[Identification of candidate genes for lung adenocarcinoma using Toppgene].

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:20677550", "kind": "science-record", "revision": 6, "content_hash": "sha256:583299e2a0212ccb22761b39ddab412836cde17d0f3a1beecf1d5620abaa23dd", "created_at": "2026-11-01T15:14:34Z", "updated_at": "2026-11-01T21:19:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[Identification of candidate genes for lung adenocarcinoma using Toppgene].", "doi": "10.3779/j.issn.1009-3419.2010.04.02", "pmid": "20677550", "authors": ["Guiping Wang", "Yun Ye", "Wenling Zheng", "Wenli Ma"], "journal": "Zhongguo fei ai za zhi = Chinese journal of lung cancer", "year": 2010, "abstract": "BACKGROUND AND OBJECTIVE: Lung adenocarcinoma (AC) is the most common type of lung cancer, however, its mechanism of oncongenesis is still unknown. The aim of this study is to screen candidate genes of lung adenocarcinoma using bioinformatics strategy and elucidate the mechanism of lung adenocarcinoma.\nMETHODS: Two published microarray data (GSE7670 and GSE10072) was obtained from Gene Expression Omnibus (GEO). Significance analysis of microarrays was performed with the software dchip, and differential expression genes from dchip analysis were defined as \"test gene set\". Genes correlated with lung adenocarcinoma, obtained by data mining tools genecard and Fable were regarded as \"train gene set\". Finally, candidate genes of lung adenocarcinoma were screened by the tool \"Toppgene\".\nRESULTS: Three hundred and forty-four differential genes were defined as \"test gene set\", and 277 genes correlated with lung adenocarcinoma were regarded as \"train gene set\". Thirty-six candidate genes were screened out by Toppgene, among them, 21 genes had nearly no report in cancer. In the following QRT-PCR experiment, CD36, PMAIP1 and FABP4 were down-regulated expression in A549, which coincided with the gene chip.\nCONCLUSION: It is demonstrated that Toppgene is useful in identification of the candidate genes of lung adenocacinoma, which provides the proof for the discovery of the specific disease genes.", "claims": [{"id": "claim-method", "statement": "我们对GSE10072和GSE7670数据集中质量合格芯片样本分别采用dchip进行差异基因分析，具体操作方法按dchip操作指南进行（http://www.dchip.org），2-fold change的基因被选择为差异表达基因。最后，采用交集方法获得共同差异基因。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:20677550", "locator": "sections[7] \"肺腺癌差异表达基因分析[9]\" paragraph 2", "quote": "我们对GSE10072和GSE7670数据集中质量合格芯片样本分别采用dchip进行差异基因分析，具体操作方法按dchip操作指南进行（http://www.dchip.org），2-fold change的基因被选择为差异表达基因。最后，采用交集方法获得共同差异基因。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "首先，我们从NCBI的GEO数据库（http:www.ncbi.nlm.nih.gov/geo）中下载2个基因表达谱数据集，即GSE7670和GSE10072。其中，GSE7670数据集来源于台湾台北荣民总医院（Taipei veterans general hospital），采用GPL96芯片平台（[HG-U133A] Affymetrix Human Genome U133A Array），包括27个配对的正常肺组织与肺腺癌组织、2个混合组织、2个商业化的正常肺组织、1个正常肺上皮细胞株与7个商业化肺癌细胞株，共64个样本；而另一个数据集GSE10072则来源于美国N.I.H遗传流行病学部（Genetic Epidemiology Branch），也采用GPL96芯片平台，疾病组织类型为肺腺癌，包括58个腺癌和49个正常肺组织，共107个样本。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:20677550", "locator": "sections[6] \"获取GEO数据集\" paragraph 2", "quote": "首先，我们从NCBI的GEO数据库（http:www.ncbi.nlm.nih.gov/geo）中下载2个基因表达谱数据集，即GSE7670和GSE10072。其中，GSE7670数据集来源于台湾台北荣民总医院（Taipei veterans general hospital），采用GPL96芯片平台（[HG-U133A] Affymetrix Human Genome U133A Array），包括27个配对的正常肺组织与肺腺癌组织、2个混合组织、2个商业化的正常肺组织、1个正常肺上皮细胞株与7个商业化肺癌细胞株，共64个样本；而另一个数据集GSE10072则来源于美国N.I.H遗传流行病学部（Genetic Epidemiology Branch），也采用GPL96芯片平台，疾病组织类型为肺腺癌，包括58个腺癌和49个正常肺组织，共107个样本。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "该研究从GEO数据库获取GSE10072和GSE7670数据集，经dchip差异表达分析形成检测基因集，并将Genecards与Fable挖掘的已知疾病基因作为训练基因集，利用Toppgene筛选出36个候选疾病基因，其中21个在肿瘤方面的研究几无报道。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:20677550", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "从GEO数据库中获得GSE10072和GSE7670两个数据集，然后利用dchip软件进行差异表达基因分析，将其获得的差异基因定义为“检测基因集”（test gene set）；采用genecard和Fable文献挖掘已知肺腺癌疾病基因，并将其定义为“训练基因集”（train gene set）；最后，利用Toppgene筛选肺腺癌候选基因，并通过荧光定量PCR对其获得的部分基因进行验证。"}, {"asset": "source:pmid:20677550", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "采用Toppgene共获得36个候选疾病基因，其中21个基因则在肿瘤方面的研究几无报道。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "该研究从GEO数据库获取GSE10072和GSE7670数据集，经dchip差异表达分析形成检测基因集，并将Genecards与Fable挖掘的已知疾病基因作为训练基因集，利用Toppgene筛选出36个候选疾病基因，其中21个在肿瘤方面的研究几无报道。", "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:20677550"], "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:GSE10072"], "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:GSE10072"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:20677550", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3779/j.issn.1009-3419.2010.04.02", "sha256": "sha256:893f95788f370551261a6d63a0afbc3c0778b2f3621339db39152b7b13b79247", "bytes": 6026, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3779/j.issn.1009-3419.2010.04.02", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6000438", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10072", "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=GSE10072", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10072", "version": null, "note": "首先，我们从NCBI的GEO数据库（http:www.ncbi.nlm.nih.gov/geo）中下载2个基因表达谱数据集，即GSE7670和GSE10072。其中，GSE7670数据集来源于台湾台北荣民总医院（Taipei veterans general hospital），采用GPL96芯片平台（[HG-U133A] Affymetrix Human Genome U133A Array），包括27个配对的正常肺组织与肺腺癌组织、2个混合组织、2个商业化的正常肺组织、1个正常肺上皮细胞株与7个商业化肺癌细胞株，共64个样本；而另一个数据集GSE10072则来源于美国N.I.H遗传流行病学部（Genetic Epidemiology Branch），也采用GPL96芯片平台，疾病组织类型为肺腺癌，包括58个腺癌和49个正常肺组织，共107个样本。", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "首先，我们从NCBI的GEO数据库（http:www.ncbi.nlm.nih.gov/geo）中下载2个基因表达谱数据集，即GSE7670和GSE10072。其中，GSE7670数据集来源于台湾台北荣民总医院（Taipei veterans general hospital），采用GPL96芯片平台（[HG-U133A] Affymetrix Human Genome U133A Array），包括27个配对的正常肺组织与肺腺癌组织、2个混合组织、2个商业化的正常肺组织、1个正常肺上皮细胞株与7个商业化肺癌细胞株，共64个样本；而另一个数据集GSE10072则来源于美国N.I.H遗传流行病学部（Genetic Epidemiology Branch），也采用GPL96芯片平台，疾病组织类型为肺腺癌，包括58个腺癌和49个正常肺组织，共107个样本。", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM254625", "GSM254626", "GSM254627", "GSM254628", 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"resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7670", "version": null, "note": "首先，我们从NCBI的GEO数据库（http:www.ncbi.nlm.nih.gov/geo）中下载2个基因表达谱数据集，即GSE7670和GSE10072。其中，GSE7670数据集来源于台湾台北荣民总医院（Taipei veterans general hospital），采用GPL96芯片平台（[HG-U133A] Affymetrix Human Genome U133A Array），包括27个配对的正常肺组织与肺腺癌组织、2个混合组织、2个商业化的正常肺组织、1个正常肺上皮细胞株与7个商业化肺癌细胞株，共64个样本；而另一个数据集GSE10072则来源于美国N.I.H遗传流行病学部（Genetic Epidemiology Branch），也采用GPL96芯片平台，疾病组织类型为肺腺癌，包括58个腺癌和49个正常肺组织，共107个样本。", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "首先，我们从NCBI的GEO数据库（http:www.ncbi.nlm.nih.gov/geo）中下载2个基因表达谱数据集，即GSE7670和GSE10072。其中，GSE7670数据集来源于台湾台北荣民总医院（Taipei veterans general hospital），采用GPL96芯片平台（[HG-U133A] Affymetrix Human Genome U133A Array），包括27个配对的正常肺组织与肺腺癌组织、2个混合组织、2个商业化的正常肺组织、1个正常肺上皮细胞株与7个商业化肺癌细胞株，共64个样本；而另一个数据集GSE10072则来源于美国N.I.H遗传流行病学部（Genetic Epidemiology Branch），也采用GPL96芯片平台，疾病组织类型为肺腺癌，包括58个腺癌和49个正常肺组织，共107个样本。", 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null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from Lung cancer", "resolution_checked_at": "2026-11-01T15:14:33Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:20677550:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7904443232ba033d06e9ffb63d737317b11d3c8cd7d5fb3d2219529900d2b982", "bytes": 488, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Table1", "version": null, "note": "GSE7670和GSE10072中芯片样本差异表达基因分析结果Analysis of lung adenocarcinoma differential expression genes against two GEO gene sets GSE10072 and GSE7670", "structure": {"pmcid": "PMC6000438", "section_index": 13, "section_title": "肺腺癌差异表达基因", "row_count": 4, "column_count": 4}, "table": {"label": "1", "caption": "GSE7670和GSE10072中芯片样本差异表达基因分析结果Analysis of lung adenocarcinoma differential expression genes against two GEO gene sets GSE10072 and GSE7670", "rows": [["GEO datasets", "Platform", "Up-expressed gene", "Down-expressed gene"], ["GSE7670", "GPL96", "123", "385"], ["GSE10072", "GPL96", "198", "363"], ["Co-expressed gene", "", "94", "285"]], "row_count": 4, "column_count": 4, "numeric_cells": 10, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Table1"}}, {"id": "asset:table:pmid:20677550:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4e76db5ca4678f1d5db1f869eae800bd6435be5239995d04e77a7ed1504340a8", "bytes": 2161, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Table2", "version": null, "note": "Toppgene筛选新的肺腺癌疾病候选基因（注：选取P < 0.01的基因）The screen of lung adenocarcinoma candidate genes using Toppgene (Note: Genes were selected based on P < 0.01)", "structure": {"pmcid": "PMC6000438", "section_index": 15, "section_title": "筛选新的肺腺癌疾病基因", "row_count": 37, "column_count": 5}, "table": {"label": "2", "caption": "Toppgene筛选新的肺腺癌疾病候选基因（注：选取P < 0.01的基因）The screen of lung adenocarcinoma candidate genes using Toppgene (Note: Genes were selected based on P < 0.01)", "rows": [["Rank", "Gene Symbol", "Gene ID", "Average score", "P"], ["1", "CD36", "948", "0.470 761 5", "0.000 000 1"], ["2", "HBEGF", "1839", "0.529 077 5", "0.000 000 6"], ["3", "PMAIP1", "5366", "0.572 612 2", "0.000 001 1"], ["4", "TYMS", "7298", "0.485 545 3", "0.000 001 8"], ["5", "TEK", "7010", "0.486 797 7", "0.000 001 8"], ["6", "COL1A1", "1277", "0.319 382 1", "0.000 004"], ["7", "IGFBP3", "3486", "0.456 963 2", "0.000 006 9"], ["8", "SPP1", "6696", "0.503 422 5", "0.000 007"], ["9", "EDN1", "1906", "0.471 195 9", "0.000 008 1"], ["10", "TIE1", "7075", "0.541 537 4", "0.000 010 4"], ["11", "TGFBR3", "7049", "0.497 567 5", "0.000 010 4"], ["12", "CDKN1C", "1028", "0.431 009 4", "0.000 013 1"], ["13", "NR4A1", "3164", "0.401 529 2", "0.000 017 5"], ["14", "CXCL2", "2920", "0.455 321 7", "0.000 030 6"], ["15", "BMP2", "650", "0.380 468 4", "0.000 039 1"], ["16", "CSF3", "1440", "0.438 977 1", "0.000 200 2"], ["17", "SFN", "2810", "0.455 187 2", "0.000 266 3"], ["18", "MMP7", "4316", "0.398 214 1", "0.000 267"], ["19", "COL1A2", "1278", "0.362 644 5", "0.000 572 2"], ["20", "FABP4", "2167", "0.330 210 4", "0.000 708 5"], ["21", "CEACAM1", "634", "0.404 989 1", "0.000 729 4"], ["22", "LEPR", "3953", "0.370 081 7", "0.001 032 8"], ["23", "DST", "667", "0.388 865 5", "0.001 492 4"], ["24", "UBE2C", "11065", "0.345 610 4", "0.001 553 9"], ["25", "GATA6", "2627", "0.280 920 4", "0.001 912 6"], ["26", "ATF3", "467", "0.307 962 8", "0.002 073 1"], ["27", "SORBS1", "10580", "0.395 258 5", "0.002 167 8"], ["28", "CXCL3", "2921", "0.384 477 2", "0.002 625 5"], ["29", "CRYAB", "1410", "0.352 635 4", "0.002 788 1"], ["30", "EDNRB", "1910", "0.334 035 3", "0.003 291 3"], ["31", "DLC1", "10395", "0.407 277 2", "0.003 520 2"], ["32", "HBB", "3043", "0.283 212 9", "0.004 263 6"], ["33", "CP", "1356", "0.349 502 5", "0.004 849 8"], ["34", "COL3A1", "1281", "0.291 960 6", "0.006 152 1"], ["35", "SLC2A1", "6513", "0.263 899 8", "0.006 28"], ["36", "NME1", "4830", "0.338 435 6", "0.010 138 1"]], "row_count": 37, "column_count": 5, "numeric_cells": 145, "header_rows": 1, "locator": "section[15]/table-wrap[1]#Table2"}}, {"id": "asset:table:pmid:20677550:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dc52b4566c53c2ab48491e25bc6508b5dbdcbb3dd0f5f7c0e9b4f8e143c041f0", "bytes": 912, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#Table3", "version": null, "note": "CD36、PMAIP1及FABP4的荧光定量PCR实验结果Expression of three genes CD36, PMAIP1 and FABP4 using fluorescent quantitation PCR", "structure": {"pmcid": "PMC6000438", "section_index": 16, "section_title": "荧光定量PCR实验验证", "row_count": 10, "column_count": 6}, "table": {"label": "3", "caption": "CD36、PMAIP1及FABP4的荧光定量PCR实验结果Expression of three genes CD36, PMAIP1 and FABP4 using fluorescent quantitation PCR", "rows": [["Gene", "Sample", "Average Ct", "Average△CT", "Average △△CT", "2-△△Ct"], ["△Ct=target gene Ct-actin Ct; △△Ct=sample target gene△Ct-reference sample target gene△Ct; when the amplification rate of PCR get close to 100%, relative sample template product=2-△△Ct."], ["CD36", "16-HBE", "31.41", "13.43", "0", "1"], ["CD36", "A549", "32.21", "13.73", "0.285", "0.821"], ["PMAIP1", "16-HBE", "34.34", "16.36", "0", "1"], ["PMAIP1", "A549", "40.96", "22.48", "7.12", "0.0072"], ["FABP4", "16-HBE", "31.24", "13.26", "0", "1"], ["FABP4", "A549", "32.51", "14.03", "0.77", "0.588"], ["β-actin", "16-HBE", "17.98", "", "", ""], ["β-actin", "A549", "18.48", "", "", ""]], "row_count": 10, "column_count": 6, "numeric_cells": 38, "header_rows": 1, "locator": "section[16]/table-wrap[1]#Table3"}}], "gaps": ["asset:data:geo:GSE10072 not downloaded", "asset:data:geo:GSE10072 licence not read", "asset:data:geo:GSE7670 not downloaded", "asset:data:geo:GSE7670 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "dchip软件差异表达基因分析，采用2-fold change筛选并以交集法获得共同差异基因", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "我们对GSE10072和GSE7670数据集中质量合格芯片样本分别采用dchip进行差异基因分析，具体操作方法按dchip操作指南进行（http://www.dchip.org），2-fold change的基因被选择为差异表达基因。最后，采用交集方法获得共同差异基因。"}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (dchip软件差异表达基因分析，采用2-fold change筛选并以交集法获得共同差异基因), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE7670", "GSE10072"], "resolved_accessions": ["GSE7670", "GSE10072"], "statements": ["首先，我们从NCBI的GEO数据库（http:www.ncbi.nlm.nih.gov/geo）中下载2个基因表达谱数据集，即GSE7670和GSE10072。其中，GSE7670数据集来源于台湾台北荣民总医院（Taipei veterans general hospital），采用GPL96芯片平台（[HG-U133A] Affymetrix Human Genome U133A Array），包括27个配对的正常肺组织与肺腺癌组织、2个混合组织、2个商业化的正常肺组织、1个正常肺上皮细胞株与7个商业化肺癌细胞株，共64个样本；而另一个数据集GSE10072则来源于美国N.I.H遗传流行病学部（Genetic Epidemiology Branch），也采用GPL96芯片平台，疾病组织类型为肺腺癌，包括58个腺癌和49个正常肺组织，共107个样本。"], "basis": "The paper names GSE7670, GSE10072 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:20677550", "data:geo:GSE10072", "asset:table:pmid:20677550:1", "asset:table:pmid:20677550:2", "asset:table:pmid:20677550:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10072"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:45Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 30616, "completion_tokens": 5500, "cached_tokens": 23532}}, "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:20677550", "type": "paper", "label": "pmid:20677550"}, {"id": "source:pmid:20677550", "type": "manuscript", "label": "PMID 20677550 full text"}, {"id": "data:geo:GSE10072", "type": "dataset", "label": "GEO GSE10072"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:20677550", "type": "paper", "label": "pmid:20677550"}, {"id": "source:pmid:20677550", "type": "manuscript", "label": "PMID 20677550 full text"}, {"id": "data:geo:GSE10072", "type": "dataset", "label": "GEO GSE10072"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-20677550", "type": "extraction", "used": ["source:pmid:20677550"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10072", "type": "accession_resolution", "used": ["data:geo:GSE10072"], "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:20677550", "parent_hash": "sha256:69aba93e4f2a77d495f9141a863b6cb51b597ec27742800b81d03eddf454778f", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE10072 licence not read", "asset:data:geo:GSE10072 not downloaded", "asset:data:geo:GSE7670 licence not read", "asset:data:geo:GSE7670 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["lung adenocarcinoma. METHODS: Two published microarray data (GSE7670 and GSE10072) was obtained fro"], "order_basis": "paper_text_order:359", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["and FABP4 were down-regulated expression in A549, which coincided with the gene chip. CONCLUS"], "order_basis": "paper_text_order:1203", "id": "assay:2"}]}