A microarray analysis of two distinct lymphatic endothelial cell populations.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484194", "kind": "science-record", "revision": 8, "content_hash": "sha256:a0b7fdaee335a1d2d73087a0ee2f88579ee318568cd100c7026deaa3010f058b", "created_at": "2026-11-01T15:40:12Z", "updated_at": "2026-11-01T22:42:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A microarray analysis of two distinct lymphatic endothelial cell populations.", "doi": "10.1016/j.gdata.2015.04.005", "pmid": "26484194", "authors": ["Bernhard Schweighofer", "Sabrina Rohringer", "Johannes Pröll", "Wolfgang Holnthoner"], "journal": "Genomics data", "year": 2015, "abstract": "We have recently identified lymphatic endothelial cells (LECs) to form two morphologically different populations, exhibiting significantly different surface protein expression levels of podoplanin, a major surface marker for this cell type. In vitro shockwave treatment (IVSWT) of LECs resulted in enrichment of the podoplanin(high) cell population and was accompanied by markedly increased cell proliferation, as well as 2D and 3D migration. Gene expression profiles of these distinct populations were established using Affymetrix microarray analyses. Here we provide additional details about our dataset (NCBI GEO accession number GSE62510) and describe how we analyzed the data to identify differently expressed genes in these two LEC populations.", "claims": [{"id": "claim-method", "statement": "Using Carmaweb, a moderated t-test (limma) was performed on the RMA normalized datasets, restricted to the 40% of the probesets with the biggest variance over all samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484194", "locator": "sections[7] \"Enhanced transcriptome analysis to exclude false positive transcripts\" paragraph 2", "quote": "Using Carmaweb, a moderated t-test (limma) was performed on the RMA normalized datasets, restricted to the 40% of the probesets with the biggest variance over all samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw and RMA normalized array data were submitted to Gene Expression Omnibus (GEO) and are available under the accession number GSE62510.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484194", "locator": "sections[6] \"Standard transcriptome analysis\" paragraph 2", "quote": "Raw and RMA normalized array data were submitted to Gene Expression Omnibus (GEO) and are available under the accession number GSE62510."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used moderated t-tests (limma) on RMA- and MAS5-normalized microarray data to identify differentially expressed genes between the two lymphatic endothelial cell populations, and deposited the raw and normalized data in GEO under accession GSE62510.", "kind": "quantitative", "target": {"value": 40.0, "unit": "per cent", "tolerance": null, "source": "Using Carmaweb, a moderated t-test (limma) was performed on the RMA normalized datasets, restricted to the 40% of the probesets with the biggest variance over all samples."}, "evidence": [{"asset": "source:pmid:26484194", "locator": "sections[7] \"Enhanced transcriptome analysis to exclude false positive transcripts\" paragraph 2", "quote": "Using Carmaweb, a moderated t-test (limma) was performed on the RMA normalized datasets, restricted to the 40% of the probesets with the biggest variance over all samples."}, {"asset": "source:pmid:26484194", "locator": "sections[6] \"Standard transcriptome analysis\" paragraph 2", "quote": "Raw and RMA normalized array data were submitted to Gene Expression Omnibus (GEO) and are available under the accession number GSE62510."}, {"asset": "source:pmid:26484194", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide additional details about our dataset (NCBI GEO accession number GSE62510) and describe how we analyzed the data to identify differently expressed genes in these two LEC populations."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used moderated t-tests (limma) on RMA- and MAS5-normalized microarray data to identify differentially expressed genes between the two lymphatic endothelial cell populations, and deposited the raw and normalized data in GEO under accession GSE62510.", "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:26484194"], "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:GSE62510"], "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:GSE62510"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484194", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.04.005", "sha256": "sha256:202c92ab72ae8c765d29171d668a01d4058d3d975ac41007818474bf2b1b60c2", "bytes": 8573, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.04.005", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4535941", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62510", "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=GSE62510", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62510", "version": null, "note": "Raw and RMA normalized array data were submitted to Gene Expression Omnibus (GEO) and are available under the accession number GSE62510.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw and RMA normalized array data were submitted to Gene Expression Omnibus (GEO) and are available under the accession number GSE62510.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1528088", "GSM1528089", "GSM1528090", "GSM1528091", "GSM1528092", "GSM1528093"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from two sorted lymphatic endothelial cell (LEC) populations, podoplanin-high versus podoplanin low", "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:26484194:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eafbc03a2400462cf67f9e133a9ebc31f0153e0bba38b961c36f13af18c935ea", "bytes": 2800, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#t0005", "version": null, "note": "RMA normalization versus MAS5 normalization, 100 genes with lowest raw p-values shown for both methods. Genes are ranked from lower to higher p-values for each given normalization method. For annotated genes, HGNC gene symbols are shown, else Affymetrix probeset IDs (xxxxx…_at) are given. Bold characters indicate genes common to both datasets.", "structure": {"pmcid": "PMC4535941", "section_index": 7, "section_title": "Enhanced transcriptome analysis to exclude false positive transcripts", "row_count": 102, "column_count": 2}, "table": {"label": "Table 1", "caption": "RMA normalization versus MAS5 normalization, 100 genes with lowest raw p-values shown for both methods. Genes are ranked from lower to higher p-values for each given normalization method. For annotated genes, HGNC gene symbols are shown, else Affymetrix probeset IDs (xxxxx…_at) are given. Bold characters indicate genes common to both datasets.", "rows": [["Gene symbol or probeset ID,RMA normalized", "Gene symbol or probeset ID,MAS5 normalized"], ["", ""], ["1558048_x_at", "SYTL4"], ["234675_x_at", "1570071_at"], ["BMX", "AKAP14"], ["242881_x_at", "LOC100289550"], ["RASEF", "LIMCH1"], ["RASEF", "239089_at"], ["AFFX-r2-Bs-thr-5_s_at", "PSMG4"], ["SERPINE2", "244791_at"], ["224549_x_at", "RASEF"], ["M10098_3_at", "FLT1"], ["ANKRD11", "BRD8"], ["M10098_M_at", "MMP7"], ["NEAT1", "232107_at"], ["TMEM71", "241618_at"], ["HIP1", "TCL1A"], ["MGP", "INPP4A"], ["VWF", "1569515_a_at"], ["TPR", "ZNF536"], ["AFFX-r2-Bs-phe-M_at", "CLIP1"], ["PDPK1", "1552955_at"], ["M10098_5_at", "RERE"], ["AFFX-r2-Bs-dap-5_at", "DYNC1H1"], ["215626_at", "C3"], ["231199_at", "UBE3B"], ["BMP6", "NLRP14"], ["CDC27", "MGP"], ["RAD21", "LOC650392"], ["MDM4", "GRM2"], ["AFFX-DapX-5_at", "FGF11"], ["1565717_s_at", "HMX2"], ["230655_at", "C21orf58"], ["FMO3", "C19orf21"], ["PHACTR2", "FOXP4"], ["220038_at", "243281_at"], ["CAB39", "C17orf52"], ["SART3", "1566042_at"], ["239355_at", "MTOR"], ["RGS20", "ZNF704"], ["GPX3", "CYP2A7"], ["IDH3A", "EVI5L"], ["ITCH", "MCM6"], ["PPP1R3C", "C3orf75"], ["GATC", "SERPINE2"], ["FOXO3", "hCG_1646157"], ["P4HB", "GPX3"], ["PRUNE2", "RANBP2"], ["GPX3", "SLC7A4"], ["PICALM", "SCARB2"], ["SLC16A6", "CIDEC"], ["NEAT1", "SH3GL1P2"], ["AFFX-M27830_5_at", "KLK8"], ["PTER", "CDK1"], ["VEZF1", "C11orf53"], ["CPNE3", "SNHG4"], ["CD47", "P4HB"], ["SKIL", "PAPPA"], ["FNIP2", "1564620_at"], ["TMED2", "242611_at"], ["MARCH6", "RAD21"], ["ALDH1A1", "NFKBIB"], ["PALMD", "HARBI1"], ["ABCG1", "M10098_M_at"], ["ARHGAP18", "FLJ10213"], ["AFFX-r2-Bs-thr-M_s_at", "224549_x_at"], ["HTR2B", "ARHGEF1"], ["PAPPA", "233687_s_at"], ["SERPINE1", "227223_at"], ["MBNL1", "RFFL"], ["ZNF207", "1558670_at"], ["KSR2", "SAMD1"], ["ATP6V0E1", "HORMAD2"], ["AFFX-r2-Bs-phe-5_at", "238796_at"], ["SCD5", "DEAF1"], ["FMO3", "KLF2"], ["ZNF638", "CDK1"], ["SCARB2", "222524_s_at"], ["SNAP23", "242276_at"], ["AFFX-ThrX-M_at", "FMO3"], ["241773_at", "LOC100130998"], ["AFFX-r2-Bs-lys-5_at", "C19orf34"], ["DIRAS3", "235355_at"], ["COQ2", "230750_at"], ["242787_at", "C14orf118"], ["SMAD7", "LOC643201"], ["ARF6", "RYK"], ["MGEA5", "207047_s_at"], ["DLC1", "HSP90B1"], ["LOC100190986", "OR1Q1"], ["CXADR", "PRIM2"], ["S100A10", "TNK2"], ["IFITM1", "SLC7A11"], ["MSI2", "208451_s_at"], ["ID2", "ONECUT3"], ["SFRS6", "ZNF207"], ["AFFX-r2-Bs-dap-M_at", "LIN7C"], ["JAG1", "CPNE3"], ["LPCAT2", "P2RX2"], ["SBNO1", "231005_at"], ["MAT2A", "GIMAP6"], ["ANKHD1", "234860_at"]], "row_count": 102, "column_count": 2, "numeric_cells": 82, "header_rows": 1, "locator": "section[7]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26484194:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8ebe32db8335df0852da0c23956efde8c695bed31fd762f87d8ac9ad860b4d9e", "bytes": 8654, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[2]#t0010", "version": null, "note": "MeanM based ranking of combined lists (100 genes each with lowest p-value for RMA normalization and MAS5 normalization, meanM values averaged). For annotated genes, HGNC gene symbols are shown, else Affymetrix probeset IDs (xxxxx…_at) are given.", "structure": {"pmcid": "PMC4535941", "section_index": 7, "section_title": "Enhanced transcriptome analysis to exclude false positive transcripts", "row_count": 189, "column_count": 4}, "table": {"label": "Table 2", "caption": "MeanM based ranking of combined lists (100 genes each with lowest p-value for RMA normalization and MAS5 normalization, meanM values averaged). For annotated genes, HGNC gene symbols are shown, else Affymetrix probeset IDs (xxxxx…_at) are given.", "rows": [["Gene symbol or probeset ID", "meanM average", "Raw p RMA", "Raw p MAS5"], ["1558048_x_at", "− 3.58", "1.13E-25", "2.15E-02"], ["SYTL4", "− 2.26", "3.26E-16", "1.66E-05"], ["SNHG4", "− 2.19", "5.13E-14", "1.82E-03"], ["UBE3B", "− 2.09", "9.12E-14", "3.90E-04"], ["238796_at", "− 2.09", "2.44E-12", "2.41E-03"], ["MMP7", "− 2.09", "2.57E-12", "1.45E-04"], ["1552955_at", "− 2.08", "1.16E-11", "2.90E-04"], ["DYNC1H1", "− 2.07", "3.14E-11", "3.11E-04"], ["INPP4A", "− 2.04", "3.45E-11", "2.14E-04"], ["NLRP14", "− 1.98", "9.15E-11", "4.13E-04"], ["RASEF", "− 1.91", "1.93E-10", "1.01E-04"], ["ANKRD11", "− 1.82", "2.18E-10", "2.05E-01"], ["C17orf52", "− 1.75", "2.35E-10", "8.46E-04"], ["224549_x_at", "− 1.74", "6.10E-10", "2.17E-03"], ["234675_x_at", "− 1.70", "1.07E-09", "1.73E-02"], ["FLT1", "− 1.67", "1.13E-09", "1.28E-04"], ["OR1Q1", "− 1.66", "1.34E-09", "2.99E-03"], ["242276_at", "− 1.65", "1.69E-09", "2.47E-03"], ["227223_at", "− 1.63", "3.16E-09", "2.25E-03"], ["1570071_at", "− 1.62", "5.97E-09", "2.60E-05"], ["ZNF638", "− 1.61", "1.29E-08", "2.03E-01"], ["NEAT1", "− 1.56", "1.40E-08", "7.25E-02"], ["BRD8", "− 1.52", "2.01E-08", "1.38E-04"], ["1566042_at", "− 1.50", "3.02E-08", "8.71E-04"], ["215626_at", "− 1.48", "3.17E-08", "1.79E-01"], ["FGF11", "− 1.44", "4.78E-08", "5.88E-04"], ["232107_at", "− 1.41", "7.11E-08", "1.61E-04"], ["RASEF", "− 1.41", "8.14E-08", "3.25E-02"], ["207047_s_at", "− 1.36", "1.40E-07", "2.89E-03"], ["242881_x_at", "− 1.34", "1.60E-07", "1.27E-02"], ["PDPK1", "− 1.33", "1.72E-07", "8.48E-02"], ["M10098_M_at", "− 1.31", "2.04E-07", "2.09E-03"], ["M10098_5_at", "− 1.30", "2.06E-07", "4.04E-02"], ["AFFX-r2-Bs-thr-5_s_at", "− 1.28", "2.55E-07", "1.05E-02"], ["ITCH", "− 1.28", "2.83E-07", "3.66E-02"], ["M10098_3_at", "− 1.27", "3.09E-07", "1.49E-02"], ["TMEM71", "− 1.27", "4.95E-07", "5.18E-03"], ["NEAT1", "− 1.21", "7.36E-07", "4.53E-02"], ["1558670_at", "− 1.20", "7.91E-07", "2.30E-03"], ["TCL1A", "− 1.19", "9.28E-07", "1.68E-04"], ["230750_at", "− 1.18", "1.04E-06", "2.61E-03"], ["231199_at", "− 1.15", "1.06E-06", "7.31E-02"], ["HIP1", "− 1.15", "1.08E-06", "2.53E-02"], ["RAD21", "− 1.14", "1.16E-06", "1.92E-03"], ["AFFX-r2-Bs-dap-5_at", "− 1.12", "1.31E-06", "7.41E-03"], ["1565717_s_at", "− 1.11", "1.33E-06", "7.37E-02"], ["SART3", "− 1.11", "1.42E-06", "2.05E-02"], ["C11orf53", "− 1.08", "2.35E-06", "1.74E-03"], ["C3orf75", "− 1.07", "2.38E-06", "1.29E-03"], ["GATC", "− 1.06", "2.68E-06", "1.09E-01"], ["FOXP4", "− 1.06", "2.69E-06", "7.63E-04"], ["CD47", "− 1.02", "2.86E-06", "5.20E-02"], ["KLF2", "− 1.01", "3.80E-06", "2.44E-03"], ["ATP6V0E1", "− 1.00", "4.23E-06", "5.23E-02"], ["AFFX-DapX-5_at", "− 0.99", "4.56E-06", "2.44E-02"], ["CPNE3", "− 0.99", "5.00E-06", "3.30E-03"], ["AFFX-r2-Bs-phe-M_at", "− 0.99", "5.14E-06", "1.35E-01"], ["SCARB2", "− 0.98", "5.45E-06", "1.47E-03"], ["MARCH6", "− 0.98", "7.30E-06", "6.71E-02"], ["RANBP2", "− 0.98", "9.07E-06", "1.42E-03"], ["CDC27", "− 0.97", "9.56E-06", "8.96E-02"], ["MDM4", "− 0.96", "1.01E-05", "2.95E-01"], ["MBNL1", "− 0.95", "1.02E-05", "6.66E-03"], ["FNIP2", "− 0.95", "1.13E-05", "8.85E-02"], ["ZNF207", "− 0.93", "1.15E-05", "3.23E-03"], ["TMED2", "− 0.93", "1.19E-05", "3.00E-02"], ["230655_at", "− 0.93", "1.26E-05", "8.48E-02"], ["VEZF1", "− 0.92", "1.48E-05", "1.72E-01"], ["ARF6", "− 0.92", "1.51E-05", "7.04E-03"], ["P4HB", "− 0.91", "1.72E-05", "1.84E-03"], ["SFRS6", "− 0.91", "2.10E-05", "8.20E-03"], ["RGS20", "− 0.89", "2.14E-05", "1.69E-01"], ["CAB39", "− 0.89", "2.50E-05", "1.56E-01"], ["SNAP23", "− 0.89", "2.86E-05", "1.29E-02"], ["AFFX-r2-Bs-thr-M_s_at", "− 0.89", "3.01E-05", "4.15E-02"], ["PHACTR2", "− 0.89", "3.35E-05", "1.07E-01"], ["FOXO3", "− 0.86", "3.40E-05", "2.33E-01"], ["NFKBIB", "− 0.85", "3.45E-05", "1.93E-03"], ["JAG1", "− 0.85", "3.01E-05", "3.02E-03"], ["IDH3A", "− 0.84", "2.04E-07", "2.88E-03"], ["RYK", "− 0.84", "7.30E-04", "3.29E-03"], ["SMAD7", "− 0.84", "1.13E-05", "1.42E-03"], ["ID2", "− 0.84", "2.14E-05", "1.66E-05"], ["AFFX-ThrX-M_at", "− 0.84", "7.30E-06", "2.23E-04"], ["AFFX-M27830_5_at", "− 0.83", "7.91E-07", "2.47E-03"], ["SERPINE1", "− 0.83", "2.68E-06", "9.90E-05"], ["MSI2", "− 0.82", "2.10E-05", "2.25E-03"], ["MAT2A", "− 0.82", "3.40E-05", "3.11E-04"], ["ARHGAP18", "− 0.81", "2.35E-06", "1.82E-03"], ["TPR", "− 0.81", "6.10E-10", "1.38E-04"], ["DLC1", "− 0.81", "1.26E-05", "3.19E-03"], ["AFFX-r2-Bs-lys-5_at", "− 0.80", "9.56E-06", "6.68E-04"], ["241773_at", "− 0.80", "9.07E-06", "1.19E-03"], ["AFFX-r2-Bs-dap-M_at", "− 0.80", "2.86E-05", "2.29E-03"], ["SBNO1", "− 0.80", "3.35E-05", "1.29E-03"], ["PRIM2", "− 0.79", "1.80E-04", "3.90E-04"], ["LIN7C", "− 0.77", "3.37E-03", "1.61E-04"], ["PTER", "− 0.75", "9.28E-07", "2.41E-03"], ["LOC100190986", "− 0.75", "1.48E-05", "2.42E-03"], ["SCD5", "− 0.74", "4.56E-06", "1.28E-04"], ["CXADR", "− 0.74", "1.51E-05", "2.44E-03"], ["222524_s_at", "− 0.73", "2.73E-02", "2.99E-03"], ["AFFX-r2-Bs-phe-5_at", "− 0.71", "4.23E-06", "2.89E-03"], ["220038_at", "− 0.71", "8.14E-08", "1.74E-03"], ["MGEA5", "− 0.70", "1.19E-05", "4.13E-04"], ["SLC7A11", "− 0.70", "5.51E-02", "2.47E-03"], ["SKIL", "− 0.70", "1.16E-06", "2.14E-04"], ["COQ2", "− 0.68", "1.01E-05", "7.63E-04"], ["DEAF1", "− 0.66", "3.48E-01", "1.45E-04"], ["242787_at", "− 0.65", "1.02E-05", "1.86E-03"], ["S100A10", "− 0.63", "1.72E-05", "6.26E-04"], ["ANKHD1", "− 0.61", "3.45E-05", "2.30E-03"], ["HARBI1", "− 0.39", "1.24E-02", "1.68E-04"], ["PICALM", "− 0.34", "4.95E-07", "3.27E-05"], ["C14orf118", "− 0.34", "1.66E-01", "2.55E-03"], ["GIMAP6", "0.62", "5.47E-03", "8.46E-04"], ["SAMD1", "0.64", "5.54E-02", "2.84E-03"], ["239355_at", "0.73", "1.65E-07", "9.59E-05"], ["ARHGEF1", "0.76", "1.50E-01", "3.36E-03"], ["CDK1", "0.77", "2.10E-04", "2.90E-04"], ["PRUNE2", "0.80", "4.50E-07", "7.42E-04"], ["CDK1", "0.80", "1.00E-04", "5.88E-04"], ["242611_at", "0.81", 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