← All .science files
pmid:26693507
The dynamic interactome of human Aha1 upon Y223 phosphorylation.
Donald Wolfgeher · Diana M Dunn · Mark R Woodford · Dimitra Bourboulia · Gennady Bratslavsky · Mehdi Mollapour · Stephen J Kron · Andrew W Truman
Data in brief · 2015 doi:10.1016/j.dib.2015.10.028
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 · 8 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
target object · 4 fields
evidence array · 4 items
[0] object · 3 fields
[1] object · 3 fields
[2] 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 · 0 fields
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 · 3 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 · 9 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 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 · 0 fields
data_shapes array · 1 item
targets array · 2 items
[0] object · 8 fields
[1] 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 · 3 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 · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[2] 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:26693507", "kind": "science-record", "revision": 8, "content_hash": "sha256:a4ddb9b9b36a2a0cbb491ed95fbcec84fdc43dddc89ae9d5288d7848ff6734fb", "created_at": "2026-11-01T15:40:14Z", "updated_at": "2026-11-01T22:42:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The dynamic interactome of human Aha1 upon Y223 phosphorylation.", "doi": "10.1016/j.dib.2015.10.028", "pmid": "26693507", "authors": ["Donald Wolfgeher", "Diana M Dunn", "Mark R Woodford", "Dimitra Bourboulia", "Gennady Bratslavsky", "Mehdi Mollapour", "Stephen J Kron", "Andrew W Truman"], "journal": "Data in brief", "year": 2015, "abstract": "Heat Shock Protein 90 (Hsp90) is an essential chaperone that supports the function of a wide range of signaling molecules. Hsp90 binds to a suite of co-chaperone proteins that regulate Hsp90 function through alteration of intrinsic ATPase activity. Several studies have determined Aha1 to be an important co-chaperone whose binding to Hsp90 is modulated by phosphorylation, acetylation and SUMOylation of Hsp90 [1], [2]. In this study, we applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand how phosphorylation of hAha1 at Y223 altered global client/co-chaperone interaction [3]. Specifically, we characterized and compared the interactomes of Aha1-Y223F (phospho-mutant form) and Aha1-Y223E (phospho-mimic form). We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.", "claims": [{"id": "claim-method", "statement": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26693507", "locator": "sections[8] \"LC–MS/MS data analysis, statistical analysis\" paragraph 4", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26693507", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the R statistical package with ANOVA testing and data deposited through ProteomeXchange via the PRIDE partner repository under PXD001737, the study identified 99 statistically significant hAha1 interactors, 84% of which preferentially bound the phospho-mimic form of hAha1.", "kind": "quantitative", "target": {"value": 84.0, "unit": "per cent", "tolerance": null, "source": "We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1."}, "evidence": [{"asset": "source:pmid:26693507", "locator": "sections[8] \"LC–MS/MS data analysis, statistical analysis\" paragraph 4", "quote": "Further statistical analysis was performed using the R statistical package (http://www.r-project.org/)."}, {"asset": "source:pmid:26693507", "locator": "sections[8] \"LC–MS/MS data analysis, statistical analysis\" paragraph 4", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}, {"asset": "source:pmid:26693507", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737."}, {"asset": "source:pmid:26693507", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the R statistical package with ANOVA testing and data deposited through ProteomeXchange via the PRIDE partner repository under PXD001737, the study identified 99 statistically significant hAha1 interactors, 84% of which preferentially bound the phospho-mimic form of hAha1.", "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:26693507"], "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:PXD001737"], "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:PXD001737"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26693507", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.10.028", "sha256": "sha256:285bb668764e516276a8306c7e0f25fad1f0ad0cea7f3003e2527f5e84437ee4", "bytes": 10863, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.10.028", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4659802", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001737", "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=PXD001737", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001737", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "c-Abl Dependent Tyrosine Phosphorylation of theCo-chaperone Aha1 Regulates Interaction with Hsp90", "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:26693507:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e022115a3822defd81a98a1dbb9a35a08cd45cc7d810c1b2b761b6a5afad108b", "bytes": 1005, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4659802", "section_index": 1, "section_title": "Specifications table", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Molecular chaperones, Mass spectrometry, phosphorylation"], ["Type of data", "18O Quant LC–MS/MS Mass spectrometry data"], ["How data was acquired", "Mass spectrometry. Thermo Q-Exactive Orbitrap"], ["Data format", "*.Raw"], ["Experimental factors", "HEK293 cells expressing either FLAG–hAha1–Y223E or FLAG–Aha1–Y223F"], ["Experimental features", "FLAG–hAha1–Y223E or FLAG–Aha1–Y223F complexes were purified by magnetic bead immunoprecipitation and processed by mass spectrometry"], ["Data source location", "The University of Chicago, Chicago, Illinois, USA"], ["Data accessibility", "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001737."]], "row_count": 9, "column_count": 2, "numeric_cells": 4, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:PXD001737 not downloaded", "asset:data:geo:PXD001737 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": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 84.0, "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": "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": ["PXD001737"], "resolved_accessions": ["PXD001737"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737."], "basis": "The paper names PXD001737 in ProteomeXchange Consortium 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:26693507", "data:geo:PXD001737", "asset:table:pmid:26693507:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001737"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:29Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 28413, "completion_tokens": 2484, "cached_tokens": 1817}}, "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:26693507", "type": "paper", "label": "pmid:26693507"}, {"id": "source:pmid:26693507", "type": "manuscript", "label": "PMID 26693507 full text"}, {"id": "data:geo:PXD001737", "type": "dataset", "label": "GEO PXD001737"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26693507", "type": "paper", "label": "pmid:26693507"}, {"id": "source:pmid:26693507", "type": "manuscript", "label": "PMID 26693507 full text"}, {"id": "data:geo:PXD001737", "type": "dataset", "label": "GEO PXD001737"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26693507", "type": "extraction", "used": ["source:pmid:26693507"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001737", "type": "accession_resolution", "used": ["data:geo:PXD001737"], "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:26693507", "parent_hash": "sha256:f7c9861d73171e39d04d5170d4ccf3c7759f8e531d7b019c9ac330cf62d0e385", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD001737 licence not read", "asset:data:geo:PXD001737 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand how phospho", "ding to the phospho-mimic form of hAha1. The mass spectrometry proteomics data have been deposited to the P", "inity-purification mass spectrometry (AP-MS) proteomics to understand how phosphorylation of hAha1 a", "biological replicates within each group. The mass spectrometry proteomic data have been deposited to the Pr"], "order_basis": "paper_text_order:502", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Experimental design, materials and methods HEK293 cell lines expressing either hAha1–Y223F–FLA", "taining 5% CO2. Protein extraction from both HEK293 cells was carried out using methods previous"], "order_basis": "paper_text_order:1202", "id": "assay:2"}, {"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": ["An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}