Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:40165474

CENPF as a Potential Biomarker Associated with the Immune Microenvironment of Renal Cancer.

Technology in cancer research & treatment · 2025 doi:10.1177/15330338251330791

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

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
id
pmid:40165474
kind
science-record
content_hash
sha256:3407dac6d5454dcb3d531e713d793729332c3b729bd7f882152ae8209052df6a
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:50Z
updated_at
2026-11-01T14:01:38Z
generator object · 3 fields
name
corpus-assay-engine
converter
sep_to_sci_v1
source_package_schema
urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
CENPF as a Potential Biomarker Associated with the Immune Microenvironment of Renal Cancer.
doi
10.1177/15330338251330791
pmid
40165474
authors
null
journal
Technology in cancer research & treatment
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
id
claim-1
statement
the headline numerical result the paper states for its main finding
kind
qualitative
state
blocked
target object · 4 fields
value
null
unit
null
tolerance
null
source
null
evidence array · 0 items
gaps array · 2 items
[0]
abstract
[1]
authors
experiment object · 8 fields
state
partial
objective
the headline numerical result the paper states for its main finding
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate and its interval from the source
kind
other
state
complete
blocked_on
null
description
The number a replication must land on, and the sentence it came from.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40165474
outputs array · 1 item
[0]
the published estimate, its unit and its interval
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data behind the published result
kind
data-preparation
state
blocked
blocked_on
data:not_downloaded
description
The published result cannot be recomputed without the data the paper analysed.
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the source data with its provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the analysis programme
kind
analysis
state
blocked
blocked_on
no owned computational capability is bound to this experiment
description
Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40165474
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
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 · 3 items
[0]
step:obtain_source_data blocked on data:not_downloaded
[1]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[2]
step:run_analysis input 'materials:the source data behind the published result in pmid:40165474' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 3 items
[0] object · 15 fields
id
source:pmid:40165474
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1177/15330338251330791
sha256
sha256:5c162c140d1103276ddcc7420674bc9ddc7b2a1a35ce0a8670d9652377f12692
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1177/15330338251330791
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
[1] object · 16 fields
id
asset:table:pmid:40165474:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:df97685ba608605da7884996277a0404ba108b5a56b58632835c5e930cc35c61
bytes
228
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[6]/table-wrap[1]#table1-15330338251330791
version
null
note
Demographic and Clinical Characteristics of KIRC Patients.
structure object · 5 fields
pmcid
PMC11960158
section_index
6
section_title
Study Population
row_count
0
column_count
0
table object · 8 fields
label
Table 1.
caption
Demographic and Clinical Characteristics of KIRC Patients.
rows array · 0 items
locator
section[6]/table-wrap[1]#table1-15330338251330791
[2] object · 16 fields
id
asset:table:pmid:40165474:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:3f9f4fef2fe563807d0cd17abc13a895cebcca07eda143545e26491527d16191
bytes
231
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[6]/table-wrap[2]#table2-15330338251330791
version
null
note
Demographic and Clinical Characteristics of Healthy Controls.
structure object · 5 fields
pmcid
PMC11960158
section_index
6
section_title
Study Population
row_count
0
column_count
0
table object · 8 fields
label
Table 2.
caption
Demographic and Clinical Characteristics of Healthy Controls.
rows array · 0 items
locator
section[6]/table-wrap[2]#table2-15330338251330791
gaps array · 1 item
[0]
asset:source:pmid:40165474 not verified
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
state
absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
readiness object · 8 fields
state
partial
tier
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
[0]
source:pmid:40165474
[1]
asset:table:pmid:40165474:1
[2]
asset:table:pmid:40165474:2
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:40165474
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 2 items
[0] object · 7 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
full-text-reading-v1
prompt_hash
6ff735bf2c4592ec80e9fee4f8c8490a2ba71d5b226cbbbf11e5f9c0917f0f95
source_hash
5c162c140d1103276ddcc7420674bc9ddc7b2a1a35ce0a8670d9652377f12692
raw_response_sha256
sha256:2be808ffc73022f33fd60a1233bbe2cdf0700e5ac1beb302a7677d228a267094
raw_response_chars
4515
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
e4ecb640dfe4b3420df340d86ab0aac87cb1b7edc9c1138e3547a9edab205a79
source_hash
5c162c140d1103276ddcc7420674bc9ddc7b2a1a35ce0a8670d9652377f12692
raw_response_sha256
sha256:52bc598aa8a9a00576f4a8e298899b508b904f9f348af192f63e457d1a2e322c
raw_response_chars
54157
target_providers array · 0 items
agreement
false
disagreements object · 3 fields
target_result object · 3 fields
minimax
No numerical headline result is stated. The main finding is that CENPF is a hub gene upregulated in renal cancer subtypes and that its overexpression is associated with poorer prognosis in KIRC.
minimax_alt
No numerical headline effect estimate is reported. The stated main finding is that CENPF was identified as a hub gene significantly upregulated in renal cancer subtypes, with overexpression linked to worse survival outcomes in KIRC patients.
decisive
false
analysis_methods object · 3 fields
minimax array · 9 items
[0]
Differential expression analysis
[1]
Molecular Complex Detection (MCODE)
[2]
Univariate Cox regression analyses
[3]
Single-cell sequencing analysis
[4]
CIBERSORT algorithm
[5]
Seurat package in R
[6]
STRING 18
[7]
Cytoscape 19
[8]
limma package
minimax_alt array · 8 items
[0]
differential expression analysis
[1]
Molecular Complex Detection (MCODE)
[2]
univariate Cox regression
[3]
STRING 18 protein-protein interaction network analysis
[4]
Cytoscape 19 network visualization
[5]
limma
[6]
Seurat
[7]
CIBERSORT
decisive
false
statistical_method object · 3 fields
minimax
univariate Cox regression analyses
minimax_alt
univariate Cox regression
decisive
true
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 2 items
[0] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[1] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 2 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 1 item
[0] object · 3 fields
id
package:d4d22f122a693fdbf65a318f04e18f08905a1619eae4cae8f02978606879e3c8
type
sep_package
label
SEP v1 package for pmid:40165474
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40165474
type
conversion
used array · 1 item
[0]
package:d4d22f122a693fdbf65a318f04e18f08905a1619eae4cae8f02978606879e3c8
agent
agent:corpus-assay-engine
agents array · 3 items
[0] object · 3 fields
id
agent:minimax
type
model
label
minimax
[1] object · 3 fields
id
agent:minimax_alt
type
model
label
minimax_alt
[2] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
source_run_id
run-20261023T122449232913
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:40165474
parent_hash
sha256:d1b39ddd3a9b7566c449ab306cea4c7cd5e19c29e085ab906867b5eca7e455de
fork_of
null
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40165474 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
step:obtain_source_data blocked on data:not_downloaded
[10]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[11]
step:run_analysis input 'materials:the source data behind the published result in pmid:40165474' does not resolve to a declared asset
[12]
targets
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40165474", "kind": "science-record", "revision": 2, "content_hash": "sha256:3407dac6d5454dcb3d531e713d793729332c3b729bd7f882152ae8209052df6a", "created_at": "2026-11-01T10:25:50Z", "updated_at": "2026-11-01T14:01:38Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "CENPF as a Potential Biomarker Associated with the Immune Microenvironment of Renal Cancer.", "doi": "10.1177/15330338251330791", "pmid": "40165474", "authors": null, "journal": "Technology in cancer research & treatment", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40165474"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40165474", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40165474' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40165474", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/15330338251330791", "sha256": "sha256:5c162c140d1103276ddcc7420674bc9ddc7b2a1a35ce0a8670d9652377f12692", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/15330338251330791", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40165474:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:df97685ba608605da7884996277a0404ba108b5a56b58632835c5e930cc35c61", "bytes": 228, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#table1-15330338251330791", "version": null, "note": "Demographic and Clinical Characteristics of KIRC Patients.", "structure": {"pmcid": "PMC11960158", "section_index": 6, "section_title": "Study Population", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1.", "caption": "Demographic and Clinical Characteristics of KIRC Patients.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[6]/table-wrap[1]#table1-15330338251330791"}}, {"id": "asset:table:pmid:40165474:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3f9f4fef2fe563807d0cd17abc13a895cebcca07eda143545e26491527d16191", "bytes": 231, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[2]#table2-15330338251330791", "version": null, "note": "Demographic and Clinical Characteristics of Healthy Controls.", "structure": {"pmcid": "PMC11960158", "section_index": 6, "section_title": "Study Population", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2.", "caption": "Demographic and Clinical Characteristics of Healthy Controls.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[6]/table-wrap[2]#table2-15330338251330791"}}], "gaps": ["asset:source:pmid:40165474 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40165474", "asset:table:pmid:40165474:1", "asset:table:pmid:40165474:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40165474"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "6ff735bf2c4592ec80e9fee4f8c8490a2ba71d5b226cbbbf11e5f9c0917f0f95", "source_hash": "5c162c140d1103276ddcc7420674bc9ddc7b2a1a35ce0a8670d9652377f12692", "raw_response_sha256": "sha256:2be808ffc73022f33fd60a1233bbe2cdf0700e5ac1beb302a7677d228a267094", "raw_response_chars": 4515}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "e4ecb640dfe4b3420df340d86ab0aac87cb1b7edc9c1138e3547a9edab205a79", "source_hash": "5c162c140d1103276ddcc7420674bc9ddc7b2a1a35ce0a8670d9652377f12692", "raw_response_sha256": "sha256:52bc598aa8a9a00576f4a8e298899b508b904f9f348af192f63e457d1a2e322c", "raw_response_chars": 54157}], "target_providers": [], "agreement": false, "disagreements": {"target_result": {"minimax": "No numerical headline result is stated. The main finding is that CENPF is a hub gene upregulated in renal cancer subtypes and that its overexpression is associated with poorer prognosis in KIRC.", "minimax_alt": "No numerical headline effect estimate is reported. The stated main finding is that CENPF was identified as a hub gene significantly upregulated in renal cancer subtypes, with overexpression linked to worse survival outcomes in KIRC patients.", "decisive": false}, "analysis_methods": {"minimax": ["Differential expression analysis", "Molecular Complex Detection (MCODE)", "Univariate Cox regression analyses", "Single-cell sequencing analysis", "CIBERSORT algorithm", "Seurat package in R", "STRING 18", "Cytoscape 19", "limma package"], "minimax_alt": ["differential expression analysis", "Molecular Complex Detection (MCODE)", "univariate Cox regression", "STRING 18 protein-protein interaction network analysis", "Cytoscape 19 network visualization", "limma", "Seurat", "CIBERSORT"], "decisive": false}, "statistical_method": {"minimax": "univariate Cox regression analyses", "minimax_alt": "univariate Cox regression", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:d4d22f122a693fdbf65a318f04e18f08905a1619eae4cae8f02978606879e3c8", "type": "sep_package", "label": "SEP v1 package for pmid:40165474"}], "activities": [{"id": "activity:conversion:pmid:40165474", "type": "conversion", "used": ["package:d4d22f122a693fdbf65a318f04e18f08905a1619eae4cae8f02978606879e3c8"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40165474", "parent_hash": "sha256:d1b39ddd3a9b7566c449ab306cea4c7cd5e19c29e085ab906867b5eca7e455de", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40165474 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40165474' does not resolve to a declared asset", "targets"]}