Comparing endocervical mucus proteome of humans and rhesus macaques.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33991406", "kind": "science-record", "revision": 5, "content_hash": "sha256:921e7237f690fa71825e80c0c3253f99f88e33f851205db28ada58ffbfca0cf6", "created_at": "2026-11-01T17:35:17Z", "updated_at": "2026-11-01T22:46:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparing endocervical mucus proteome of humans and rhesus macaques.", "doi": "10.1002/prca.202100023", "pmid": "33991406", "authors": ["Leo Han", "Daye Park", "Ashok Reddy", "Phillip A Wilmarth", "Jeffrey T Jensen"], "journal": "Proteomics. Clinical applications", "year": 2021, "abstract": "PURPOSE: Endocervical mucus changes play a key role in regulating fertility throughout the menstrual cycle and in response to hormonal contraceptives. Non-human primates (NHP) provide the most translational animal model for reproductive tract studies, as they have hormonally-regulated menstrual cycles and mucus changes, similar to women.\nEXPERIMENTAL DESIGN: We used TMT labelling and LC-LC/MS to compare the proteins found in the mucus of the rhesus macaque to the mucus of the human endocervix. Data are available via ProteomeXchange with identifier PXD021710.\nRESULTS: We found 3048 total proteins present in both rhesus mucus and human mucus, and of these, 57% showed a similar expression pattern. An even higher similarity occurred in the top 500 most prevalent proteins, with overlap in 341 (68%) proteins. Mucin MUC5B was the most highly expressed mucin protein (top 10 expressed proteins in both) but other key proteins related to mucus structure were present in both samples.\nCONCLUSIONS AND CLINICAL RELEVANCE: We find that the mucus proteome of the endocervical mucus is highly conserved in NHP and women. This supports use of the NHP model system for studies of the endocervix and trials of novel fertility treatments targeting the cervix.", "claims": [{"id": "claim-method", "statement": "We conducted differential expression testing using edgeR[11] from Bioconductor.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33991406", "locator": "sections[8] \"p\" paragraph 1", "quote": "We conducted differential expression testing using edgeR[11] from Bioconductor."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD021710.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33991406", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD021710."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The rhesus macaque and human endocervical mucus proteomes were highly conserved: 3,048 proteins were present in both, and 57% showed a similar expression pattern.", "kind": "quantitative", "target": {"value": 57.0, "unit": "per cent", "tolerance": null, "source": "We found 3,048 total proteins present in both rhesus mucus and human mucus, and of these, 57% showed a similar expression pattern."}, "evidence": [{"asset": "source:pmid:33991406", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found 3,048 total proteins present in both rhesus mucus and human mucus, and of these, 57% showed a similar expression pattern."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The rhesus macaque and human endocervical mucus proteomes were highly conserved: 3,048 proteins were present in both, and 57% showed a similar expression pattern.", "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:33991406"], "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:PXD021710"], "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:PXD021710"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33991406", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/prca.202100023", "sha256": "sha256:2ea9d5d0bdee0304fee2101575bdd04673791ac704aadecfd30e8f5673f4713b", "bytes": 15170, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/prca.202100023", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8653767", "source": "ncbi_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD021710", "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=PXD021710", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD021710", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD021710.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD021710.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comparing Endocervical Mucus Proteome of Humans and Rhesus Macaques", "resolution_checked_at": "2026-11-01T17:30:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD021710 not downloaded", "asset:data:geo:PXD021710 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We conducted differential expression testing using edgeR[11] from Bioconductor."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 57.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. 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