← All .science files
pmid:29681787
The response to neoadjuvant chemoradiotherapy with 5-fluorouracil in locally advanced rectal cancer patients: a predictive proteomic signature.
Anaïs Chauvin · Chang-Shu Wang · Sameh Geha · Perrine Garde-Granger · Alex-Ane Mathieu · Vincent Lacasse · François-Michel Boisvert
Clinical proteomics · 2018 doi:10.1186/s12014-018-9192-2
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 7 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
target object · 4 fields
evidence array · 3 items
[0] object · 3 fields
[1] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 1 field
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 6 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 27 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[24] array · 6 items
[25] array · 6 items
[26] array · 6 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 29 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[24] array · 6 items
[25] array · 6 items
[26] array · 6 items
[27] array · 6 items
[28] array · 6 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 26 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[24] array · 6 items
[25] array · 6 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 7 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 1 field
data_shapes array · 1 item
evidence object · 3 fields
targets array · 1 item
[0] object · 8 fields
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 4 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 4 items
assets array · 6 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[1] object · 11 fields
required_operations array · 4 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29681787", "kind": "science-record", "revision": 8, "content_hash": "sha256:0ee26f58b9f8c7ae5b6e2e7f4a63b781e947ce4a85076ff7f1f8a6e8e2b94b5b", "created_at": "2026-11-01T15:40:33Z", "updated_at": "2026-11-01T22:43:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The response to neoadjuvant chemoradiotherapy with 5-fluorouracil in locally advanced rectal cancer patients: a predictive proteomic signature.", "doi": "10.1186/s12014-018-9192-2", "pmid": "29681787", "authors": ["Anaïs Chauvin", "Chang-Shu Wang", "Sameh Geha", "Perrine Garde-Granger", "Alex-Ane Mathieu", "Vincent Lacasse", "François-Michel Boisvert"], "journal": "Clinical proteomics", "year": 2018, "abstract": "BACKGROUND: Colorectal cancer is the third most common and the fourth most lethal cancer in the world. In the majority of cases, patients are diagnosed at an advanced stage or even metastatic, thus explaining the high mortality. The standard treatment for patients with locally advanced non-metastatic rectal cancer is neoadjuvant radio-chemotherapy (NRCT) with 5-fluorouracil (5-FU) followed by surgery, but the resistance rate to this treatment remains high with approximately 30% of non-responders. The lack of evidence available in clinical practice to predict NRCT resistance to 5-FU and to guide clinical practice therefore encourages the search for biomarkers of this resistance.\nMETHODS: From twenty-three formalin-fixed paraffin-embedded (FFPE) biopsies performed before NRCT with 5-FU of locally advanced non-metastatic rectal cancer patients, we extracted and analysed the tumor proteome of these patients. From clinical data, we were able to classify the twenty-three patients in our cohort into three treatment response groups: non-responders (NR), partial responders (PR) and total responders (TR), and to compare the proteomes of these different groups.\nRESULTS: We have highlighted 384 differentially abundant proteins between NR and PR, 248 between NR and TR and 417 between PR and TR. Among these proteins, we have identified many differentially abundant proteins identified as having a role in cancer (IFIT1, FASTKD2, PIP4K2B, ARID1B, SLC25A33: overexpressed in TR; CALD1, CPA3, B3GALT5, CD177, RIPK1: overexpressed in NR). We have also identified that DPYD, the main degradation enzyme of 5-FU, was overexpressed in NR, as well as several ribosomal and mitochondrial proteins also overexpressed in NR. Data are available via ProteomeXchange with identifier PXD008440.\nCONCLUSIONS: From these retrospective study, we implemented a protein extraction protocol from FFPE biopsy to highlight protein differences between different response groups to RCTN with 5-FU in patients with locally advanced non-metastatic rectal cancer. These results will pave the way for a larger cohort for better sensitivity and specificity of the signature to guide decisions in the choice of treatment.", "claims": [{"id": "claim-method", "statement": "Finally, the analysis of mass spectrometry data were next carried out with the Perseus software package [19] and subjected to a normalization (z-score) and an ANOVA statistical test (comparison of the three groups) or Student’s T test (comparison of two groups), both corrected with a p value of 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29681787", "locator": "sections[13] \"Quantification and bioinformatics analysis\" paragraph 2", "quote": "Finally, the analysis of mass spectrometry data were next carried out with the Perseus software package [19] and subjected to a normalization (z-score) and an ANOVA statistical test (comparison of the three groups) or Student’s T test (comparison of two groups), both corrected with a p value of 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the datasets included in the present manuscript are presented in the main manuscript or additional supporting files. The complete data, including the raw files and all extracted peptides information can be found at the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD008440.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29681787", "locator": "sections[26] \"ack\" paragraph 1", "quote": "All the datasets included in the present manuscript are presented in the main manuscript or additional supporting files. The complete data, including the raw files and all extracted peptides information can be found at the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD008440."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper highlighted 384 differentially abundant proteins between non-responders and partial responders, using ANOVA and Student’s T test for statistical comparisons, and deposited the source proteomics data in ProteomeXchange under identifier PXD008440.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Statistical tests used for these analyses are ANOVA test (1) and Student’s T test (2) both corrected with a p value of 0.05."}, "evidence": [{"asset": "source:pmid:29681787", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We have highlighted 384 differentially abundant proteins between NR and PR, 248 between NR and TR and 417 between PR and TR."}, {"asset": "source:pmid:29681787", "locator": "sections[19] \"Identification of differentially abundant proteins between groups\" paragraph 3", "quote": "Statistical tests used for these analyses are ANOVA test (1) and Student’s T test (2) both corrected with a p value of 0.05."}, {"asset": "source:pmid:29681787", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Data are available via ProteomeXchange with identifier PXD008440."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper highlighted 384 differentially abundant proteins between non-responders and partial responders, using ANOVA and Student’s T test for statistical comparisons, and deposited the source proteomics data in ProteomeXchange under identifier PXD008440.", "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:29681787"], "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:PXD008440"], "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": {"p_value": ", both corrected with a p value of 0"}, "inputs": ["data:geo:PXD008440"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29681787", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12014-018-9192-2", "sha256": "sha256:75275a7d036c6c519b66605147a8a5c48fd56a9a13457c9b81305d26f0a5903a", "bytes": 51777, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12014-018-9192-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5898006", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD008440", "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=PXD008440", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD008440", "version": null, "note": "All the datasets included in the present manuscript are presented in the main manuscript or additional supporting files. The complete data, including the raw files and all extracted peptides information can be found at the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD008440.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the datasets included in the present manuscript are presented in the main manuscript or additional supporting files. The complete data, including the raw files and all extracted peptides information can be found at the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD008440.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "The response to neoadjuvant chemoradiotherapy to 5-fluorouracil in locally advanced colorectal cancer patients: a predictive proteomic signature.", "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:29681787:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:68526178f158fa1a73fac12b97c5bcf1740f4c6fb9c80c26dfcb0f8e840269dc", "bytes": 1462, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Baseline patient characteristics", "structure": {"pmcid": "PMC5898006", "section_index": 3, "section_title": "Study design and clinical protocol", "row_count": 27, "column_count": 6}, "table": {"label": "Table 1", "caption": "Baseline patient characteristics", "rows": [["Characteristics", "All patients23 (100)a", "NR7 (30)", "PR10 (43)", "TR6 (26)", "p valueb"], ["Age (years)", "", "", "", "", ""], ["Median", "58.6 ± 11.1", "54.7 ± 14.3", "59.7 ± 10.2", "61.3 ± 8.6", ""], ["Range", "31–75", "31–72", "47–75", "48–71", ""], ["Sex", "", "", "", "", "0.324"], ["Male", "19 (83)", "7 (100)", "7 (70)", "5 (83)", ""], ["Female", "4 (17)", "0", "3 (30)", "1 (17)", ""], ["Tumor location from anal verge (cm)", "", "", "", "", "0.961"], ["3–5", "10 (43)", "3 (43)", "5 (50)", "2 (33)", ""], ["6–10", "11 (48)", "3 (43)", "4 (40)", "4 (67)", ""], ["> 10", "2 (9)", "1 (14)", "1 (10)", "0", ""], ["Tumor differentiation", "", "", "", "", "0.884"], ["Missing value", "9 (39)", "3 (43)", "3 (30)", "3 (50)", ""], ["Well", "5 (22)", "2 (29)", "2 (20)", "1 (17)", ""], ["Moderately", "9 (39)", "2 (29)", "5 (50)", "2 (33)", ""], ["Undifferentiated", "0", "0", "0", "0", ""], ["Pre-treatment stage", "", "", "", "", "0.441"], ["IIA", "3 (13)", "0", "2 (20)", "1 (17)", ""], ["IIIA", "1 (4)", "0", "1 (10)", "0", ""], ["IIIA–IIIB", "2 (9)", "0", "0", "2 (33)", ""], ["IIIB", "4 (17)", "1 (14)", "2 (20)", "1 (17)", ""], ["IIIB–IIIC", "12 (52)", "5 (71)", "5 (50)", "2 (33)", ""], ["IIIC", "1 (4)", "1 (14)", "0", "0", ""], ["iT", "", "", "", "", "0.560"], ["T2", "3 (13)", "0", "1 (10)", "2 (33)", ""], ["T3", "18 (78)", "6 (86)", "8 (80)", "4 (67)", ""], ["T4", "2 (9)", "1 (14)", "1 (10)", "0", ""]], "row_count": 27, "column_count": 6, "numeric_cells": 92, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:29681787:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:039fbae5bd86cb235ff2fbf6c907d0b5f642a8fd87906283c36ab717b9029cca", "bytes": 1520, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab2", "version": null, "note": "Surgical treatment and complications", "structure": {"pmcid": "PMC5898006", "section_index": 17, "section_title": "Surgical treatment and complications", "row_count": 29, "column_count": 6}, "table": {"label": "Table 2", "caption": "Surgical treatment and complications", "rows": [["Characteristics", "All patients23 (100%)a", "NR7 (30%)", "PR10 (43%)", "TR6 (26%)", "p valueb"], ["Radiotherapy", "", "", "", "", "0.822"], ["45 Gy", "1 (4)", "0", "1 (10)", "0", ""], ["45 Gy + 5.4 Gy", "21 (91)", "6 (86)", "9 (90)", "6 (100)", ""], ["50.5 Gy", "1 (4)", "1 (14)", "0", "0", ""], ["Chemotherapy", "", "", "", "", "3.2e−05"], ["Xeloda®", "22 (96)", "7 (100)", "9 (90)", "6 (100)", ""], ["5-FU", "1 (4)", "0", "1 (10)", "0", ""], ["Radiodermatitis", "", "", "", "", "0.962"], ["−", "7 (30)", "2 (29)", "3 (30)", "2 (33)", ""], ["Non-severe", "13 (57)", "4 (57)", "5 (50)", "4 (67)", ""], ["Severe", "3 (13)", "1 (14)", "2 (20)", "0", ""], ["Proctitis", "", "", "", "", "0.211"], ["+", "11 (48)", "2 (29)", "7 (70)", "2 (33)", ""], ["−", "12 (52)", "5 (71)", "3 (30)", "4 (67)", ""], ["Colitis", "", "", "", "", "1"], ["+", "0", "0", "0", "0", ""], ["−", "23 (100)", "7 (100)", "10 (100)", "6 (100)", ""], ["Mucositis", "", "", "", "", "1"], ["+", "0", "0", "0", "0", ""], ["−", "23 (100)", "7 (100)", "10 (100)", "6 (100)", ""], ["Surgical resection type", "", "", "", "", "0.004"], ["Low anterior", "17 (74)", "7 (100)", "8 (80)", "2 (33)", ""], ["Abdomino-perineal", "2 (9)", "0", "2 (20)", "0", ""], ["Endo-anal", "1 (4)", "0", "0", "1 (17)", ""], ["Refused", "3 (13)", "0", "0", "3 (50)", ""], ["Surgery delay", "", "", "", "", ""], ["Median", "8.6 ± 2.8", "9.3 ± 2.7", "8.3 ± 3.1", "8.1 ± 2.6", ""], ["Range", "1.4–13.1", "5.3–13.1", "1.4–12.9", "6.0–11.0", ""]], "row_count": 29, "column_count": 6, "numeric_cells": 95, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:29681787:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:17e17bd057aafd7a6687321e931f8b5d7cb34e8bc78e0e633bd25d8365c8f272", "bytes": 1312, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#Tab3", "version": null, "note": "Post-treatment patient characteristics", "structure": {"pmcid": "PMC5898006", "section_index": 18, "section_title": "Neoadjuvant chemoradiotherapy post-treatment results", "row_count": 26, "column_count": 6}, "table": {"label": "Table 3", "caption": "Post-treatment patient characteristics", "rows": [["Characteristics", "All patients 23 (100%)a", "NR 7 (30%)", "PR 10 (43%)", "TR 6 (26%)", "p valueb"], ["Tumor diff. after treatment", "", "", "", "", "0.064"], ["No surgery", "3 (13)", "0", "0", "3 (50)", ""], ["Missing value", "5 (22)", "2 (29)", "1 (10)", "2 (33)", ""], ["Well", "5 (22)", "1 (14)", "4 (40)", "0", ""], ["Moderately", "9 (39)", "3 (43)", "5 (50)", "1 (17)", ""], ["Undifferentiated", "1 (4)", "1 (14)", "0", "0", ""], ["Post-treatment stage", "", "", "", "", "3.3e−08"], ["0", "6 (26)", "0", "0", "6 (100)", ""], ["I", "7 (30)", "0", "7 (70)", "0", ""], ["IIA", "3 (13)", "2 (29)", "1 (10)", "0", ""], ["IIIA", "2 (9)", "0", "2 (20)", "0", ""], ["IIIB", "2 (9)", "2 (29)", "0", "0", ""], ["IIIB–IIIC", "3 (13)", "3 (43)", "0", "0", ""], ["ypT", "", "", "", "", "4.6e−08"], ["T0", "6 (26)", "0", "0", "6 (100)", ""], ["T1", "3 (13)", "0", "3 (30)", "0", ""], ["T2", "6 (26)", "0", "6 (60)", "0", ""], ["T3", "7 (30)", "6 (86)", "1 (10)", "0", ""], ["T4", "1 (4)", "1 (14)", "0", "0", ""], ["PNI", "", "", "", "", "1"], ["+", "2 (9)", "1 (14)", "1 (10)", "0", ""], ["−", "21 (91)", "6 (86)", "9 (90)", "6 (100)", ""], ["LVI", "", "", "", "", "0.002"], ["+", "8 (35)", "6 (86)", "2 (20)", "0", ""], ["−", "15 (65)", "1 (14)", "8 (80)", "6 (100)", ""]], "row_count": 26, "column_count": 6, "numeric_cells": 90, "header_rows": 1, "locator": "section[18]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:29681787:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ee58fe6a84ea3505ccb78f22335b267edb0974965969b49c86b57ad486de896f", "bytes": 501, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#Tab4", "version": null, "note": "Numbers of differentially abundant proteins between each group of responders", "structure": {"pmcid": "PMC5898006", "section_index": 19, "section_title": "Identification of differentially abundant proteins between groups", "row_count": 7, "column_count": 5}, "table": {"label": "Table 4", "caption": "Numbers of differentially abundant proteins between each group of responders", "rows": [["", "Total", "NR", "PR", "TR"], ["NR versus PR versus TRa", "402", "", "", ""], ["NR versus PRb", "384", "180", "204", ""], ["NR versus TRb", "248", "139", "", "109"], ["PR versus TRb", "417", "", "294", "123"], ["NR versus PR + TRb", "282", "139", "143", ""], ["NR + PR versus TRb", "368", "93", "275", ""]], "row_count": 7, "column_count": 5, "numeric_cells": 16, "header_rows": 1, "locator": "section[19]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:PXD008440 not downloaded", "asset:data:geo:PXD008440 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {"p_value": ", both corrected with a p value of 0"}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Finally, the analysis of mass spectrometry data were next carried out with the Perseus software package [19] and subjected to a normalization (z-score) and an ANOVA statistical test (comparison of the three groups) or Student’s T test (comparison of two groups), both corrected with a p value of 0.05."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.05, "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": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD008440"], "resolved_accessions": ["PXD008440"], "statements": ["All the datasets included in the present manuscript are presented in the main manuscript or additional supporting files. The complete data, including the raw files and all extracted peptides information can be found at the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD008440."], "basis": "The paper names PXD008440 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:29681787", "data:geo:PXD008440", "asset:table:pmid:29681787:1", "asset:table:pmid:29681787:2", "asset:table:pmid:29681787:3", "asset:table:pmid:29681787:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD008440"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:24Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 108044, "completion_tokens": 3578, "cached_tokens": 1560}}, "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:29681787", "type": "paper", "label": "pmid:29681787"}, {"id": "source:pmid:29681787", "type": "manuscript", "label": "PMID 29681787 full text"}, {"id": "data:geo:PXD008440", "type": "dataset", "label": "GEO PXD008440"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29681787", "type": "paper", "label": "pmid:29681787"}, {"id": "source:pmid:29681787", "type": "manuscript", "label": "PMID 29681787 full text"}, {"id": "data:geo:PXD008440", "type": "dataset", "label": "GEO PXD008440"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29681787", "type": "extraction", "used": ["source:pmid:29681787"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD008440", "type": "accession_resolution", "used": ["data:geo:PXD008440"], "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:29681787", "parent_hash": "sha256:b2ff0fd46bd727ca4c5b476eb7f10e25795e2009efa80bd21c72c17105d872ea", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD008440 licence not read", "asset:data:geo:PXD008440 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tial responders, RT radiotherapy, TMA tissue microarray, TR total responders Table 1Baseline patient", "the paraffin blocks (Fig. 2b) using a Tissue Microarray (TMA) Master II (3DHISTECH) (Fig. 1b).Fig. 2", "formalin-fixed paraffin-embedded, TMA tissue microarray Statistical analysis The different groups of"], "order_basis": "paper_text_order:6711", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Finally, the analysis of mass spectrometry data were next carried out with the Perseus software package [19] and subjected to a normalization (z-score) and an ANOVA statistical test (comparison of the three groups) or Student’s T test (comparison of two groups), both corrected with a p value of 0.05."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}