{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24641125", "kind": "science-record", "revision": 4, "content_hash": "sha256:0817409d1d8a6277bbccd6008fc8dcc92d61f4bdcc32665be8e259bbcae5475d", "created_at": "2026-11-01T15:40:04Z", "updated_at": "2026-11-01T21:19:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts.", "doi": "10.1186/1471-2180-14-70", "pmid": "24641125", "authors": ["Clifford G Clark", "Patrick M Chong", "Stuart J McCorrister", "Philippe Simon", "Matthew Walker", "David M Lee", "Kimberly Nguy", "Keding Cheng", "Matthew W Gilmour", "Garrett R Westmacott"], "journal": "BMC microbiology", "year": 2014, "abstract": "BACKGROUND: The presence of Campylobacter jejuni temperate bacteriophages has increasingly been associated with specific biological effects. It has recently been demonstrated that the presence of the prophage CJIE1 is associated with increased adherence and invasion of C. jejuni isolates in cell culture assays.\nRESULTS: Quantitative comparative proteomics experiments were undertaken using three closely related isolates with CJIE1 and one isolate without CJIE1 to determine whether there was a corresponding difference in protein expression levels. Initial experiments indicated that about 2% of the total proteins characterized were expressed at different levels in isolates with or without the prophage. Some of these proteins regulated by the presence of CJIE1 were associated with virulence or regulatory functions. Additional experiments were conducted using C. jejuni isolates with and without CJIE1 grown on four different media: Mueller Hinton (MH) media containing blood; MH media containing 0.1% sodium deoxycholate, which is thought to result in increased expression of virulence proteins; MH media containing 2.5% Oxgall; and MHwithout additives. These experiments provided further evidence that CJIE1 affected protein expression, including virulence-associated proteins. They also demonstrated a general bile response involving a majority of the proteome and clearly showed the induction of almost all proteins known to be involved with iron acquisition. The data have been deposited to the ProteomeXchange with identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nCONCLUSION: The presence of the CJIE1 prophage was associated with differences in protein expression levels under different conditions. Further work is required to determine what genes are involved in causing this phenomenon.", "claims": [{"id": "claim-method", "statement": "A total of 25 proteins were differentially expressed in these experiments (Table 2; Additional file 3); all had P values of <0.05 in the Permutation test (see Additional file 3) except for hypothetical protein ICDCCJ07001_1249, for which differences were not statistically significant at 75% (P = 0.20).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24641125", "locator": "sections[4] \"Comparison of C. jejuni on two additional media, MH and MH + SD, demonstrated similar patterns of protein expression, experiment 2\" paragraph 5", "quote": "A total of 25 proteins were differentially expressed in these experiments (Table 2; Additional file 3); all had P values of <0.05 in the Permutation test (see Additional file 3) except for hypothetical protein ICDCCJ07001_1249, for which differences were not statistically significant at 75% (P = 0.20)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24641125", "locator": "sections[26] \"Availability of supporting data\" paragraphs 1-7", "quote": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The presence of the CJIE1 prophage was associated with differences in protein expression levels under different conditions.", "kind": "quantitative", "target": {"value": 75.0, "unit": "per cent", "tolerance": null, "source": "A total of 25 proteins were differentially expressed in these experiments (Table 2; Additional file 3); all had P values of <0.05 in the Permutation test (see Additional file 3) except for hypothetical protein ICDCCJ07001_1249, for which differences were not statistically significant at 75% (P = 0.20)."}, "evidence": [{"asset": "source:pmid:24641125", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The presence of the CJIE1 prophage was associated with differences in protein expression levels under different conditions."}, {"asset": "source:pmid:24641125", "locator": "sections[4] \"Comparison of C. jejuni on two additional media, MH and MH + SD, demonstrated similar patterns of protein expression, experiment 2\" paragraph 5", "quote": "A total of 25 proteins were differentially expressed in these experiments (Table 2; Additional file 3); all had P values of <0.05 in the Permutation test (see Additional file 3) except for hypothetical protein ICDCCJ07001_1249, for which differences were not statistically significant at 75% (P = 0.20)."}, {"asset": "source:pmid:24641125", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The data have been deposited to the ProteomeXchange with identifiers PXD000798, PXD000799, PXD000800, and PXD000801."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The presence of the CJIE1 prophage was associated with differences in protein expression levels under different conditions.", "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:24641125"], "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:PXD000798"], "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:PXD000798"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24641125", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/1471-2180-14-70", "sha256": "sha256:bd0eb9b1ed264a1b128b842ba0114b4039b4d2a3a85796e6d113ac6b47564f2a", "bytes": 82174, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/1471-2180-14-70", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4004267", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000798", "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=PXD000798", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000798", "version": null, "note": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD000799", "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=PXD000799", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000799", "version": null, "note": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD000800", "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=PXD000800", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000800", "version": null, "note": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD000801", "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=PXD000801", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000801", "version": null, "note": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4", "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:24641125:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cec586215a7f72c99f92259cfbf0925fcef25443fd1a348812c2db6053394dba", "bytes": 2638, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Proteins regulated with ≥0.6 log 2 change in three isolates carrying CJIE1 versus the isolate without CJIE1 when grown on MH + 10% sheep blood", "structure": {"pmcid": "PMC4004267", "section_index": 3, "section_title": "Differential expression of proteins in isolates with and without the CJIE1 prophage in rich medium, experiment 1", "row_count": 23, "column_count": 5}, "table": {"label": "Table 1", "caption": "Proteins regulated with ≥0.6 log 2 change in three isolates carrying CJIE1 versus the isolate without CJIE1 when grown on MH + 10% sheep blood", "rows": [["Protein name", "GI number", "Locus in NCTC11168 a", "Protein function", "log 2 change b"], ["CJIE1 phage repressor protein CJE0215", "gi|57237226", "Not present", "Maintenance of lysogeny", "3.10 ± 1.27*"], ["CJIE1 hypothetical protein CJE0246", "gi|315124241", "Not present", "CJIE1 prophage capsid protein", "2.95 ± 0.07*"], ["CJIE1 00–2425 ORF 11", "gi|313116388", "Not present", "Unknown", "2.67 ± 0.65"], ["CJIE1 extracellular deoxyribonuclease CJE0256", "gi|57237266", "Not present", "Degradation of DNA", "2.3 ± 0.53"], ["CJIE1 phage major tail tube protein CJE0226", "gi|315124254", "Not present", "Prophage structural protein", "2.20 ± 0*"], ["CJIE1 major tail sheath protein CJE0227", "gi|315124253", "Not present", "Prophage structural protein", "2.20 (single value)"], ["CJIE1 signal peptidase I associated with PanB", "gi|315124225", "Not present", "Prophage repressor", "1.57 ± 0.78"], ["CJIE1 hypothetical protein ICDCCJ07001_659 ORF7", "gi|315124224", "Not present", "Unknown", "2.95 ± 0.35*"], ["Flagellar protein FlaG", "gi|157414828", "Cj0547", "Flagellar protein", "−0.77 ± 0.76"], ["Flagellar protein FliS", "gi|121612919", "Cj0549", "Flagellin specific chaperone", "−1.00 ± 0.44"], ["Invasion phenotype protein CipA", "gi|157414972", "Cj0685c", "Sugar transferase", "2.97 ± 0.40"], ["Phosphate acetyltransferase Pta", "gi|121613717", "Cj0688", "Acetate metabolism, regulation", "2.30 ± 0.26"], ["Acetate kinase AckA", "gi|57236992", "Cj0689", "Acetate metabolism, regulation", "2.00 ± 0.26"], ["Integral membrane protein CstA", "gi|218562536", "Cj0917c", "Carbon starvation protein", "−0.73 ± 0.42"], ["Aspartate carbamoyltransferase catalytic subunit PyrB", "gi|218562712", "Cj1098", "Pyrimidine biosynthesis", "1.66 ± 0.10"], ["Oligoendopeptidase F PepF", "gi|218562713", "Cj1099", "Degradation of macromolecules", "1.73 ± 0.31"], ["Hypothetical protein CJJ81176_1118", "gi|121613077", "Cj1100", "Unknown", "1.50 ± 0.44"], ["ATP-dependent DNA helicase UvrD", "gi|121612511", "Cj1101", "DNA helicase", "1.70 ± 0.35"], ["Hypothetical protein CJE1504", "gi|57238362", "Cj1305c", "Unknown", "−0.93 ± 0.4"], ["Hypothetical protein ICDCCJ07001_1249", "gi|315124755", "Cj1305c", "Unknown", "−2.70 ± 0.85*"], ["Methyltransferase protein", "gi|218563030", "Cj1426c", "Part of capsule locus", "−1.23 ± 0.38"], ["Hypothetical protein Cj1429c", "gi|218563033", "Cj1429c", "Capsule biosynthesis", "1.73 ± 1.33"]], "row_count": 23, "column_count": 5, "numeric_cells": 71, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:24641125:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8a81f35217e5d49f95c250c914892ba73c4c12489b2d07e17d2675e666ee30bc", "bytes": 3888, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T2", "version": null, "note": "Proteins regulated with ≥0.6 log 2 change in isolate 00–2426 (no CJIE1) compared with isolate 00–2425 (with CJIE1, grown on MH) as reference when isolates were grown on MH and MH + SD", "structure": {"pmcid": "PMC4004267", "section_index": 4, "section_title": "Comparison of C. jejuni on two additional media, MH and MH + SD, demonstrated similar patterns of protein expression, experiment 2", "row_count": 26, "column_count": 7}, "table": {"label": "Table 2", "caption": "Proteins regulated with ≥0.6 log 2 change in isolate 00–2426 (no CJIE1) compared with isolate 00–2425 (with CJIE1, grown on MH) as reference when isolates were grown on MH and MH + SD", "rows": [["Protein name a", "GI number", "Locus in NCTC 11168", "Protein function or region", "log 2 change 00–2425 MH + SD agar", "log 2 change 00–2426 MH agar", "log 2 change 00–2426 MH + SD agar"], ["CJIE1 00–2425 ORF 11", "gi|313116388", "Not present", "Unknown", "0.67 ± 0.40", "−2.43 ± 0.70", "−2.13 ± 1.27"], ["CJIE1 signal peptidase I associated with PanB", "gi|315124225", "Not present", "Prophage repressor", "0.50 ± 0.20", "−3.75 ± 0.64", "−3.15 ± 0.78"], ["Hypothetical protein CJJ81176_0110", "gi|121613178", "Cj0073c", "Unknown", "0.83 ± 0.21", "0.87 ± 0.99", "1.27 ± 0.67"], ["Iron-sulfur cluster binding protein", "gi|121612415", "Cj0074c", "Unknown", "0.57 ± 0.6", "0.63 ± 1.01", "1.00 ± 0.61"], ["Anaerobic C4-dicarboxylate transporter", "gi|218561769", "Cj0088", "", "1.03 ± 1.04", "1.13 ± 0.40", "2.17 ± 0.38"], ["Hypothetical protein Cj0170", "gi|218561850", "Cj0170", "Unknown", "−0.30 ± 0.10", "−2.80 ± 0.90", "−2.97 ± 0.31"], ["Hypothetical protein CJJ81176_0447", "gi|121613189", "Cj0427", "Unknown", "0.33 ± 1.46", "1.33 ± 1.12", "1.07 ± 1.66"], ["Invasion phenotype protein CipA", "gi|157414972", "Cj0685c", "Sugar transferase", "0.70 ± 0.20", "−2.87 ± 0.21", "−2.43 ± 0.47"], ["Phosphate acetyltransferase Pta", "gi|121613717", "Cj0688", "Acetate metabolism, regulation", "−0.03 ± 0.21", "−2.43 ± 0.31", "−2.67 ± 0.58"], ["Acetate kinase AckA", "gi|384443065", "Cj0689", "Acetate metabolism, regulation", "−0.33 ± 0.64", "−3.37 ± 0.25", "−2.70 ± 1.00"], ["Oxidoreductase", "gi|218562461", "Cj0833c", "Oxidoreductase", "−0.10 ± 0.10", "−0.96 ± 1.76", "−1.10 ± 0.95"], ["Ankyrin repeat-containing periplasmic protein", "gi|218562462", "Cj0834c", "Mediates protein-protein interactions", "−0.67 ± 0.25", "−1.20 ± 2.42", "−1.60 ± 1.05"], ["Amino acid ABC transporter, ATP-binding protein PEB1", "gi|121612723", "Cj0922c", "Amino-acid ABC transporter", "0.77 ± 0.21", "0.63 ± 0.68", "1.03 ± 0.45"], ["Aspartate carbamoyltransferase catalytic subunit PyrB", "gi|218562712", "Cj1098", "Pyrimidine biosynthesis", "0.20 ± 0.35", "−1.70 ± 0.17", "−1.57 ± 0.21"], ["Oligoendopeptidase F PepF", "gi|218562713", "Cj1099", "Degradation of macromolecules", "−0.20 ± 0.10", "−1.43 ± 0.32", "−1.63 ± 0.23"], ["ATP-dependent DNA helicase UvrD", "gi|384448349", "Cj1101", "DNA helicase", "0.73 ± 0.42", "−1.65 ± 0.21*", "−1.23 ± 0.47"], ["Hypothetical protein ICDCCJ07001_1249", "gi|315124755", "Cj1305", "Part of O-linked glycosylation locus", "−0.35 ± 0.35*", "1.30 ± 1.56*", "2.53 ± 2.60"], ["Hypothetical protein Cj1310c", "gi|218562921", "Cj1310c", "Part of O-linked glycosylation locus", "−0.23 ± 0.25", "1.33 ± 1.02", "0.87 ± 0.81"], ["Motility accessory factor", "gi|407942710", "Cj1318", "Part of O-linked glycosylation locus", "0.03 ± 0.32", "0.93 ± 0.98", "1.00 ± 0.17"], ["Maf7; hypothetical protein C8J_1258", "gi|157415578", "Cj1342c", "Motility accessory factor", "0.20 ± 0.10", "1.57 ± 0.31", "1.87 ± 0.31"], ["Sugar transferase", "gi|218563025", "Cj1421c", "Part of capsule locus", "0.50 ± 0.17", "0.80 ± 0.66", "1.3 ± 0.60"], ["Methyltransferase protein", "gi|218563030", "Cj1426c", "Part of capsule locus", "0.57 ± 0.72", "1.13 ± 0.72", "1.03 ± 0.65"], ["Hypothetical protein Cj1429c", "gi|218563033", "Cj1429c", "Capsule biosynthesis", "0.33 ± 0.32", "−2.50 ± 0.36", "−1.80 ± 1.25"], ["Aminotransferase", "gi|218563040", "Cj1436c", "Part of capsule locus", "−0.30 ± 0.30", "−1.53 ± 1.26", "−2.03 ± 0.25"], ["Hypothetical protein CJJ81176_1657", "gi|121612948", "Cj1666c", "Probable periplasmic protein", "−0.63 ± 0.46", "−0.63 ± 0.51", "−1.43 ± 0.38"]], "row_count": 26, "column_count": 7, "numeric_cells": 136, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:24641125:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eabab93c2317b4147b41bfbf7ee2e622fbd5ae92a61532d93391ace852f598cd", "bytes": 1828, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T3", "version": null, "note": "Proteins detected only in C. jejuni 00–2425 (carrying CJIE1) or in C. jejuni 00–2426 (without CJIE1)", "structure": {"pmcid": "PMC4004267", "section_index": 5, "section_title": "Growth of C. jejuni on different media revealed different patterns of expression, experiments 3 (using isolate 00–2425) and 4 (using isolate 00–2426)", "row_count": 23, "column_count": 4}, "table": {"label": "Table 3", "caption": "Proteins detected only in C. jejuni 00–2425 (carrying CJIE1) or in C. jejuni 00–2426 (without CJIE1)", "rows": [["Protein designation", "", "Protein name", "GI Number"], ["Detected only in isolate 00–2425 (carrying CJIE1)"], ["CJIE1", "Prophage indel", "00-2425 hotspot protein ORF11", "gi|313116388"], ["CJIE1", "Prophage", "Signal peptidase I prophage repressor", "gi|315124225"], ["CJIE1", "Prophage ORF7", "Hypothetical protein ICDCCJ07001_659", "gi|315124224"], ["CJE0269", "Prophage", "Bacteriophage DNA transposition protein B, putative", "gi|57237279"], ["CJE0256", "Prophage", "Extracellular deoxyribonuclease", "gi|57237266"], ["CJE0246", "Prophage", "Hypothetical protein ICDCCJ07001_677", "gi|315124241"], ["CJE0228", "Prophage", "Hypothetical protein ICDCCJ07001_690", "gi|315124252"], ["CJE0226", "Prophage", "Phage major tail tube protein", "gi|315124254"], ["CJE0215", "Prophage", "Phage repressor protein", "gi|157414969"], ["Cj1620c", "MutY", "A/G-specific adenine glycosylase", "gi|218563209"], ["Cj1588c", "putative MFS transport protein", "gi|218563177"], ["Thauera spp.", "pyruvate phosphate dikinase PEP/pyruvate-binding", "gi|217970436"], ["Detected only in isolate 00–2426 without CJIE1"], ["Cj0065c", "FolK", "2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase", "gi|157414379"], ["Cj1731c", "Holliday junction resolvase", "gi|121612651"], ["Cj0566", "Hypothetical protein Cj0566", "gi|218562217"], ["Cj0620", "Hypothetical protein Cj0620", "gi|218562271"], ["CJE1531", "Hypothetical protein CJE1531", "gi|57238385"], ["Cj1113", "Hypothetical protein CJJ81176_1131", "gi|121613282"], ["Cj1193c", "Hypothetical protein CJJ81176_1208", "gi|121613678"], ["CJE0735", "IlvC", "Ketol-acid reductoisomerase", "gi|152990905"]], "row_count": 23, "column_count": 4, "numeric_cells": 48, "header_rows": 1, "locator": "section[5]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:24641125:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:62f011f044bd4f87f351d38e4f5beab8dfc70c0dc4d1e15b980cd6134d54661f", "bytes": 864, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#T4", "version": null, "note": "Protein expression showing ≥ log 2 0.6 change in isolates grown on different media", "structure": {"pmcid": "PMC4004267", "section_index": 5, "section_title": "Growth of C. jejuni on different media revealed different patterns of expression, experiments 3 (using isolate 00–2425) and 4 (using isolate 00–2426)", "row_count": 10, "column_count": 8}, "table": {"label": "Table 4", "caption": "Protein expression showing ≥ log 2 0.6 change in isolates grown on different media", "rows": [["Comparison", "Number of proteins up-regulated", "Total regulated", "Total proteins", "% of total regulated"], ["", "In MH", "In MH", "In SD", "In OX", "", "", ""], ["00- 2425 MH + blood vs MH", "44", "70", "", "", "114", "1366", "8.3"], ["00- 2426 MH + blood vs MH", "37", "53", "", "", "90", "1363", "6.6"], ["00-2425 MH vs SD", "", "426", "568", "", "994", "1365", "72.8"], ["00-2426 MH vs SD", "", "463", "615", "", "1078", "1362", "79.1"], ["00-2425 MH vs OX", "", "426", "", "531", "957", "1366", "70.1"], ["00-2426 MH vs OX", "", "439", "", "503", "942", "1362", "69.2"], ["00-2425 SD vs OX", "", "", "124", "29", "153", "1375", "11.1"], ["00-2426 SD vs OX", "", "", "40", "33", "73", "1375", "5.3"]], "row_count": 10, "column_count": 8, "numeric_cells": 48, "header_rows": 2, "locator": "section[5]/table-wrap[2]#T4"}}, {"id": "asset:table:pmid:24641125:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:265bf8d5baa125e8543c09389e7a4022ce74b31d5b67782b12be34de99a6bf86", "bytes": 1521, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T5", "version": null, "note": "Effect of media differing in iron concentration and inclusion of bile salts on expression of consensus proteins differentially regulated by the presence or absence of CJIE1 in initial experiments", "structure": {"pmcid": "PMC4004267", "section_index": 7, "section_title": "Bile salts affect the expression of proteins regulated by CJIE1", "row_count": 11, "column_count": 8}, "table": {"label": "Table 5", "caption": "Effect of media differing in iron concentration and inclusion of bile salts on expression of consensus proteins differentially regulated by the presence or absence of CJIE1 in initial experiments", "rows": [["", "", "", "", "Log 2 change"], ["Protein", "COG", "GI number", "Locus in NCTC 11168", "0.1% sodium deoxycholate", "2.5% Oxgall"], ["", "00-2425", "00-2426", "00-2425", "00-2426"], ["Invasion phenotype protein CipA", "R", "gi|157414972", "Cj0685c", "1.17 ± 0.30", "1.57 ± 0.35", "1.13 ± 0.46", "1.20 ± 0.66"], ["phosphate acetyltransferase Pta", "R", "gi|121613717", "Cj0688", "0.07 ± 0.30", "1.10 (n = 1)", "−0.93 ± 0.21", "1.90 (n = 1)"], ["Acetate kinase AckA", "C", "gi|57236992", "Cj0689", "−1.27 ± 0.10", "−1.00 ± 0.60", "−0.57 ± 0.50", "−0.50 ± 0.36"], ["Aspartate carbamoyltransferase catalytic subunit PyrB", "F", "gi|218562712", "Cj1098", "0.80 ± 0.30", "1.00 ± 0.20", "0.50 ± 0.40", "0.73 ± 0.25"], ["Oligoendopeptidase F PepF", "E", "gi|218562713", "Cj1099", "−0.87 ± 0.20", "−0.90 ± 0.17", "−0.03 ± 0.06", "−0.13 ± 0.23"], ["ATP-dependent DNA helicase UvrD", "L", "gi|121612511", "Cj1101", "1.20 ± 0.30", "1.40 ± 0.17", "1.40 ± 0.36", "1.40 ± 0.10"], ["Hypothetical protein Cj1429c", "S", "gi|218563033", "Cj1429c", "0.33 ± 0.40", "1.45 ± 0.49", "1.13 ± 0.25", "2.5 ± 0"], ["Methyltransferase protein", "", "gi|218563030", "Cj1426c", "0.43 ± 0.30", "0.97 ± 0.21", "0.23 ± 0.40", "0.33 ± 0.70"]], "row_count": 11, "column_count": 8, "numeric_cells": 57, "header_rows": 3, "locator": "section[7]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:24641125:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e071af8bf821b2006066aa0b924ad876d20b6bc7adc60c171c0a0130fab40953", "bytes": 10493, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T6", "version": null, "note": "C. jejuni proteins responding to decreased iron concentration assessed by comparing protein expression after growth on MH + blood and on MH medium", "structure": {"pmcid": "PMC4004267", "section_index": 10, "section_title": "Growth of bacteria on medium without blood induces proteins involved in iron acquisition and oxidative stress responses", "row_count": 110, "column_count": 5}, "table": {"label": "Table 6", "caption": "C. jejuni proteins responding to decreased iron concentration assessed by comparing protein expression after growth on MH + blood and on MH medium", "rows": [["Protein", "Locus in NCTC11168", "GI number", "Log 2 change in MH medium"], ["", "", "", "00-2425", "00-2426"], ["Iron acquisition", "", "", "", ""], ["Iron-uptake ABC transporter ATP-binding protein CfbpC, putative", "Cj0173c", "gi|218561852", "1.27 ± 0.75", "1.10 ± 0.53"], ["Iron ABC transporter, permease CfbpB, putative", "Cj0174c", "gi|121612175", "0.80 ± 0.71", "0.90 ± 0"], ["Iron-uptake ABC transporter, periplasmic iron-binding protein CfbpA, putative", "Cj0175c", "gi|218561854", "2.00 ± 1.30", "1.97 ± 1.27"], ["Iron transport protein, putative", "Cj0177", "gi|218561856", "3.30 ± 0.17", "2.73 ± 1.05"], ["TonB-denpendent outer membrane receptor, putative", "Cj0178", "gi|218561857", "2.70 ± 0.56", "2.97 ± 0.29"], ["Biopolymer transport ExbB protein, TonB transport system", "Cj0179", "gi|218561858", "3.03 ± 0.32", "3.37 ± 1.61"], ["Periplasmic TonB transport protein", "Cj0753c", "gi|315124276", "3.5 (single value)", "3.5 (single value)"], ["Ferric receptor CfrA", "Cj0755", "gi|57237601", "2.37 ± 0.15", "2.23 ± 0.81"], ["Enterochelin uptake ATP-binding protein CeuD", "Cj1354", "gi|218562963", "2.00 ± 1.06", "2.00 ± 0.56"], ["Enterochelin ABC transporter, periplasmic enterochelin-binding protein CeuE", "Cj1355", "gi|121612138", "1.80 ± 0.66", "1.40 ± 0.26"], ["Periplasmic protein P19", "Cj1659", "gi|157415879", "1.97 ± 1.50", "2.10 ± 1.04"], ["Iron permease, putative", "Cj1658", "gi|218563246", "1.97 ± 1.04", "1.70 ± 1.01"], ["Heme iron utilization protein, putative", "Cj1613c", "gi|121612296", "3.60 ± 0.95", "3.70 ± 0.5"], ["TonB-dependent heme receptor ChuA", "Cj1614", "gi|57238627", "3.35 ± 0.35", "4.20 ± 0"], ["TonB-dependent heme receptor ChuA", "Cj1614", "gi|157415833", "1.80 ± 0.70", "1.73 ± 0.87"], ["TonB-dependent heme receptor ChuA", "Cj1614", "gi|121613006", "1.20 ± 0.56", "0.33 ± 0.64"], ["Hemin ABC transporter, permease protein, putative ChuB", "Cj1615", "gi|153951720", "3.17 ± 0.55", "2.93 ± 1.19"], ["Hemin uptake system ATP-binding protein ChuC , putative", "Cj1616", "gi|218563205", "2.97 ± 0.74", "3.07 ± 0.50"], ["Hemin uptake system periplasmic hemin-binding protein, putative", "Cj1617", "gi|218563206", "2.83 ± 0.59", "2.53 ± 0.42"], ["Biopolymer transport ExbD protein, TonB transport system", "Cj1629", "gi|153952038", "1.63 ± 0.81", "1.57 ± 0.49"], ["Integral membrane protein, putative", "Cj1660", "gi|218563248", "1.27 ± 0.81", "1.5 ± 0.79"], ["ABC transporter permease, putative", "Cj1661", "gi|218563249", "1.67 ± 0.97", "1.57 ± 0.67"], ["Integral membrane protein, putative", "Cj1662", "gi|218563250", "1.93 ± 1.15", "1.60 ± 0.87"], ["ABC transporter ATP-binding protein", "Cj1663", "gi|157415883", "1.53 ± 0.80", "1.53 ± 0.51"], ["Oxidative stress", "", "", "", ""], ["Thioredoxin reductase", "Cj0146c", "gi|218561827", "0.93 ± 0.47", "0.87 ± 0.5"], ["Antioxidant, AhpC/Tsa family", "Cj0334", "gi|157414631", "0.97 ± 0.32", "0.70 ± 0.20"], ["Catalase", "Cj1385", "gi|121612952", "3.37 ± 0.23", "2.80 ± 0.56"], ["Thioredoxin-like protein", "Cj1664", "gi|121613144", "1.23 ± 0.91", "1.27 ± 1.08"], ["Anthranilate synthesis", "", "", "", ""], ["Anthranilate synthase component I", "Cj0345", "gi|121612335", "0.80 ± 0.75", "0.87 ± 0.71"], ["Anthranilate synthase component II", "Cj0346", "gi|121612640", "0.67 ± 0.60", "0.60 ± 0.46"], ["N-(5′phosphoribosyl)anthranilate isomerase", "Cj0347", "gi|157414644", "1.00 ± 0.53", "0.83 ± 0.65"], ["Chemotaxis", "", "", "", ""], ["Methyl-accepting chemotaxis protein", "Cj1189c", "gi|121613242", "0.70 ± 1.10", "0.07 ± 0.06"], ["Methyl-accepting chemotaxis protein", "Cj1506c", "gi|121613017", "2.0 ± 1.31", "3.23 ± 2.40"], ["Methionine biosynthesis", "", "", "", ""], ["5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE", "Cj1201", "gi|157415465", "0.50 ± 0.35", "1.20 ± 0.26"], ["Homoserine O-succinyltransferase MetA", "Cj1726c", "gi|121613233", "0.80 ± 0.35", "1.53 ± 0.55"], ["Homoserine O-acetyltransferase MetB", "Cj1727c", "gi|315125108", "1.27 ± 0.57", "1.93 ± 0.9"], ["Molybdate transport", "", "", "", ""], ["Molybdate transport system ATP-binding protein", "Cj0300c", "gi|157414597", "0.67 ± 0.15", "0.77 ± 0.25"], ["Hypothetical protein C8J_0279 molybdenum-pterin-binding protein", "Cj0302", "gi|157414599", "0.30 (single value)", "0.67 ± 0.21"], ["Molybdate transport system substrate-binding protein", "Cj0303", "gi|157414600", "0.83 ± 0.75", "0.77 ± 0.25"], ["Hypothetical proteins", "", "", "", ""], ["Hypothetical protein C8J_0062", "Cj0069", "gi|157414383", "−0.63 ± 0.06", "−0.60 ± 0.17"], ["Hypothetical protein CJJ81176_0110", "Cj0073c", "gi|121613178", "−0.93 ± 0.68", "−0.57 ± 0.35"], ["Hypothetical protein C8J_0189", "Cj0200c", "gi|157414509", "0.67 ± 0.81", "0.80 ± 0.78"], ["Hypothetical protein Cj0427", "Cj0427", "gi|218562085", "−1.47 ± 0.67", "0.07 ± 0.58"], ["Hypothetical protein CJJ81176_0676", "Cj0648", "gi|121613289", "0.70 ± 0.28", "0.50 ± 0.36"], ["Hypothetical protein C8J_1185", "Cj1242", "gi|157415505", "−0.60 (single value)", "−1.10 ± 0.71"], ["Hypothetical protein C8J_1529", "Cj1627c", "gi|157415847", "0.60 ± 0.20", "0.50 ± 0.61"], ["Hypothetical protein CJJ81176_1628", "Cj1637c", "gi|121613390", "−0.33 ± 0.15", "−0.73 ± 0.35"], ["Hypothetical protein C8J_1561", "Cj1659", "gi|157415879", "1.97 ± 1.50", "2.10 ± 1.04"], ["Hypothetical protein CJE0598 CJIE2 prophage", "not present", "gi|57238304", "1.10 ± 0.28", "0.77 ± 0.40"], ["Hypothetical protein CXIVA_22050", "not present", "gi|339443269", "0.67 ± 0.57", "0.50 ± 0.53"], ["Transporters", "", "", "", ""], ["Sodium/dicarboxylate symporter", "Cj0025c", "gi|121612756", "0.80 ± 0.66", "0.40 ± 0.44"], ["Anaerobic C4-dicarboxylate transporter", "Cj0088", "gi|218561769", "−1.10 ± 0.61", "−0.63 ± 0.23"], ["OPT family oligopeptide transporter", "Cj0204", "gi|121613125", "0.73 ± 0.21", "0.50 ± 0.17"], ["Other function or unknown function", "", "", "", ""], ["Non-haem iron protein", "Cj0012c", "gi|218561705", "−0.83 ± 0.61", "−0.77 ± 0.64"], ["Cytochrome c family protein", "Cj0037c", "gi|121612292", "0.93 ± 0.21", "1.03 ± 0.35"], ["Aspartate ammonia-lyase", "Cj0087", "gi|157414400", "−1.10 ± 0.50", "−1.1 ± 0.40"], ["Periplasmic protein, putative", "Cj0093", "gi|218561774", "0.80 ± 0.53", "0.80 ± 0.56"], ["Superoxide dismutase, Fe", "Cj0169", "gi|157414485", "−1.23 ± 0.84", "−1.20 ± 1.47"], ["Superoxide dismutase, Fe", "Cj0169", "gi|153951398", "−3.70 ± 2.95", "−0.93 ± 0.97"], ["Integral membrane protein", "Cj0236c", "gi|153952171", "0.53 ± 0.75", "0.97 ± 0.76"], ["Chemotaxis histidine kinase", "Cj0284c", "gi|218561946", "−0.83 ± 0.61", "−0.53 ± 0.42"], ["Ferredoxin 4Fe-4S", "Cj0333c", "gi|121612302", "−1.10 ± 0.89", "0.53 ± 0.15"], ["Tryptophan synthase subunit alpha", "Cj0349", "gi|121613100", "0.67 ± 0.47", "0.80 ± 0.56"], ["Cytochrome c551 peroxidase", "Cj0358", "gi|121612870", "−0.67 ± 0.55", "0.50 ± 0.17"], ["Putative integral membrane protein", "Cj0421c", "gi|218562079", "1.00 ± 0.71", "0.73 ± 0.12"], ["Putative periplasmic protein", "Cj0425", "gi|218562083", "1.70 (single value)", "1.10 (single value)"], ["Succinate dehydrogenase flavoprotein subunit", "Cj0437", "gi|218562095", "−0.70 ± 0.44", "−0.6 ± 0.87"], ["DNA polymerase III subunit epsilon", "Cj0452", "gi|218562107", "−0.23 ± 0.21", "−0.67 ± 0.31"], ["Thiamine biosynthesis protein ThiC", "Cj0453", "gi|121613325", "−2.23 ± 0.38", "−1.83 ± 0.32"], ["ATP-dependent chaperone protein ClpB", "Cj0509c", "gi|121613623", "−0.33 ± 0.15", "−0.67 ± 0.15"], ["2-oxoglutarate-acceptor oxidoreductase subunit OorD", "Cj0535", "gi|157414816", "−0.87 ± 0.55", "0.63 ± 0.66"], ["2-oxoglutarate-acceptor oxidoreductase subunit OorA", "Cj0536", "gi|157414817", "−0.73 ± 0.32", "−0.67 ± 0.15"], ["Aminohydrolase family protein, putative", "Cj0556", "gi|218562208", "0.90 ± 0.57", "1.13 ± 0.71"], ["Quinol dehydrogenase membrane component NapH", "Cj0782", "gi|121612888", "−0.67 ± 0.49", "−0.55 ± 0.35"], ["Bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase", "Cj0835c", "gi|218562463", "−1.00 ± 0.26", "−0.93 ± 0.59"], ["Thermonuclease family protein", "Cj0979c", "gi|121612563", "−0.83 ± 0.38", "−0.73 ± 0.68"], ["Amino acid transporter, periplasmic solute-binding protein, putative", "Cj0982c", "gi|218562598", "1.03 ± 0.38", "0.77 ± 0.4"], ["Arginyl-tRNA-protein transferase", "Cj1035c", "gi|121613462", "−0.73 ± 0.29", "−0.60 ± 0.26"], ["Flippase", "Cj1130c", "gi|218562744", "−0.27 ± 0.38", "−0.67 ± 0.42"], ["Cytochrome c553", "Cj1153", "gi|157415419", "−0.77 ± 0.25", "−0.53 ± 0.38"], ["Cyclopropane fatty acid biosynthesis", "Cj1183c", "gi|57238055", "1.07 ± 0.67", "0.73 ± 0.32"], ["NLPA family lipoprotein, putative", "Cj1200", "gi|218562812", "0.47 ± 0.83", "1.20 ± 0.56"], ["Hemerythrin family non-heme iron protein", "Cj1224", "gi|121612625", "−0.73 ± 0.25", "−0.07 ± 0.21"], ["Quinone-reactive Ni/Fe-hydrogenase, small subunit", "Cj1267c", "gi|157415531", "−0.63 ± 0.46", "−0.57 ± 0.21"], ["Endoribonuclease L-PSP, putative", "Cj1388", "gi|218562997", "0.77 ± 0.21", "0.40 ± 0.36"], ["Putative Ni/Fe-hydrogenase small subunit", "Cj1399c", "gi|218563003", "0.73 ± 0.31", "0.57 ± 0.15"], ["Hypothetical protein C8J_1356 ATP/GTP-binding protein", "Cj1450", "gi|157415675", "−0.87 ± 0.38", "−0.80 ± 0.46"], ["Transformation system protein CtsX", "Cj1472", "gi|121612126", "−0.55 ± 0.7", "−1.20 (single value)"], ["Transformation system protein CtsP", "Cj1473c", "gi|121613067", "−0.65 ± 0.07", "−0.13 ± 0.31"], ["Pyruvate-flavodoxin oxidoreductase", "Cj1476c", "gi|315124909", "−0.87 ± 0.38", "0.63 ± 0.42"], ["Formate dehydrogenase, iron-sulfur subunit", "Cj1510c", "gi|157415732", "−0.73 ± 0.71", "−0.73 ± 0.45"], ["Dephospho-CoA kinase", "Cj1530", "gi|218563123", "0.73 ± 0.68", "0.57 ± 0.74"], ["Multidrug transporter membrane component/ATP-binding component", "Cj1587c", "gi|121613099", "1.40 ± 0.53", "1.00 ± 0.44"], ["Two-component regulator (DNA binding response regulator), putative", "Cj1608", "gi|218563197", "−0.07 ± 0.31", "−2.50 ± 1.65"], ["Citrate synthase", "Cj1682c", "gi|157415898", "−0.80 ± 0.36", "−0.73 ± 0.21"], ["50S ribosomal protein L2", "Cj1704c", "gi|121612340", "−0.47 ± 0.85", "−0.80 ± 0.46"], ["2-isopropylmalate synthase", "Cj1719c", "gi|121612265", "0.83 ± 0.68", "0.67 ± 0.21"], ["Hypothetical protein CJE0598 CJIE2 prophage", "CJE0598", "gi|57238304", "1.10 ± 0.28", "0.77 ± 0.4"], ["Flagellin", "CJE1526", "gi|57238729", "−0.87 ± 0.25", "−0.80 ± 0.44"]], "row_count": 110, "column_count": 5, "numeric_cells": 423, "header_rows": 2, "locator": "section[10]/table-wrap[1]#T6"}}], "gaps": ["asset:data:geo:PXD000798 not downloaded", "asset:data:geo:PXD000798 licence not read", "asset:data:geo:PXD000799 not downloaded", "asset:data:geo:PXD000799 licence not read", "asset:data:geo:PXD000800 not downloaded", "asset:data:geo:PXD000800 licence not read", "asset:data:geo:PXD000801 not downloaded", "asset:data:geo:PXD000801 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Permutation test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A total of 25 proteins were differentially expressed in these experiments (Table 2; Additional file 3); all had P values of <0.05 in the Permutation test (see Additional file 3) except for hypothetical protein ICDCCJ07001_1249, for which differences were not statistically significant at 75% (P = 0.20)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 75.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.2, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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 (Permutation test), 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": ["PXD000798", "PXD000799", "PXD000800", "PXD000801"], "resolved_accessions": ["PXD000798", "PXD000799", "PXD000800", "PXD000801"], "statements": ["Some of the supporting data have been included as Additional files 1, 3, and 4. These files represent the Excel Samples Report created by the Scaffold software after removal of entries for which there was no log2 change values and after calculating means for each group of data. Accession numbers for whole genome sequences are 00–2425, CP006729; 00–2426, CP006708; 00–2538, CP006707; 00–2544, CP006709 (genome) and CP006710 (plasmid).\nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [55] with the dataset identifiers PXD000798, PXD000799, PXD000800, and PXD000801.\nData for experiment 1 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1” with the dataset identifier PXD000798. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate: 00–2425, 114; 00–2426, 115; 00–2538, 116, 00–2544, 117.\nData for experiment 2 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 2” with the dataset identifier PXD000799. The iTRAQ labels for this experiment were different for each replicate experiment as in the following description. Replicate Y1: 00–2425 grown on MH agar, 114; 00–2425 grown on MH + SD, 115; 00–2426 grown on MH agar, 116; 00–2426 grown on MH + SD, 117. Replicate Y2: 00–2425 grown on MH agar, 115; 00–2425 grown on MH + SD, 116; 00–2426 grown on MH agar, 117; 00–2426 grown on MH + SD, 114. Replicate Y3: 00–2425 grown on MH agar, 116; 00–2425 grown on MH + SD, 117; 00–2426 grown on MH agar, 114; 00–2426 grown on MH + SD, 115.\nData for experiment 3 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 3” with the dataset identifier PXD000800. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2425 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117.\nData for experiment 4 have been deposited under the ProteomeXchange title “Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 4” with the dataset identifier PXD000801. The iTRAQ labels for this experiment (all three replicates) were for C. jejuni isolate 00–2426 grown on: MH + blood, 114; MH agar, 115; MH + SD, 116; MH + OX, 117."], "basis": "The paper names PXD000798, PXD000799, PXD000800, PXD000801 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:24641125", "data:geo:PXD000798", "asset:table:pmid:24641125:1", "asset:table:pmid:24641125:2", "asset:table:pmid:24641125:3", "asset:table:pmid:24641125:4", "asset:table:pmid:24641125:5", "asset:table:pmid:24641125:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000798"]}, "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": "2026-10-31T18:22:19Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 153862, "completion_tokens": 7187, "cached_tokens": 39660}}, "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:24641125", "type": "paper", "label": "pmid:24641125"}, {"id": "source:pmid:24641125", "type": "manuscript", "label": "PMID 24641125 full text"}, {"id": "data:geo:PXD000798", "type": "dataset", "label": "GEO PXD000798"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:24641125", "type": "paper", "label": "pmid:24641125"}, {"id": "source:pmid:24641125", "type": "manuscript", "label": "PMID 24641125 full text"}, {"id": "data:geo:PXD000798", "type": "dataset", "label": "GEO PXD000798"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-24641125", "type": "extraction", "used": ["source:pmid:24641125"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000798", "type": "accession_resolution", "used": ["data:geo:PXD000798"], "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:24641125", "parent_hash": "sha256:12c6b57a858a85084797e22135ce55354a05c1cbf15197b1c3342c3951626ddc", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD000798 licence not read", "asset:data:geo:PXD000798 not downloaded", "asset:data:geo:PXD000799 licence not read", "asset:data:geo:PXD000799 not downloaded", "asset:data:geo:PXD000800 licence not read", "asset:data:geo:PXD000800 not downloaded", "asset:data:geo:PXD000801 licence not read", "asset:data:geo:PXD000801 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:33:23+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. 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}}}