Comparison of a human neuronal model proteome upon Japanese encephalitis or West Nile Virus infection and potential role of mosquito saliva in neuropathogenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32374750", "kind": "science-record", "revision": 7, "content_hash": "sha256:857fbcfc8a551d424725f01ac06b3ed67abe58ea20e7baebe05faae7943c37ba", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T22:01:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparison of a human neuronal model proteome upon Japanese encephalitis or West Nile Virus infection and potential role of mosquito saliva in neuropathogenesis.", "doi": "10.1371/journal.pone.0232585", "pmid": "32374750", "authors": ["Benoit Besson", "Justine Basset", "Sandrine Gatellier", "Hélène Chabrolles", "Thibault Chaze", "Véronique Hourdel", "Mariette Matondo", "Nathalie Pardigon", "Valérie Choumet"], "journal": "PloS one", "year": 2020, "abstract": "Neurotropic flavivirus Japanese encephalitis virus (JEV) and West Nile virus (WNV) are amongst the leading causes of encephalitis. Using label-free quantitative proteomics, we identified proteins differentially expressed upon JEV (gp-3, RP9) or WNV (IS98) infection of human neuroblastoma cells. Data are available via ProteomeXchange with identifier PXD016805. Both viruses were associated with the up-regulation of immune response (IFIT1/3/5, ISG15, OAS, STAT1, IRF9) and the down-regulation of SSBP2 and PAM, involved in gene expression and in neuropeptide amidation respectively. Proteins associated to membranes, involved in extracellular matrix organization and collagen metabolism represented major clusters down-regulated by JEV and WNV. Moreover, transcription regulation and mRNA processing clusters were also heavily regulated by both viruses. The proteome of neuroblastoma cells infected by JEV or WNV was significantly modulated in the presence of mosquito saliva, but distinct patterns were associated to each virus. Mosquito saliva favored modulation of proteins associated with gene regulation in JEV infected neuroblastoma cells while modulation of proteins associated with protein maturation, signal transduction and ion transporters was found in WNV infected neuroblastoma cells.", "claims": [{"id": "claim-method", "statement": "Statistical analysis of label free data was performed using the MS-Stat package on R environment [29].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32374750", "locator": "sections[7] \"Statistical analysis of label free MS data\" paragraph 2", "quote": "Statistical analysis of label free data was performed using the MS-Stat package on R environment [29]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All relevant data are within the manuscript and its Supporting Information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32374750", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "All relevant data are within the manuscript and its Supporting Information files."}], "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:32374750"], "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:PXD016805"], "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:PXD016805"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32374750", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0232585", "sha256": "sha256:e35ead43302cf58cb65504b196b143a3e8b043becfb61c89a57e42cbbd470ab3", "bytes": 59967, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0232585", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7202638", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD016805", "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=PXD016805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD016805", "version": null, "note": "All relevant data are within the manuscript and its Supporting Information files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All relevant data are within the manuscript and its Supporting Information files.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comparison of the Human Neuronal Proteome upon Japanese Encephalitis or West Nile Virus Infection and potential role of mosquito saliva in neuropathogenesis", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32374750:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:53b53adc1f432713174e8b0a0bc60e65a3ebf7c3a8068f00e0eadb8e3cbd7b1b", "bytes": 4131, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone.0232585.t001", "version": null, "note": "Top 10 up-regulated proteins during JEV and/or WNV infection.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells compared to the Mock. For complete list, see S1 Table.", "structure": {"pmcid": "PMC7202638", "section_index": 12, "section_title": "Identification of differentially expressed proteins following JEV or WNV infection", "row_count": 31, "column_count": 8}, "table": {"label": "Table 1", "caption": "Top 10 up-regulated proteins during JEV and/or WNV infection.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells compared to the Mock. For complete list, see S1 Table.", "rows": [["Effect", "Uniprot #", "GeneID #", "Gene symbol", "Name", "Clusters", "JEV/Mock FC (pValue)", "WNV/Mock FC (pValue)"], ["Up-regulated during JEV infection", "P32886", "1489713", "N/A", "JEV genomic polyprotein", "", "65.95 (0.00E+00)", ""], ["Q5EBM0-4", "129607", "CMPK2", "UMP-CMP kinase 2, mitochondrial", "Nucleotide-binding", "3.82 (3.25E-02)", ""], ["O60664", "10226", "PLIN3", "Perilipin-3", "Cell-cell adhesion", "1.82 (1.81E-06)", ""], ["P11047", "3915", "LAMC1", "Laminin subunit gamma-1", "Collagen metabolism, EGF-like domain, Extracellular matrix org., Glycoprotein", "1.80 (5.28E-06)", ""], ["Q9BXJ9", "80155", "NAA15", "N-alpha-acetyltransferase 15, NatA auxiliary subunit", "Tetratricopeptide repeat, Transcription regulation", "1.78 (1.80E-02)", ""], ["O00622", "3491", "CYR61", "Protein CYR61", "Glycoprotein, Nucleotide-binding", "1.76 (1.82E-02)", ""], ["Q9Y520-4", "23215", "PRRC2C", "Protein PRRC2C", "", "1.76 (1.16E-02)", ""], ["Q9Y3Z3", "25939", "SAMHD1", "Deoxynucleoside triphosphate triphosphohydrolase SAMHD1", "Innate immunity", "1.74 (1.58E-05)", ""], ["F8VVL1", "8562", "DENR", "Density-regulated protein", "", "1.66 (2.90E-02)", ""], ["Q9UNF0-2", "11252", "PACSIN2", "Protein kinase C and casein kinase substrate in neurons protein 2", "Cell-cell adhesion", "1.66 (2.26E-02)", ""], ["Up-regulated during both JEV and WNV infection", "P09914", "3434", "IFIT1", "Interferon-induced protein with tetratricopeptide repeats 1", "Innate immunity, Tetratricopeptide repeat", "13.60 (1.34E-13)", "7.838 (2.36E-09)"], ["O14879", "3437", "IFIT3", "Interferon-induced protein with tetratricopeptide repeats 3", "Innate immunity, Tetratricopeptide repeat", "12.31 (0.00E+00)", "6.944 (3.20E-13)"], ["P05161", "9636", "ISG15", "Ubiquitin-like protein ISG15", "Anchored protein, Innate immunity", "9.08 (7.93E-09)", "4.59 (4.85E-05)"], ["Q9Y6K5", "4940", "OAS3", "2'-5'-oligoadenylate synthase 3", "Innate immunity, Nucleotide-binding, Transmembrane protein", "5.32 (0.00E+00)", "3.17 (0.00E+00)"], ["P42224", "6772", "STAT1", "Signal transducer and activator of transcription 1-alpha/beta", "Cell-cell adhesion, Innate immunity, Transcription regulation", "3.96 (0.00E+00)", "2.49 (0.00E+00)"], ["Q9BQE5", "23780", "APOL2", "Apolipoprotein L2", "Transmembrane protein", "3.04 (9.67E-04)", "2.13 (4.43E-02)"], ["Q13325", "24138", "IFIT5", "Interferon-induced protein with tetratricopeptide repeats 5", "Innate immunity, Tetratricopeptide repeat, Transmembrane protein", "2.98 (5.96E-11)", "1.93 (6.50E-05)"], ["Q8WUP2-3", "54751", "FBLIM1", "Filamin-binding LIM protein 1", "", "2.96 (4.13E-02)", "2.94 (4.26E-02)"], ["Q5K651", "54809", "SAMD9", "Sterile alpha motif domain-containing protein 9", "2.61 (9.24E-05)", "2.11 (4.97E-04)"], ["Q9NUQ6-2", "26010", "SPATS2L", "SPATS2-like protein", "", "2.47 (2.95E-09)", "2.02 (2.37E-06)"], ["Up-regulated during WNV infection", "P06935", "912267", "N/A", "WNV genomic polyprotein", "", "", "271.78 (3.88E-04)"], ["Q6GMV3", "391356", "PTRHD1", "Putative peptidyl-tRNA hydrolase PTRHD1", "", "4.22 (3.58E-02)"], ["Q5QNY5", "5824", "PEX19", "Peroxisomal biogenesis factor 19", "Transmembrane", "", "3.35 (1.43E-03)"], ["Q96C90", "26472", "PP1R14B", "Protein phosphatase 1 regulatory subunit 14B", "", "2.21 (1.43E-02)"], ["P0DMV8/9", "3303", "HSPA1A", "Heat shock 70 kDa protein 1A", "Cell-cell adhesion, Nucleotide-binding", "2.03 (4.86E-11)"], ["Q9Y6G9", "51143", "YNC1LI1", "Cytoplasmic dynein 1 light intermediate chain 1", "Nucleotide-binding", "", "2.01 (2.58E-02)"], ["Q8TDX7", "140609", "NEK7", "Serine/threonine-protein kinase Nek7", "Kinase, Nucleotide-binding", "1.99 (8.66E-03)"], ["Q9BUF5", "84617", "TUBB6", "Tubulin beta-6 chain", "Nucleotide-binding", "", "1.96 (2.40E-02)"], ["O95817", "9531", "BAG3", "BAG family molecular chaperone regulator 3", "Cell-cell adhesion", "", "1.96 (6.14E-03)"], ["O00592-2", "5420", "PODXL", "Podocalyxin", "Glycoprotein, Transmembrane", "1.77 (1.43E-02)"]], "row_count": 31, "column_count": 8, "numeric_cells": 115, "header_rows": 1, "locator": "section[12]/table-wrap[1]#pone.0232585.t001"}}, {"id": "asset:table:pmid:32374750:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3c8b10ec08c1673efd3255b77dc5b095e8cab8db459cc4e4156b3344319afa75", "bytes": 4295, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#pone.0232585.t002", "version": null, "note": "Top 10 down-regulated proteins during JEV and/or WNV infection.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells compared to the Mock. For complete list, see S2 Table.", "structure": {"pmcid": "PMC7202638", "section_index": 12, "section_title": "Identification of differentially expressed proteins following JEV or WNV infection", "row_count": 31, "column_count": 8}, "table": {"label": "Table 2", "caption": "Top 10 down-regulated proteins during JEV and/or WNV infection.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells compared to the Mock. For complete list, see S2 Table.", "rows": [["Effect", "Uniprot #", "GeneID #", "Gene symbol", "Name", "Clusters", "JEV/Mock FC (pValue)", "WNV/Mock FC (pValue)"], ["Down-regulated during JEV infection", "Q99797", "4285", "MIPEP", "Mitochondrial intermediate peptidase", "Metalloprotease", "7.84 (1.53E-03)", ""], ["P21810", "633", "BGN", "Biglycan", "Extracellular matrix org., Glycoprotein, Leucine-rich repeat", "3.21 (4.36E-02)", ""], ["Q8WZ42-5", "7273", "TTN", "Titin", "Immunoglobulin domain, Nucleotide-binding, Tetratricopeptide repeat", "3.12 (2.25E-02)", ""], ["O14657", "27348", "TOR1B", "Torsin-1B", "Glycoprotein, Nucleotide-binding", "3.09 (6.62E-03)", ""], ["P55083", "4239", "MFAP4", "Microfibril-associated glycoprotein 4", "Extracellular matrix org., Glycoprotein", "2.95 (6.07E-03)", ""], ["O75063", "9917", "FAM20B", "Glycosaminoglycan xylosylkinase", "Glycoprotein, Nucleotide-binding, Transmembrane protein", "2.70 (3.24E-02)", ""], ["Q9P032", "29078", "NDUFAF4", "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 4", "", "2.37 (2.00E-02)", ""], ["Q13641", "7162", "TPBG", "Trophoblast glycoprotein", "Glycoprotein, Leucine-rich repeat, Transmembrane protein", "2.36 (4.55E-02)", ""], ["Q86UV5-2", "84196", "USP48", "Ubiquitin carboxyl-terminal hydrolase 48", "", "2.24 (3.92E-02)", ""], ["P63218", "2787", "GNG5", "Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-5", "Anchored protein, Collagen metabolism", "2.22 (4.35E-02)", ""], ["Down-regulated during both JEV and WNV infection", "P81877-2", "23635", "SSBP2", "Single-stranded DNA-binding protein 2", "", "26.22 (2.60E-02)", "15,05 (3.46E-02)"], ["P19021-2", "5066", "PAM", "Peptidyl-glycine alpha-amidating monooxygenase", "Glycoprotein, Transmembrane protein", "5.05 (3.74E-02)", "9,23 (2.02E-02)"], ["P02452", "1277", "COL1A1", "Collagen alpha-1(I) chain", "Extracellular matrix org., Collagen metabolism, Glycoprotein, Transmembrane protein", "4.65 (0.00E+00)", "2,96 (0.00E+00)"], ["P08123", "1278", "COL1A2", "Collagen alpha-2(I) chain", "Extracellular matrix org., Collagen metabolism, Glycoprotein", "4.29 (0.00E+00)", "2,16 (5.21E-09)"], ["P02461", "1281", "COL3A1", "Collagen alpha-1(III) chain", "Extracellular matrix org., Collagen metabolism, Glycoprotein", "4.28 (0.00E+00)", "2,16 (1.89E-11)"], ["Q9H3M7", "10628", "TXNIP", "Thioredoxin-interacting protein", "Transcription regulation", "4.13 (1.20E-04)", "4,98 (1.82E-04)"], ["Q96CG8", "115908", "CTHRC1", "Collagen triple helix repeat-containing protein 1", "Extracellular matrix org., Collagen metabolism, Glycoprotein", "3.98 (0.00E+00)", "2,54 (0.00E+00)"], ["O95864", "9415", "FADS2", "Fatty acid desaturase 2", "Transmembrane protein", "3.41 (1.60E-12)", "3,36 (3.20E-11)"], ["Q15113", "5118", "PCOLCE", "Procollagen C-endopeptidase enhancer 1", "Extracellular matrix org., Collagen metabolism, Glycoprotein", "3.35 (0.00E+00)", "1,81 (3.60E-08)"], ["C9JEZ4", "10602", "CDC42EP3", "Cdc42 effector protein 3", "Transmembrane protein", "3.09 (8.20E-05)", "2,26 (1.88E-02)"], ["Down-regulated during WNV infection", "P33908", "4121", "MAN1A1", "Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA", "Glycoprotein, Transmembrane", "", "4.52 (4.01E-02)"], ["B4DWB0", "80224", "NUBPL", "Iron-sulfur protein NUBPL", "Glycoprotein, Nucleotide-binding", "", "4.30 (3.39E-02)"], ["Q8N129", "245812", "CNPY4", "Protein canopy homolog 4", "Glycoprotein", "", "3.65 (2.81E-02)"], ["H3BQR0", "10073", "SNUPN", "Snurportin-1", "", "", "3.10 (4.33E-02)"], ["Q16706", "4124", "MAN2A1", "Alpha-mannosidase 2", "Glycoprotein, Transmembrane", "", "2.98 (3.58E-02)"], ["Q9Y294", "25842", "ASF1A", "Histone chaperone ASF1A", "Transcription regulation", "", "2.93 (4.58E-02)"], ["Q9NRX1", "56902", "PNO1", "RNA-binding protein PNO1", "", "", "2.70 (4.97E-03)"], ["P07711", "1514", "CTSL", "Cathepsin L1", "Collagen metabolism, Glycoprotein, Lysosome", "", "2.63 (4.66E-02)"], ["P38571-2", "3988", "LIPA", "Lysosomal acid lipase/cholesteryl ester hydrolase", "Glycoprotein, Lysosome", "", "2.58 (1.19E-02)"], ["O00754-2", "4125", "MAN2B1", "Lysosomal alpha-mannosidase", "Glycoprotein, Lysosome", "", "2.53 (6.58E-03)"]], "row_count": 31, "column_count": 8, "numeric_cells": 115, "header_rows": 1, "locator": "section[12]/table-wrap[2]#pone.0232585.t002"}}, {"id": "asset:table:pmid:32374750:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:049af42cb7cffc470bd8f2359c9f456a537b01ff0d39fd4ed04971c878e60ea2", "bytes": 1268, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#pone.0232585.t003", "version": null, "note": "Effect of SGE on non infected human neuroblastoma cells.", "structure": {"pmcid": "PMC7202638", "section_index": 14, "section_title": "Role of mosquito saliva in a neuron model of infection", "row_count": 13, "column_count": 7}, "table": {"label": "Table 3", "caption": "Effect of SGE on non infected human neuroblastoma cells.", "rows": [["Effect", "Uniprot #", "GeneID #", "Gene symbol", "Name", "Fold change (adjusted pValue)", ""], ["Up-regulated in presence of SGE", "O95218-2", "9406", "ZRANB2", "zinc finger RANBP2-type containing 2", "3.04 (2,33E-03)", ""], ["Down-regulated in presence of SGE", "Q5QNY5", "5824", "PEX19", "peroxisomal biogenesis factor 19", "2.45 (3,45E-02)", ""], ["E9PJ95", "29099", "COMMD9", "COMM domain containing 9", "2.08 (1,87E-02)", ""], ["E7EQI7", "9897", "KIAA0196", "KIAA0196", "2.04 (1,77E-02)", ""], ["Q9NRG7-2", "56948", "SDR39U1", "short chain dehydrogenase/reductase family 39U member 1", "1.91 (1,49E-02)", ""], ["Q66K74", "55201", "MAP1S", "microtubule associated protein 1S", "1.79 (1,49E-02)", ""], ["O43592", "11260", "XPOT", "exportin for tRNA", "1.79 (2,33E-03)", "*"], ["Q9BZH6", "55717", "WDR11", "WD repeat domain 11", "1.68 (1,87E-02)", "*"], ["O60443", "1687", "DFNA5", "deafness associated tumor suppressor", "1.58 (1,65E-02)", ""], ["Q9HAV4", "57510", "XPO5", "exportin 5", "1.56 (5,53E-03)", "*"], ["O95373", "10527", "IPO7", "importin 7", "1.51 (1,58E-02)", "*"], ["* involved in nuclear transport", ""]], "row_count": 13, "column_count": 7, "numeric_cells": 42, "header_rows": 1, "locator": "section[14]/table-wrap[1]#pone.0232585.t003"}}, {"id": "asset:table:pmid:32374750:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e1c8a8539d7bd1cc25642a98d503a95590c949a89f3f872230dea79bb4a51bf0", "bytes": 2485, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#pone.0232585.t004", "version": null, "note": "Top 10 proteins up-regulated by SGE in JEV and/or WNV infected cells.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells treated or not with SGE. For complete list, see S5 Table.", "structure": {"pmcid": "PMC7202638", "section_index": 14, "section_title": "Role of mosquito saliva in a neuron model of infection", "row_count": 23, "column_count": 7}, "table": {"label": "Table 4", "caption": "Top 10 proteins up-regulated by SGE in JEV and/or WNV infected cells.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells treated or not with SGE. For complete list, see S5 Table.", "rows": [["Effect", "Protein #", "Gene ID #", "Gene", "Gene name", "JEV infected FC (adj. pValue)", "WNV infected FC (adj. pValue)"], ["Up-regulated proteins during JEV infection", "Q15388", "9804", "TOMM20", "translocase of outer mitochondrial membrane 20", "3.52 (1,94E-02)", ""], ["P16403", "3006", "HIST1H1C", "histone cluster 1 H1 family member c", "2.28 (2,48E-02)", ""], ["P07305", "3005", "H1F0", "H1 histone family member 0", "1.96 (7,76E-05)", ""], ["P53999", "10923", "SUB1", "SUB1 homolog transcriptional regulator", "1.92 (1,93E-02)", ""], ["Q5TAQ0", "84300", "UQCC2", "ubiquinol-cytochrome c reductase complex assembly factor 2", "1.85 (4,01E-02)", ""], ["Q9NR30", "9188", "DDX21", "DExD-box helicase 21", "1.70 (3,02E-09)", ""], ["P11387", "7150", "TOP1", "topoisomerase DNA I", "1.64 (1,27E-03)", ""], ["O15446", "10849", "CD3EAP", "CD3e molecule associated protein", "1.60 (2,48E-02)", ""], ["Q9UIG0-2", "9031", "BAZ1B", "bromodomain adjacent to zinc finger domain 1B", "1.59 (1,85E-03)", ""], ["P11388", "7153", "TOP2A", "topoisomerase DNA II alpha", "1.57 (2,48E-02)", ""], ["Up-regulated proteins during JEV and WNV infection", "Q9BZF1-3", "114882", "OSBPL8", "oxysterol binding protein like 8", "1.57 (1,65E-04)", "1.55 (2,83E-05)"], ["P16401", "3009", "HIST1H1B", "histone cluster 1 H1 family member b", "2.01 (1,98E-06)", "1.50 (2,85E-03)"], ["Up-regulated proteins during WNV infection", "P60468", "10952", "SEC61B", "Sec61 translocon beta subunit", "", "7.71 (1,61E-07)"], ["H0YI58", "51290", "ERGIC2", "ERGIC and golgi 2", "", "3.90 (1,23E-02)"], ["Q9P0L0", "9218", "VAPA", "VAMP associated protein A", "", "3.78 (8,72E-04)"], ["P07099", "2052", "EPHX1", "epoxide hydrolase 1", "", "2.18 (5,44E-08)"], ["O15427", "9123", "SLC16A3", "solute carrier family 16 member 3", "", "2.10 (4,83E-02)"], ["Q13619", "8451", "CUL4A", "cullin 4A", "", "2.09 (3,11E-02)"], ["O00264", "10857", "PGRMC1", "progesterone receptor membrane component 1", "", "2.04 (2,72E-03)"], ["Q9BT22", "56052", "ALG1", "ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase", "2.01 (1,08E-02)"], ["P04844", "6185", "RPN2", "ribophorin II", "", "1.98 (1,66E-06)"], ["Q9HC07", "55858", "TMEM165", "transmembrane protein 165", "", "1.97 (2,59E-02)"]], "row_count": 23, "column_count": 7, "numeric_cells": 86, "header_rows": 1, "locator": "section[14]/table-wrap[2]#pone.0232585.t004"}}, {"id": "asset:table:pmid:32374750:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9aa0116fde97ae86f6af37dbb11c38d16b287369b3393109022957cfb65e1beb", "bytes": 2757, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[3]#pone.0232585.t005", "version": null, "note": "Top 10 proteins down-regulated by SGE in JEV and/or WNV infected cells.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells treated or not with SGE. For complete list, see S6 Table.", "structure": {"pmcid": "PMC7202638", "section_index": 14, "section_title": "Role of mosquito saliva in a neuron model of infection", "row_count": 26, "column_count": 7}, "table": {"label": "Table 5", "caption": "Top 10 proteins down-regulated by SGE in JEV and/or WNV infected cells.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells treated or not with SGE. For complete list, see S6 Table.", "rows": [["Effect", "Uniprot #", "GeneID #", "Gene symbol", "Name", "JEV infected FC (adj. pValue)", "WNV infected FC (adj. pValue)"], ["Down-regulated proteins during JEV infection", "Q99797", "4285", "MIPEP", "mitochondrial intermediate peptidase", "4.61 (3,06E-02)", ""], ["Q9Y6W5-2", "10163", "WASF2", "WAS protein family member 2", "3.67 (4,08E-05)", ""], ["E7ESU0", "10869", "USP19", "ubiquitin specific peptidase 19", "3.24 (4,61E-02)", ""], ["Q9BZX2", "7371", "UCK2", "uridine-cytidine kinase 2", "2.58 (1,85E-03)", ""], ["O95400", "10421", "CD2BP2", "CD2 cytoplasmic tail binding protein 2", "1.82 (1,53E-02)", ""], ["P00338", "3939", "LDHA", "lactate dehydrogenase A", "1.77 (2,33E-02)", ""], ["Q9Y316", "51072", "MEMO1", "mediator of cell motility 1", "1.75 (2,34E-03)", ""], ["Q9H3M7", "10628", "TXNIP", "thioredoxin interacting protein", "1.74 (3,06E-02)", ""], ["Q9NRG7-2", "56948", "SDR39U1", "short chain dehydrogenase/reductase family 39U member 1", "1.69 (2,48E-02)", ""], ["Q9NPQ8-4", "60626", "RIC8A", "RIC8 guanine nucleotide exchange factor A", "1.66 (3,29E-02)", ""], ["Down-regulated proteins during JEV and WNV infection", "R4GN98", "6277", "S100A6", "S100 calcium binding protein A6", "2.73 (1,22E-02)", "2.78 (1,49E-02)"], ["F8VZJ2", "4666", "NACA", "nascent polypeptide-associated complex alpha subunit", "1.80 (1,94E-02)", "2.15 (1,88E-03)"], ["Q15056-2", "7458", "EIF4H", "eukaryotic translation initiation factor 4H", "1.78 (1,80E-02)", "2.05 (1,60E-03)"], ["E9PGT6", "10920", "COPS8", "COP9 signalosome subunit 8", "1.67 (9,82E-03)", "2.22 (1,93E-04)"], ["P09382", "3956", "LGALS1", "galectin 1", "1.66 (7,22E-03)", "1.98 (2,36E-04)"], ["Down-regulated proteins during WNV infection", "Q9P0S9", "51522", "TMEM14C", "transmembrane protein 14C", "", "4.12 (1,10E-02)"], ["Q9NRX1", "56902", "PNO1", "partner of NOB1 homolog", "", "3.03 (1,23E-02)"], ["P61758", "7411", "VBP1", "VHL binding protein 1", "", "2.69 (1,93E-06)"], ["P49366", "1725", "DHPS", "deoxyhypusine synthase", "", "2.56 (1,36E-02)"], ["Q99497", "11315", "PARK7", "Parkinsonism associated deglycase", "", "2.49 (1,32E-07)"], ["Q04837", "6742", "SSBP1", "single stranded DNA binding protein 1", "", "2.14 (8,85E-05)"], ["O00499-9", "274", "BIN1", "bridging integrator 1", "", "2.06 (2,90E-02)"], ["O00743", "5537", "PPP6C", "protein phosphatase 6 catalytic subunit", "", "1.85 (2,85E-03)"], ["Q9Y3B8", "25996", "REXO2", "RNA exonuclease 2", "", "1.73 (1,36E-02)"], ["P46777", "6125", "RPL5", "ribosomal protein L5", "", "1.60 (2,73E-02)"]], "row_count": 26, "column_count": 7, "numeric_cells": 92, "header_rows": 1, "locator": "section[14]/table-wrap[3]#pone.0232585.t005"}}], "gaps": ["asset:data:geo:PXD016805 not downloaded", "asset:data:geo:PXD016805 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-3", "family": null, "specific": null, "label": "MS-Stat package on R environment", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical analysis of label free data was performed using the MS-Stat package on R environment [29]."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["hierarchical_cluster"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: hierarchical."}, "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": ["PXD016805"], "resolved_accessions": ["PXD016805"], "statements": ["All relevant data are within the manuscript and its Supporting Information files."], "basis": "The paper names PXD016805 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. 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