Integrated Analysis of a Gene Correlation Network Identifies Critical Regulation of Fibrosis by lncRNAs and TFs in Idiopathic Pulmonary Fibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32596346", "kind": "science-record", "revision": 7, "content_hash": "sha256:e28c09afc49db8bfe9b63912e7d71d46dfb2358fc7e7fccedb026458983e4802", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T22:01:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Analysis of a Gene Correlation Network Identifies Critical Regulation of Fibrosis by lncRNAs and TFs in Idiopathic Pulmonary Fibrosis.", "doi": "10.1155/2020/6537462", "pmid": "32596346", "authors": ["Fan Wang", "Pei Li", "Feng-Sen Li"], "journal": "BioMed research international", "year": 2020, "abstract": "Idiopathic pulmonary fibrosis (IPF), the most frequent form of irreversible interstitial pneumonia with unknown etiology, is characterized by massive remodeling of lung architecture and followed by progressive loss of lung function. However, the key regulatory genes and the specific signaling pathways involved in the onset and progression of IPF still remain unclear. The present study is aimed at investigating the key role of long noncoding RNAs (lncRNAs) and transcription factors (TFs) involved in the pathogenesis of IPF through the integrated analysis of three gene expression profiles from the GEO dataset (GSE2052, GSE44723, and GSE24206). A total of 8483 differentially expressed genes (DEGs) including 988 upregulated and 7495 downregulated genes were filtered. Subsequently, following the intersection of these DEGs, 29 overlapping genes were identified and further analyzed using a bioinformatics approach. Furthermore, the protein-protein interaction (PPI) network was used to obtain 18 modules of related genes. The hub genes were identified through hypergeometric testing, which were closely associated with ubiquitin-mediated proteolysis, the spliceosome, and the cell cycle. The significant difference was observed in the expression of these key genes, such as lncRNA MALAT1, E2F1, and YBX1, in the peripheral blood of IPF patients when compared with those normal control subjects by real-time polymerase chain reaction (RT-PCR) analysis. This study indicated that lncRNA MALAT1, E2F1, and YBX1 may be key regulators for the pathogenesis of IPF.", "claims": [{"id": "claim-method", "statement": "After pretreatment of the genes that came from more than one probe set, the DEGs identified with cutoff criteria of |logFC| > 1 and P < 0.05 by the classic t-test were considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32596346", "locator": "sections[4] \"2.2. Identification of Differential Gene Expression in IPF\" paragraph 2", "quote": "After pretreatment of the genes that came from more than one probe set, the DEGs identified with cutoff criteria of |logFC| > 1 and P < 0.05 by the classic t-test were considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the present study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32596346", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The datasets used and/or analyzed during the present study are available from the corresponding author on reasonable request."}], "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:32596346"], "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:GSE2052"], "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:GSE2052"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32596346", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/6537462", "sha256": 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"sha256:593c7a350faaad5e91d61a83596edbe0cf96a16896235af80a786da084bbf37b", "bytes": 3415, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#tab1", "version": null, "note": "DEGs were identified from three datasets, including 262 upregulated and 191 downregulated genes in IPF compared with normal lung tissues (upregulated genes were defined with fold change (FC) > 0 as the cutoff criterion. The opposite was defined as downregulated genes).", "structure": {"pmcid": "PMC7290873", "section_index": 11, "section_title": "3.1. Identification of Differentially Expressed Genes in IPF", "row_count": 4, "column_count": 2}, "table": {"label": "Table 1", "caption": "DEGs were identified from three datasets, including 262 upregulated and 191 downregulated genes in IPF compared with normal lung tissues (upregulated genes were defined with fold change (FC) > 0 as the cutoff criterion. The opposite was defined as downregulated genes).", "rows": [["DEGs", "Gene names"], ["Upregulated", "SULF1, DEAF1, SCG5, DSG2, SLC1A4, CCND2, KCNN4, ST6GAL1, SLC38A1, SEC11C, XPOT, DPY30, PFKP, DDB1, HEPH, CXCL13, ATXN10, SEL1L3, CIAO1, CCL19, STARD5, SLFN12, ROR2, VAT1L, FPGT, GMPPA, COL18A1, COL7A1, PIGF, LMO4, FAM120A, SLC29A3, TCFL5, IGFBP2, UQCRQ, CCNA2, TWSG1, TCTN3, ASPN, PAM, BPIFB1, FAIM, FBLN2, SCARA3, COMP, ABCC5, DIO2, CHEK2, MCM4, TM9SF2, NAB1, DGKA, PTGFRN, FAT1, DOK5, CNIH1, ACTN1, PLA2G12A, MAGED1, ALG1, TWIST1, TRIM5, RCN2, CXCL14, ARMC1, STMN3, HMCN1, WDR5B, CROT, LEF1, TMEM14A, PLA2G4A, FKBP10, ABCC3, SPR, ROBO1, OXR1, CRLF1, TRIAP1, KDELR3, DIRAS3, BBS2, TGFB3, LGMN, CDK2AP1, CXCL12, RRM2, STRBP, TSPAN6, DAP, COL6A3, FZD6, TDO2, GMDS, PPP2R5E, SUPT7L, ZKSCAN7, CDKN3, CNTNAP1, IGF1, GSS, LRRC8D, TMEM98, TRIM2, LTBP1, BACE2, BRD8, COLEC11, FXN, PAFAH1B3, PGAM1, COL5A2, AOC1, ANTXR1, TMEM69, IMPACT, NET1, MXRA5, RCN1, MYO1E, DUSP23, CDH3, RHOD, CYP2S1, POSTN, ICMT, PDLIM4, C1QTNF6, ACVR1, SYTL2, PLA2G7, MFAP2, ZDHHC13, TMED10, ALDH1A3, SLN, CPOX, CDKN2C, PPIC, XRCC5, CLDN1, NSG1, ITGA7, R3HDM1, ERGIC2, TRIM36, EYA2, RPL39L, CCL13, RBP5, DONSON, SERPINB5, TXNDC15, HOMER3, ARL1, UBE2E3, CRYM, MEOX1, TMEM45A, COL15A1, ATP1B1, LDLRAD4, STEAP3, NABP2, BDKRB2, DCLK1, CFH, TRO, ECM1, PFN2, IL13RA2, MYOF, FHL2, CADPS, ITGAV, PCNA, PTK7, KIF2C, MEGF8, BMP4, PDCD2L, PRMT6, TP53BP1, OSBPL6, FMO1, PDE1A, PBX3, ELOVL4, ATF7IP, SYNDIG1, TMEM158, CFI, ALDH3A1, CKAP2, MRPL2, COL14A1, EGFL6, LHX6, THBS2, RRM1, YLPM1, TM7SF3, MLEC, CFB, BCL11A, GPR87, ZNF436, CLNS1A, ATIC, LGR4, CYP24A1, SEMA3C, PDGFC, TP63, ARMCX2, NUSAP1, ASB2, SLC39A6"], [""], ["Downregulated", "MKLN1, ECHDC3, RAB32, SLC25A51, HOPX, MATN3, MAP2, ARHGAP6, EPB41L5, NRGN, HEY1, PCTP, ACVRL1, TBX5, ERMP1, NAGA, MPP1, TXNIP, LRRN3, FLOT1AATK, RCL1, CSF3R, ANXA3, TEK, GRK5, HES1, HSPA1L, GATA6, EMP2, SLCO2A1, PMM1, STARD13, SEC14L1, SPTBN1, GHRL, TSPAN7, NEBL, ZNF655, TMEM11, UIMC1, NCOA3, ZFP36, CREBBP, LDLR, RAB20, SERTAD1, PPFIBP1, REPS2, ELF1, CALCOCO2, CSRNP1, GPM6A, DLL4, FPR1, CARHSP1, ADARB1, LMO7, RCOR1, LRRC32, CTNNBIP1, CA4, PADI4, OSGIN1, CXCL2, EGFR, CHI3L2, LPIN2, ANKHD1, ARHGEF4, ARHGAP29, VAMP5, RAI2, CYTIP, PRX, IER5, DNM2, IL17RA, BHLHE40, SLC39A8, RAPGEF5, PTPRM, CNOT8, DLC1, TLK2, EPAS1, PRELP, MAFF, ABTB1, HSD17B6, NDEL1, HYAL1, HECA, HSPB8, DNAJB1, CDH13, RGS16, PTPN12, CD55, TIPARP, CRYAB, CD36, NUP153, PTPRB, ITSN2, TNNC1, MAPT, THBD, CDKN2D, AOC3, P2RY1, ZBTB16, CSF3, EDNRB, FAM167A, SRGAP2, SLCO1A2, DAPK2, AGTR1, RIMKLB, ASRGL1, ANG, CCK, BCL2L13, OSGIN2, ACSM5, KIAA0040, KDR, FUT1, DOCK9, GADD45G, CLDN5, LIFR, STXBP6, GPR4, S1PR1, SLC1A1, PLAG1, EDA, DENND3, IDI1, KHDRBS3, CLEC1A, INMT, MPP3, PLLP, MTSS1, FSTL3, CRTAC1, GTF2IRD1, F3, KLF10, KLRD1, FBLN5IZUMO4, PIR, MAOA, C1QL1, THRB, RNF182, ALDH6A1, FAM49A, ST6GALNAC3, SSFA2, SLC25A24, AMPH, ADAMTS8, PLSCR1, BCKDHA, STXBP4, FLRT3, AOX1, SYAP1, RLF, SSH2, DERA, PIM1, STARD3NL, SUN2, SEPP1, IL1R2, EIF2A, FAH, METTL7A, EIF4E3, CHRM2, 1-Mar, PDK1, TJP2, RASL11A, NKX3-1"]], "row_count": 4, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[11]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:32596346:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ae52efda3c297e90c40e8cedcb635b14d191a6e4d27e77d62c1e207fecd3f5f4", "bytes": 2111, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab2", "version": null, "note": "The significantly enriched analysis of differentially expressed genes in idiopathic pulmonary fibrosis.", "structure": {"pmcid": "PMC7290873", "section_index": 12, "section_title": "3.2. GO and KEGG Enrichment Analyses of Differentially Expressed Genes", "row_count": 25, "column_count": 5}, "table": {"label": "Table 2", "caption": "The significantly enriched analysis of differentially expressed genes in idiopathic pulmonary fibrosis.", "rows": [["Category", "Pathway ID", "Description", "Count", "P value"], ["GOTERM_BP", "GO:0007155", "Cell adhesion", "45", "1.46327E − 09"], ["GOTERM_BP", "GO:0022610", "Biological adhesion", "45", "1.50199E − 09"], ["GOTERM_BP", "GO:0042127", "Regulation of cell proliferation", "42", "9.51714E − 07"], ["GOTERM_BP", "GO:0035295", "Tube development", "18", "1.51015E − 05"], ["GOTERM_BP", "GO:0032103", "Positive regulation of response to external stimulus", "10", "1.56397E − 05"], ["GOTERM_BP", "GO:0001501", "Skeletal system development", "22", "1.77224E − 05"], ["GOTERM_MF", "GO:0005509", "Calcium ion binding", "38", "0.000949643"], ["GOTERM_MF", "GO:0019955", "Cytokine binding", "10", "0.001081524"], ["GOTERM_MF", "GO:0008009", "Chemokine activity", "6", "0.004374834"], ["GOTERM_MF", "GO:0042802", "Identical protein binding", "27", "0.00485805"], ["GOTERM_MF", "GO:0042379", "Chemokine receptor binding", "6", "0.005747644"], ["GOTERM_MF", "GO:0008017", "Microtubule binding", "7", "0.00692901"], ["GOTERM_CC", "GO:0044421", "Extracellular region part", "54", "3.94172E − 10"], ["GOTERM_CC", "GO:0005615", "Extracellular space", "38", "4.31806E − 07"], ["GOTERM_CC", "GO:0031012", "Extracellular matrix", "24", "2.55104E − 06"], ["GOTERM_CC", "GO:0005578", "Proteinaceous extracellular matrix", "22", "8.9433E − 06"], ["GOTERM_CC", "GO:0044459", "Plasma membrane part", "76", "5.14236E − 05"], ["GOTERM_CC", "GO:0031226", "Intrinsic to plasma membrane", "48", "0.000103242"], ["KEGG_PATHWAY", "hsa04512", "ECM-receptor interaction", "9", "0.00286045"], ["KEGG_PATHWAY", "hsa04060", "Cytokine-cytokine receptor interaction", "17", "0.003658523"], ["KEGG_PATHWAY", "hsa04510", "Focal adhesion", "13", "0.01357663"], ["KEGG_PATHWAY", "hsa04610", "Complement and coagulation cascades", "7", "0.014586106"], ["KEGG_PATHWAY", "hsa05414", "Dilated cardiomyopathy", "8", "0.017081193"], ["KEGG_PATHWAY", "hsa00360", "Phenylalanine metabolism", "4", "0.024804532"]], "row_count": 25, "column_count": 5, "numeric_cells": 72, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:32596346:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a29d5634e9b50968498f8e3dcb602e64be9976ba988f13d1be0117a3a214da74", "bytes": 2609, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tab3", "version": null, "note": "The significant GO enrichment analysis of module gene function in idiopathic pulmonary fibrosis.", "structure": {"pmcid": "PMC7290873", "section_index": 13, "section_title": "3.3. Construction and Enrichment Analysis of Modules", "row_count": 31, "column_count": 5}, "table": {"label": "Table 3", "caption": "The significant GO enrichment analysis of module gene function in idiopathic pulmonary fibrosis.", "rows": [["Category", "Pathway ID", "Pathway description", "Count", "P value"], ["GO_BP_m1", "GO:0000209", "Protein polyubiquitination", "47", "1.77E − 64"], ["GO_BP_m10", "GO:0097711", "Ciliary basal body-plasma membrane docking", "32", "6.55E − 71"], ["GO_BP_m11", "GO:0048193", "Golgi vesicle transport", "30", "9.70E − 41"], ["GO_BP_m12", "GO:0006898", "Receptor-mediated endocytosis", "19", "6.36E − 21"], ["GO_BP_m13", "GO:0060337", "Type I interferon signaling pathway", "20", "1.37E − 38"], ["GO_BP_m14", "GO:0007059", "Chromosome segregation", "29", "2.58E − 38"], ["GO_BP_m15", "GO:0009165", "Nucleotide biosynthetic process", "20", "2.61E − 27"], ["GO_BP_m16", "GO:0036297", "Interstrand cross-link repair", "16", "1.73E − 32"], ["GO_BP_m17", "GO:0006289", "Nucleotide-excision repair", "26", "7.46E − 53"], ["GO_BP_m18", "GO:0000280", "Nuclear division", "24", "7.63E − 35"], ["GO_CC_m1", "GO:0000151", "Ubiquitin ligase complex", "42", "1.34E − 54"], ["GO_CC_m10", "GO:0044450", "Microtubule organizing center part", "19", "1.93E − 29"], ["GO_CC_m11", "GO:0005875", "Microtubule-associated complex", "27", "1.16E − 46"], ["GO_CC_m12", "GO:0030136", "Clathrin-coated vesicle", "22", "8.55E − 33"], ["GO_CC_m13", "GO:0042611", "MHC protein complex", "5", "6.87E − 10"], ["GO_CC_m14", "GO:0000775", "Chromosome, centromeric region", "35", "4.74E − 59"], ["GO_CC_m15", "GO:0008074", "Guanylate cyclase complex, soluble", "2", "2.57E − 06"], ["GO_CC_m16", "GO:0043240", "Fanconi anemia nuclear complex", "7", "9.55E − 17"], ["GO_CC_m17", "GO:1990391", "DNA repair complex", "9", "3.70E − 17"], ["GO_CC_m18", "GO:0005819", "Spindle", "17", "5.08E − 23"], ["GO_MF_m1", "GO:0004842", "Ubiquitin-protein transferase activity", "69", "5.10E − 99"], ["GO_MF_m10", "GO:0005200", "Structural constituent of cytoskeleton", "6", "4.58E − 08"], ["GO_MF_m11", "GO:0003777", "Microtubule motor activity", "21", "3.95E − 38"], ["GO_MF_m12", "GO:0030276", "Clathrin binding", "9", "2.00E − 14"], ["GO_MF_m13", "GO:0042605", "Peptide antigen binding", "5", "2.31E − 09"], ["GO_MF_m14", "GO:0043515", "Kinetochore binding", "4", "9.27E − 10"], ["GO_MF_m15", "GO:0016776", "Phosphotransferase activity", "10", "4.97E − 20"], ["GO_MF_m16", "GO:0140097", "Catalytic activity, acting on DNA", "13", "5.26E − 17"], ["GO_MF_m17", "GO:0003684", "Damaged DNA binding", "16", "9.67E − 31"], ["GO_MF_m18", "GO:0004674", "Protein serine/threonine kinase activity", "8", "6.57E − 07"]], "row_count": 31, "column_count": 5, "numeric_cells": 117, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:32596346:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2c8913d3a71f3fc3ec993c063b39b164196f7e079ec55e1b3e999923af9a0072", "bytes": 3491, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#tab4", "version": null, "note": "The significant KEGG enrichment analysis of module gene function in idiopathic pulmonary fibrosis.", "structure": {"pmcid": "PMC7290873", "section_index": 13, "section_title": "3.3. Construction and Enrichment Analysis of Modules", "row_count": 19, "column_count": 5}, "table": {"label": "Table 4", "caption": "The significant KEGG enrichment analysis of module gene function in idiopathic pulmonary fibrosis.", "rows": [["Pathway", "Pathway description", "Count", "P value", "Genes"], ["KEGG_Pathway_m1", "Ubiquitin mediated proteolysis", "30", "1.21E − 46", "10273, 10477, 11065, 22954, 23327, 25898, 51433, 51434, 54926, 55070, 57154, 65264, 7318, 7320, 7321, 7323, 7326, 7328, 7332, 7428, 83737, 8454, 8697, 9021, 90293, 9246, 92912, 9820, 991, 6921"], ["KEGG_Pathway_m2", "Spliceosome", "30", "1.23E − 44", "10084, 10262, 10285, 10594, 10907, 10946, 10992, 1665, 22827, 51340, 51690, 57187, 57819, 6428, 6429, 6430, 6432, 6434, 6625, 6626, 6628, 6635, 7307, 8175, 84321, 8449, 84991, 9775, 988, 9984"], ["KEGG_Pathway_m15", "Purine metabolism", "26", "8.05E − 39", "10201, 11128, 124583, 171568, 205, 2987, 29922, 3704, 4831, 4832, 4833, 4881, 50484, 50808, 51251, 5138, 5315, 5422, 6240, 6241, 84284, 953, 955, 956, 2982, 2983"], ["KEGG_Pathway_m16", "Fanconi anemia pathway", "20", "2.23E − 37", "2067, 2072, 2176, 2178, 2188, 2189, 22909, 29089, 51426, 5429, 55120, 5889, 6118, 6119, 672, 80010, 80198, 84464, 80233, 91442"], ["KEGG_Pathway_m4", "Protein digestion and absorption", "21", "1.16E − 36", "1277, 1278, 1281, 1285, 1287, 1288, 1289, 1290, 1292, 1293, 1294, 1299, 1300, 1303, 1306, 1308, 255631, 7373, 80781, 81578, 85301"], ["KEGG_Pathway_m5", "Glutathione metabolism", "20", "1.44E − 36", "124975, 2678, 2687, 27306, 2878, 2879, 2880, 2882, 2937, 2938, 2941, 2948, 2949, 2950, 2952, 373156, 4257, 4258, 493869, 51060"], ["KEGG_Pathway_m6", "Ribosome", "20", "4.77E − 35", "11222, 29088, 51069, 51073, 51116, 51263, 51264, 51318, 54460, 54948, 6183, 63875, 63931, 64928, 64963, 64965, 64983, 65003, 65008, 79590"], ["KEGG_Pathway_m17", "Nucleotide excision repair", "16", "4.27E − 30", "1022, 1069, 1642, 1643, 2067, 2072, 2968, 3978, 5111, 5425, 6118, 6119, 7507, 7508, 8451, 902"], ["KEGG_Pathway_m9", "Neuroactive ligand-receptor interaction", "25", "7.26E − 28", "10161, 10800, 1131, 1241, 148, 154, 185, 1902, 1910, 2149, 2151, 2925, 3061, 3357, 3358, 4829, 4923, 5021, 5028, 5031, 624, 680, 6915, 7201, 9002"], ["KEGG_Pathway_m3", "Neuroactive ligand-receptor interaction", "25", "3.41E − 21", "1129, 1268, 150, 152, 1813, 187, 1901, 1902, 1903, 2357, 2358, 2359, 2587, 2913, 2918, 4543, 4887, 59340, 624, 6752, 6755, 719, 728, 9294, 9568"], ["KEGG_Pathway_m8", "Ribosome biogenesis in eukaryotes", "12", "5.45E − 20", "10171, 10799, 134430, 23560, 27341, 3692, 51096, 51119, 51602, 55341, 55651, 84916"], ["KEGG_Pathway_m7", "Ribosome", "17", "7.99E − 19", "11224, 25873, 51065, 6128, 6141, 6156, 6157, 6160, 6168, 6169, 6181, 6201, 6205, 6229, 6231, 6232, 6234"], ["KEGG_Pathway_m12", "Endocytosis", "16", "3.91E − 16", "10109, 1173, 1759, 1785, 1956, 22905, 26119, 27131, 273, 3949, 408, 5868, 6456, 6643, 867, 8976"], ["KEGG_Pathway_m13", "Herpes simplex infection", "11", "8.93E − 13", "10379, 3105, 3113, 3115, 3122, 3134, 3434, 3661, 4938, 4940, 6041"], ["KEGG_Pathway_m18", "Cell cycle", "7", "9.18E − 11", "4085, 701, 7272, 8379, 890, 891, 9133"], ["KEGG_Pathway_m14", "Oocyte meiosis", "8", "8.35E − 10", "4085, 5516, 5525, 5528, 5529, 8379, 891, 9133"], ["KEGG_Pathway_m11", "Vasopressin-regulated water reabsorption", "6", "1.07E − 09", "10540, 1639, 51164, 79659, 84516, 8655"], ["KEGG_Pathway_m10", "Pathogenic Escherichia coli infection", "3", "5.99E − 05", "203068, 7277, 7846"]], "row_count": 19, "column_count": 5, "numeric_cells": 63, "header_rows": 1, "locator": "section[13]/table-wrap[2]#tab4"}}, {"id": "asset:table:pmid:32596346:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:66c2a3d19a6b05aafbef1700f48913f9842ff265a2a1ce4a1d6b63046a76f38d", "bytes": 2549, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab5", "version": null, "note": "Functional roles of the strongest correlations of lncRNAs and TFs in IPF.", "structure": {"pmcid": "PMC7290873", "section_index": 14, "section_title": "3.4. Selection and Analysis of Key Genes", "row_count": 13, "column_count": 4}, "table": {"label": "Table 5", "caption": "Functional roles of the strongest correlations of lncRNAs and TFs in IPF.", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "MALAT1", "Metastasis-associated lung adenocarcinoma transcript 1", "Form molecular scaffolds for ribonucleoprotein complexes, acting as a transcriptional regulator for numerous genes, and involved in cell cycle regulation"], ["2", "RNU1-1", "RNA, U1 small nuclear 1", "Its related pathways are spliceosomal splicing cycle"], ["3", "FENDRR", "FOXF1 adjacent noncoding developmental regulatory RNA", "Bind to polycomb repressive complex 2 and/or TrxG/MLL complexes to promote the methylation of the promoters of target genes"], ["4", "TUG1", "Taurine upregulated 1", "Interacts with the polycomb repressor complex and functions in the epigenetic regulation of transcription, acting as a sponge for microRNAs"], ["5", "E2F1", "E2F transcription factor 1", "Bind preferentially to retinoblastoma protein pRB in a cell cycle-dependent manner and mediate both cell proliferation and p53-dependent/independent apoptosis"], ["6", "TP53", "Tumor protein P53", "Regulate expression of target genes, inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism"], ["7", "SP1", "Sp1 transcription factor", "Be involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling"], ["8", "YBX1", "Y-box binding protein 1", "Be implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation, and mRNA packaging"], ["9", "BRCA1", "Breast cancer type 1 susceptibility protein", "Play a role in transcription, DNA repair of double-stranded breaks, and recombination which forms a large multisubunit protein complex known as the BRCA1-associated genome surveillance complex and interacts with histone deacetylase complexes"], ["10", "E2F4", "E2F transcription factor 4", "Act as proliferation-associated suppression genes and bind to all three of the tumor suppressor proteins pRB, p107, and p130"], ["11", "CREB1", "CAMP responsive element binding protein 1", "Its related pathways are development of HGF signaling pathway and circadian entrainment"], ["12", "CIITA", "Class II major histocompatibility complex transactivator", "Once it does not bind DNA but rather uses an intrinsic acetyltransferase activity to act in a coactivator-like fashion"]], "row_count": 13, "column_count": 4, "numeric_cells": 26, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tab5"}}, {"id": "asset:table:pmid:32596346:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d2133cec8791b6d624d010e150c6b45f86778dfe404305a9c353701194a01a97", "bytes": 886, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tab6", "version": null, "note": "Demographic and clinical characteristics of the subjects.", "structure": {"pmcid": "PMC7290873", "section_index": 15, "section_title": "3.5. 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