{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26131905", "kind": "science-record", "revision": 7, "content_hash": "sha256:43a67168e7991c5b929badea331b8ed9d755d07b56e3d6238567aa6dc7feddbc", "created_at": "2026-11-01T15:40:09Z", "updated_at": "2026-11-01T21:58:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians.", "doi": "10.1371/journal.pone.0132045", "pmid": "26131905", "authors": ["Xiaofang Geng", "Gaiping Wang", "Yanli Qin", "Xiayan Zang", "Pengfei Li", "Zhi Geng", "Deming Xue", "Zimei Dong", "Kexue Ma", "Guangwen Chen", "Cunshuan Xu"], "journal": "PloS one", "year": 2015, "abstract": "The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR) remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. 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"access_route": "GEO accession URL", "access_statement_verbatim": "All relevant data are within the paper 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": "iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians", "resolution_checked_at": "2026-11-01T15:39:58Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26131905:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0673e6d4d7f225cb8c516bd07531b070644ce6484c677a24c76768b6f0cb386f", "bytes": 5512, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone.0132045.t001", "version": null, "note": "Relative expression abundance of the representative proteins in four clusters at the early stage of planarian head regeneration.", "structure": {"pmcid": "PMC4488856", "section_index": 12, "section_title": "Functional enrichment analysis of the differentially expressed proteins at the early stage of planarian head regeneration", "row_count": 63, "column_count": 9}, "table": {"label": "Table 1", "caption": "Relative expression abundance of the representative proteins in four clusters at the early stage of planarian head regeneration.", "rows": [["Accession", "Protein Name", "Gene", "MW [kDa]", "calc. pI", "Coverage", "Unique Peptides", "2h*", "6h*"], ["Carbohydrate and energy metabolism (Cluster 1 and 3)"], ["F1R2A3", "ATP-dependent 6-phosphofructokinase, platelet type", "PFKP", "35.8", "7.0", "8.0", "2", "0.52", "1.10"], ["P85968", "6-phosphogluconate dehydrogenase, decarboxylating", "PGD", "53.2", "7.0", "29.4", "8", "0.56", "0.94"], ["P30835", "6-phosphofructokinase, liver type", "PFKL", "85.3", "7.4", "6.3", "2", "0.61", "1.14"], ["D4A7P8", "2-oxoglutarate dehydrogenase, mitochondrial", "OGDH", "115.2", "6.9", "24.1", "10", "0.65", "1.76"], ["O70199", "UDP-glucose 6-dehydrogenase", "UGDH", "54.9", "7.5", "37.9", "9", "0.66", "1.05"], ["Q64428", "Trifunctional enzyme subunit alpha, mitochondrial", "HADHA", "82.6", "9.1", "36.6", "20", "0.69", "0.83"], ["P55159", "Serum paraoxonase/arylesterase 1", "PON1", "39.3", "5.2", "23.9", "7", "0.70", "0.81"], ["O02572", "Enolase", "ENO1", "17.1", "9.0", "37.9", "4", "0.70", "0.96"], ["P21213", "Histidine ammonia-lyase", "HAL", "72.2", "6.5", "20.9", "10", "0.71", "0.83"], ["G3V945", "Aldehyde dehydrogenase family 5, subfamily A1", "ALDH5A1", "56.1", "8.1", "24.9", "10", "1.32", "0.70"], ["Q1MTI4", "Triosephosphate isomerase A", "TPI1A", "26.8", "5.0", "29.8", "2", "0.57", "0.56"], ["Q90XG0", "Triosephosphate isomerase B", "TPI1B", "26.8", "6.9", "70.6", "2", "1.41", "1.01"], ["F1QXK3", "Acyl-coenzyme A oxidase 3", "ACOX3", "70.1", "7.6", "9.9", "4", "1.41", "1.14"], ["D3ZSC5", "Cystathionine beta-synthase", "CBS", "52.4", "6.7", "33.5", "7", "1.44", "1.01"], ["A9JRE6", "Dmgdh protein (Fragment)", "DMGDH", "97.4", "7.0", "25.7", "3", "1.44", "0.95"], ["B0BNG1", "Probable proline dehydrogenase 2", "PRODH2", "51.1", "8.5", "21.1", "8", "1.46", "0.77"], ["Q5SPG8", "Acyl-coenzyme A thioesterase 1", "ACOT1", "48.6", "8.3", "9.8", "3", "1.47", "1.04"], ["Q68FT3", "Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 2", "PYROXD2", "62.8", "8.2", "4.5", "2", "1.49", "0.93"], ["Q6NZW7", "Dihydrolipoamide succinyltransferase", "DLST", "48.6", "8.7", "11.2", "2", "1.49", "0.98"], ["B1WC61", "Acad9 protein", "ACAD9", "68.8", "7.7", "23.2", "13", "1.50", "1.26"], ["Q6PBX8", "NADH dehydrogenase [ubiquinone] flavoprotein 2", "NDUFV2", "26.6", "5.6", "13.9", "3", "1.52", "1.19"], ["P21571", "ATP synthase-coupling factor 6, mitochondrial", "ATP5J", "12.5", "9.4", "46.3", "6", "1.72", "0.88"], ["Q5BK17", "Iodotyrosine dehalogenase 1", "IYD", "32.8", "6.6", "7.7", "2", "1.83", "1.14"], ["P00564", "Creatine kinase M-type", "CKM", "43.0", "7.1", "21.0", "5", "3.01", "2.89"], ["Nucleosome assembly and organization (Cluster 2)"], ["P15865", "Histone H1.4", "HIST1H1E", "22.0", "11.1", "18.7", "3", "0.44", "0.53"], ["Q7ZUY3", "Histone H2A.x", "H2AFX", "15.0", "10.7", "39.4", "3", "0.38", "0.53"], ["P0C0S7", "Histone H2A.Z", "H2AFZ", "13.5", "10.6", "31.3", "2", "0.68", "0.74"], ["A7E2M8", "Histone H2B", "HIST2H2BE", "13.6", "10.4", "48.4", "2", "0.50", "0.53"], ["A3KPR4", "Histone H4", "HIST1H4A", "11.4", "11.4", "53.4", "3", "0.61", "0.71"], ["Q6NYV3", "Histone H1.0", "H1F0", "21.2", "10.9", "9.6", "2", "0.24", "0.28"], ["B8JN00", "Histone H2A", "H2AFY2", "24.3", "10.2", "9.8", "2", "0.62", "0.56"], ["Translation (Cluster 3)"], ["P62755", "40S ribosomal protein S6", "RPS6", "28.7", "10.8", "24.9", "2", "1.41", "0.83"], ["P62083", "40S ribosomal protein S7", "RPS7", "22.1", "10.1", "44.9", "5", "1.66", "0.87"], ["P23358", "60S ribomal protein L12", "RPL12", "17.8", "9.4", "59.4", "5", "1.67", "0.90"], ["H7C5Y5", "60S ribosomal protein L6", "RPL6", "33.6", "10.7", "29.6", "7", "1.38", "0.61"], ["Q6P3V8", "Eukaryotic translation initiation factor 4A1", "EIF4A1", "46.1", "5.5", "37.0", "6", "1.58", "1.00"], ["A4V6L7", "DEAD box polypeptide 48 protein", "EIF4A3", "43.1", "7.8", "7.7", "2", "1.65", "1.01"], ["Protein localization (Cluster 3)"], ["F1M6Z1", "Apolipoprotein B-100", "APOB", "509.4", "7.2", "3.1", "11", "1.41", "1.03"], ["Q5PQK5", "Radixin", "RDX", "68.5", "6.3", "19.0", "5", "1.59", "0.91"], ["Q3B7E7", "Sorting nexin 3", "SNX3", "18.8", "8.6", "12.4", "2", "1.80", "0.81"], ["Q4KM74", "Vesicle-trafficking protein SEC22b", "SEC22B", "24.7", "8.5", "20.5", "4", "1.55", "0.92"], ["B2RZD1", "Protein Sec61b", "SEC61B", "10.0", "11.6", "33.3", "2", "1.20", "0.61"], ["Muscle contraction (Cluster 4)"], ["Q76BG8", "Fructose-bisphosphate aldolase", "ALDOA", "36.1", "7.9", "29.9", "8", "1.86", "2.15"], ["G3V885", "Myosin-6", "MYH6", "223.4", "5.7", "30.6", "3", "1.11", "1.41"], ["D3ZCV0", "Protein Actn2", "ACTN2", "103.8", "5.5", "31.0", "8", "1.66", "1.51"], ["F1M789", "Protein Myh13", "MYH13", "208.8", "5.6", "21.5", "5", "1.67", "2.36"], ["F1RBV5", "Uncharacterized protein", "MYH4", "221.6", "5.8", "26.3", "2", "1.47", "2.22"], ["B6RK61", "Myosin heavy chain 7B", "MYH7B", "221.5", "5.9", "9.07", "3", "1.45", "1.29"], ["Q7LZ84", "Myosin heavy chain, cardiac and skeletal muscle", "MYH7", "45.2", "5.8", "47.04", "6", "1.45", "1.29"], ["Extracellular matrix organization (Cluster 4)"], ["F1LNH3", "Protein Col6a2 (Fragment)", "COL6A2", "109.4", "6.6", "2.0", "2", "1.70", "1.62"], ["Q9W7R9", "Alpha1 type II collagen", "COL2A1", "135.0", "7.8", "5.2", "6", "1.85", "1.38"], ["Q9YIB4", "Collagen alpha-1(I) chain", "COL1A1", "137.5", "5.6", "21.0", "24", "2.37", "1.19"], 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["kmeans_fit"], "assets": ["source:pmid:26131905", "data:geo:PXD002100", "asset:table:pmid:26131905:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD002100"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:26131905", "type": "paper", "label": "pmid:26131905"}, {"id": "source:pmid:26131905", "type": "manuscript", "label": "PMID 26131905 full text"}, {"id": "data:geo:PXD002100", "type": "dataset", "label": "GEO PXD002100"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26131905", "type": "paper", "label": "pmid:26131905"}, {"id": "source:pmid:26131905", "type": "manuscript", "label": "PMID 26131905 full text"}, {"id": "data:geo:PXD002100", "type": "dataset", "label": "GEO PXD002100"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26131905", "type": "extraction", "used": ["source:pmid:26131905"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD002100", "type": "accession_resolution", "used": ["data:geo:PXD002100"], "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:26131905", "parent_hash": "sha256:87d70bb05e30ffa78b6948e0f53de692bf977cae1c526647777fee654d2e7852", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD002100 licence not read", "asset:data:geo:PXD002100 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Materials and Methods Quantitative real-time PCR analysis of gene expression In this study, s"], "order_basis": "paper_text_order:1806", "id": "assay:1"}, {"role": "analysis", "definition_id": "clustering", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["kmeans_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["k-means clustering was utilized to classify the differentially expressed proteins"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. 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Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}