]/table-wrap[2]#tIV-mmr-20-05-4202"}}, {"id": "asset:table:pmid:31545476:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:26ab7f246180e64f081908cdb3566f9fb417a3ea7d60378101c1f7fe3f65c746", "bytes": 1224, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#tV-mmr-20-05-4202", "version": null, "note": "Functional enrichment analysis for differentially-expressed genes between tumor and normal contained TWIST1 or COL11A1 based on GO.", "structure": {"pmcid": "PMC6797952", "section_index": 22, "section_title": "Functional enrichment analysis", "row_count": 8, "column_count": 5}, "table": {"label": "Table V.", "caption": "Functional enrichment analysis for differentially-expressed genes between tumor and normal contained TWIST1 or COL11A1 based on GO.", "rows": [["Category", "Term", "Description", "P-value", "Genes"], ["GOTERM_CC_DIRECT", "GO:0005578", "Proteinaceous extracellular matrix", "0.0022724", "MMP9, COMP, COL11A1, MMP1, COL10A1"], ["GOTERM_BP_DIRECT", "GO:0001649", "Osteoblast differentiation", "0.0028232", "MSX2, COL1A1, TWIST1, SPP1"], ["GOTERM_BP_DIRECT", "GO:0045944", "Positive regulation of transcription from RNA polymerase II promoter", "0.0096635", "CKAP2, FOXA2, ATAD2, BMP7, MYC, ETV4, TWIST1"], ["GOTERM_MF_DIRECT", "GO:0000981", "RNA polymerase II transcription factor activity, sequence-specific DNA binding", "0.0108839", "FOXA2, MYBL2, ETV4, TWIST1"], ["GOTERM_CC_DIRECT", "GO:0005581", "Collagen trimer", "0.0135131", "COL1A1, COL11A1, COL10A1"], ["GOTERM_BP_DIRECT", "GO:0002063", "Chondrocyte development", "0.04367", "MSX2, COL11A1"], ["GOTERM_CC_DIRECT", "GO:0005634", "Nucleus", "0.0498886", "FOXA2, NUF2, TPX2, MND1, ATAD2, UBE2C, MYBL2, CENPH, MSX2, SPC25, CDCA7, CENPA, MYC, ETV4, TWIST1"]], "row_count": 8, "column_count": 5, "numeric_cells": 18, "header_rows": 1, "locator": "section[22]/table-wrap[1]#tV-mmr-20-05-4202"}}], "gaps": ["asset:data:geo:GSE26906 not downloaded", "asset:data:geo:GSE26906 licence not read", "asset:data:geo:GSE31595 not downloaded", "asset:data:geo:GSE31595 licence not read", "asset:data:geo:GSE44076 not downloaded", "asset:data:geo:GSE44076 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", 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