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pmid:40547309

Mito-fission gene prognostic model for colorectal cancer.

PeerJ · 2025 doi:10.7717/peerj.19522

Paper

partial

Experiment

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Data

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Analysis

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:40547309
kind
science-record
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sha256:00368366a914518d28bb233532ea82d8ad8881565d7249d2dcf4eb49e828f508
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:51Z
updated_at
2026-11-01T14:01:42Z
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paper object · 10 fields
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partial
title
Mito-fission gene prognostic model for colorectal cancer.
doi
10.7717/peerj.19522
pmid
40547309
authors
null
journal
PeerJ
year
2025
abstract
null
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the headline numerical result the paper states for its main finding
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qualitative
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the headline numerical result the paper states for its main finding
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the published estimate, its unit and its interval
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the source data with its provenance
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List of 40 MFRGs.
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PMC12182055
section_index
3
section_title
Data extraction
row_count
41
column_count
2
table object · 8 fields
label
Table 1
caption
List of 40 MFRGs.
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[0] array · 2 items
[0]
Number
[1]
Symbol
[1] array · 2 items
[0]
1
[1]
DNM1L
[2] array · 2 items
[0]
2
[1]
RALBP1
[3] array · 2 items
[0]
3
[1]
MTFR2
[4] array · 2 items
[0]
4
[1]
LRRK2
[5] array · 2 items
[0]
5
[1]
MIEF2
[6] array · 2 items
[0]
6
[1]
COX10
[7] array · 2 items
[0]
7
[1]
C11orf65
[8] array · 2 items
[0]
8
[1]
DCN
[9] array · 2 items
[0]
9
[1]
PGAM5
[10] array · 2 items
[0]
10
[1]
DDHD2
[11] array · 2 items
[0]
11
[1]
KDR
[12] array · 2 items
[0]
12
[1]
MAPT
[13] array · 2 items
[0]
13
[1]
OPA1
[14] array · 2 items
[0]
14
[1]
PRKN
[15] array · 2 items
[0]
15
[1]
FIS1
[16] array · 2 items
[0]
16
[1]
MTFP1
[17] array · 2 items
[0]
17
[1]
CYRIB
[18] array · 2 items
[0]
18
[1]
GDAP1
[19] array · 2 items
[0]
19
[1]
MIEF1
[20] array · 2 items
[0]
20
[1]
PPARG
[21] array · 2 items
[0]
21
[1]
MARCHF5
[22] array · 2 items
[0]
22
[1]
VPS35
[23] array · 2 items
[0]
23
[1]
MTFR1L
[24] array · 2 items
[0]
24
[1]
SPIRE1
[25] array · 2 items
[0]
25
[1]
MFF
[26] array · 2 items
[0]
26
[1]
RALA
[27] array · 2 items
[0]
27
[1]
INF2
[28] array · 2 items
[0]
28
[1]
PINK1
[29] array · 2 items
[0]
29
[1]
TMEM135
[30] array · 2 items
[0]
30
[1]
BNIP3
[31] array · 2 items
[0]
31
[1]
STAT2
[32] array · 2 items
[0]
32
[1]
AURKA
[33] array · 2 items
[0]
33
[1]
UCP2
[34] array · 2 items
[0]
34
[1]
MUL1
[35] array · 2 items
[0]
35
[1]
MYO19
[36] array · 2 items
[0]
36
[1]
DDHD1
[37] array · 2 items
[0]
37
[1]
AP3B1
[38] array · 2 items
[0]
38
[1]
MCU
[39] array · 2 items
[0]
39
[1]
SLC25A46
[40] array · 2 items
[0]
40
[1]
MTFR1
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Primer sequence information for RT-qPCR.
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PMC12182055
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15
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RNA isolation and quantitative real-time polymerase chain reaction (qRT-PCR)
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9
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Table 2
caption
Primer sequence information for RT-qPCR.
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[0] array · 2 items
[0]
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[1]
Sequence
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[0]
CCDC68 F
[1]
TGCCTTGTATGAGTCTACGTCC
[2] array · 2 items
[0]
CCDC68 R
[1]
AGCCCTGTTGAAGGTTTCCAC
[3] array · 2 items
[0]
FAM151A F
[1]
CTGAATGTGGAGTGGCTGGT
[4] array · 2 items
[0]
FAM151A R
[1]
TTCTGTGTCTGGGAGGGTCA
[5] array · 2 items
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MC1R F
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GTGTCGAAATGTCCTGGGGA
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MC1R R
[1]
GACACCTCCTGGCATCTACC
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Internal reference-GAPDH F
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CGAAGGTGGAGTCAACGGATTT
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ATGGGTGGAATCATATTGGAAC
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List of functional information for ten genes from univariate Cox analysis.
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pmcid
PMC12182055
section_index
23
section_title
Identification of hub gene and risk model construction
row_count
11
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5
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label
Table 3
caption
List of functional information for ten genes from univariate Cox analysis.
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[0] array · 5 items
[0]
[1]
Full name
[2]
Function
[3]
Correlation with cancer
[4]
Correlation with mitochondrial dysregulation
[1] array · 5 items
[0]
HIGD1A
[1]
HIG1 Hypoxia Inducible Domain Family Member 1A
[2]
Regulating polyamine metabolism, inhibited tumor growth and metastasis
[3]
colon cancer (PMID: 37479180)
[4]
Mitochondrial inner membrane protein, regulating metabolic homeostasis (PMID: 37492734)
[2] array · 5 items
[0]
DIAPH3
[1]
Diaphanous Related Formin 3
[2]
Involved in actin remodeling and regulate cell movement and adhesion, promote migration and invasion of CRC cells
[3]
colorectal cancer (PMID: 39843730)
[4]
NA
[3] array · 5 items
[0]
CCDC68
[1]
Coiled-Coil Domain Containing 68
[2]
Involved in microtubule anchoring at centrosome and protein localization
[3]
colorectal cancer (PMID: 35557589)
[4]
NA
[4] array · 5 items
[0]
FAM151A
[1]
Family With Sequence Similarity 151 Member A
[2]
Highly expressed in the intestine, kidney and spleen (PMID: 31949211)
[3]
NA
[4]
NA
[5] array · 5 items
[0]
KRTAP5.1
[1]
Keratin Associated Protein 5-1
[2]
Essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins (PMID: 37014946)
[3]
NA
[4]
NA
[6] array · 5 items
[0]
HSF4
[1]
Heat Shock Transcription Factor 4
[2]
Promotes the proliferation and metastasis of CRC by regulating EMT-related signalling pathways
[3]
colorectal cancer (PMID: 39881364)
[4]
NA
[7] array · 5 items
[0]
MC1R
[1]
Melanocortin 1 Receptor
[2]
Regulates T regulatory cell differentiation through metabolic reprogramming to promote colon cancer
[3]
colorectal cancer (PMID: 38917522)
[4]
Suppressing the oxidative stress, apoptosis, and mitochondrial fission through the AMPK/SIRT1/PGC-1α signaling pathway (PMID: 33391490)
[8] array · 5 items
[0]
ZNF692
[1]
Zinc Finger Protein 692
[2]
Promotes the progression of colorectal cancer by regulating HSF4 expression
[3]
colorectal cancer (PMID: 38435777)
[4]
NA
[9] array · 5 items
[0]
LIME1
[1]
Lck Interacting Transmembrane Adaptor 1
[2]
Docking protein to recruit signaling molecules, and involved in inflammatory pathways
[3]
bladder cancer (PMID: 39429662)
[4]
NA
[10] array · 5 items
[0]
TTYH3
[1]
Tweety Family Member 3
[2]
Plays a role in tissue formation, embryonic development, and immune response to pathogen related molecules
[3]
colorectal cancer (PMID: 38827027)
[4]
NA
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Results of stepwise regression analysis.
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section_index
23
section_title
Identification of hub gene and risk model construction
row_count
4
column_count
6
table object · 8 fields
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Table 4
caption
Results of stepwise regression analysis.
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[0] array · 6 items
[0]
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[1]
coef
[2]
exp (coef)
[3]
se (coef)
[4]
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[5]
Pr (>|z|)
[1] array · 6 items
[0]
CCDC68
[1]
−0.30553
[2]
0.736733
[3]
0.141426
[4]
−2.16035
[5]
0.030746
[2] array · 6 items
[0]
FAM151A
[1]
−0.97326
[2]
0.377849
[3]
0.31981
[4]
−3.04325
[5]
0.00234
[3] array · 6 items
[0]
MC1R
[1]
0.797626
[2]
2.220264
[3]
0.181711
[4]
4.389539
[5]
1.14E−05
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Table of relevant information on 71 discrepant drugs.
structure object · 5 fields
pmcid
PMC12182055
section_index
27
section_title
Fifty-one common chemotherapeutic drugs were effective in high-risk patients for CRC
row_count
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column_count
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table object · 8 fields
label
Table 5
caption
Table of relevant information on 71 discrepant drugs.
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[0] array · 7 items
[0]
drugs
[1]
high_group_res
[2]
low_group_res
[3]
padj
[4]
pvalue
[5]
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[6]
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[2]
−1.029
[3]
0.09352216
[4]
0.048116473
[5]
0.028560435
[6]
PMID: 39531120
[2] array · 7 items
[0]
Sorafenib
[1]
3.844
[2]
3.826
[3]
0.083005791
[4]
0.042104387
[5]
0.014156188
[6]
PMID: 39577235
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VX.680
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2.364
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0.075511125
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0.039769178
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[3]
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[4]
0.035871561
[5]
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[5] array · 7 items
[0]
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0.9782
[2]
0.953
[3]
0.064334946
[4]
0.031235082
[5]
0.021896508
[6]
PMID: 363377
[6] array · 7 items
[0]
AZD.2281
[1]
4.856
[2]
4.915
[3]
0.059041856
[4]
0.028237409
[5]
−0.090080215
[6]
PMID: 36082969
[7] array · 7 items
[0]
GSK.650394
[1]
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[2]
4.187
[3]
0.055894746
[4]
0.026327236
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0.05820392
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[8] array · 7 items
[0]
CGP.082996
[1]
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[2]
4.07
[3]
0.04924791
[4]
0.022839611
[5]
−0.033324433
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[9] array · 7 items
[0]
ABT.263
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[2]
2.855
[3]
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[10] array · 7 items
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[1]
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[2]
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[11] array · 7 items
[0]
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6.134
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0.033967735
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0.015014723
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−0.022779748
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[12] array · 7 items
[0]
JNK.9L
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−0.06688
[2]
−0.0392
[3]
0.031843664
[4]
0.013845071
[5]
−0.046716942
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[13] array · 7 items
[0]
AP.24534
[1]
1.758
[2]
1.855
[3]
0.031843664
[4]
0.01364931
[5]
−0.124897566
[6]
PMID: 38722621
[14] array · 7 items
[0]
RDEA119
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2.148
[2]
1.979
[3]
0.031843664
[4]
0.013543565
[5]
0.117379887
[6]
[15] array · 7 items
[0]
Roscovitine
[1]
4.827
[2]
4.81
[3]
0.025538218
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0.010548395
[5]
0.005275309
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[16] array · 7 items
[0]
TW.37
[1]
−0.3615
[2]
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[3]
0.021059601
[4]
0.008545925
[5]
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[17] array · 7 items
[0]
Camptothecin
[1]
−3.94
[2]
−3.873
[3]
0.021059601
[4]
0.008499383
[5]
−0.189793129
[6]
PMID: 16990856
[18] array · 7 items
[0]
Rapamycin
[1]
−0.1547
[2]
−0.2284
[3]
0.021059601
[4]
0.008429995
[5]
0.028144422
[6]
PMID: 37057884
[19] array · 7 items
[0]
JNJ.26854165
[1]
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[2]
2.903
[3]
0.019286462
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[5]
−0.096412009
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[20] array · 7 items
[0]
KU.55933
[1]
5.121
[2]
5.135
[3]
0.018646596
[4]
0.007026254
[5]
−0.018304948
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[21] array · 7 items
[0]
A.770041
[1]
3.721
[2]
3.837
[3]
0.018080039
[4]
0.006681753
[5]
−0.125054936
[6]
[22] array · 7 items
[0]
Axitinib
[1]
3.562
[2]
3.638
[3]
0.016782954
[4]
0.006080781
[5]
−0.070962035
[6]
PMID: 39851927
[23] array · 7 items
[0]
IPA.3
[1]
5.828
[2]
5.935
[3]
0.016529912
[4]
0.005869317
[5]
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[24] array · 7 items
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AZD8055
[1]
0.362
[2]
0.3714
[3]
0.015447953
[4]
0.005373201
[5]
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[25] array · 7 items
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GW843682X
[1]
−2.316
[2]
−2.338
[3]
0.015309048
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0.005213951
[5]
0.008854699
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[26] array · 7 items
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AZD6482
[1]
3.629
[2]
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[3]
0.015068095
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0.005022698
[5]
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[27] array · 7 items
[0]
NSC.87877
[1]
6.735
[2]
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[3]
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[4]
0.004363873
[5]
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[28] array · 7 items
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EHT.1864
[1]
4.778
[2]
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[3]
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[29] array · 7 items
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VX.702
[1]
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[2]
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[30] array · 7 items
[0]
SB590885
[1]
4.975
[2]
4.915
[3]
0.010444852
[4]
0.003178868
[5]
0.056102008
[6]
[31] array · 7 items
[0]
BI.2536
[1]
−1.595
[2]
−1.692
[3]
0.010444852
[4]
0.003117351
[5]
0.07229982
[6]
[32] array · 7 items
[0]
AZD6244
[1]
2.899
[2]
2.721
[3]
0.010435655
[4]
0.003024827
[5]
0.119951365
[6]
[33] array · 7 items
[0]
Docetaxel
[1]
−5.362
[2]
−5.26
[3]
0.007690955
[4]
0.002173531
[5]
−0.177536721
[6]
PMID: 39911148
[34] array · 7 items
[0]
NVP.BEZ235
[1]
−2.387
[2]
−2.266
[3]
0.007245434
[4]
0.00199512
[5]
−0.119126921
[6]
[35] array · 7 items
[0]
NU.7441
[1]
3.534
[2]
3.595
[3]
0.006978244
[4]
0.001870979
[5]
−0.078773514
[6]
[36] array · 7 items
[0]
Bryostatin.1
[1]
−1.129
[2]
−1.09
[3]
0.006422026
[4]
0.001675311
[5]
−0.037451029
[6]
[37] array · 7 items
[0]
NVP.TAE684
[1]
1.689
[2]
1.721
[3]
0.006218487
[4]
0.001577153
[5]
−0.062869173
[6]
[38] array · 7 items
[0]
ZM.447439
[1]
2.739
[2]
2.766
[3]
0.005392136
[4]
0.001328497
[5]
−0.029209727
[6]
[39] array · 7 items
[0]
Metformin
[1]
10.65
[2]
10.53
[3]
0.005392136
[4]
0.001300887
[5]
0.083124597
[6]
PMID: 39861414
[40] array · 7 items
[0]
PD.173074
[1]
4.122
[2]
4.184
[3]
0.005392136
[4]
0.00128624
[5]
−0.080062717
[6]
[41] array · 7 items
[0]
OSI.906
[1]
3.718
[2]
3.84
[3]
0.005392136
[4]
0.001217238
[5]
−0.132662293
[6]
[42] array · 7 items
[0]
Midostaurin
[1]
0.8398
[2]
0.9802
[3]
0.004306115
[4]
0.000936112
[5]
−0.127502408
[6]
PMID: 28644114
[43] array · 7 items
[0]
Dasatinib
[1]
2.085
[2]
2.413
[3]
0.003827739
[4]
0.00080438
[5]
−0.290838304
[6]
PMID: 36322825
[44] array · 7 items
[0]
Bexarotene
[1]
4.739
[2]
4.761
[3]
0.003827739
[4]
0.000803033
[5]
−0.029905707
[6]
PMID: 39007945
[45] array · 7 items
[0]
GDC.0449
[1]
5.653
[2]
5.714
[3]
0.003030732
[4]
0.000592969
[5]
−0.055388504
[6]
PMID: 24756807
[46] array · 7 items
[0]
AZD7762
[1]
0.1399
[2]
0.3149
[3]
0.002536853
[4]
0.000477958
[5]
−0.17295287
[6]
[47] array · 7 items
[0]
Imatinib
[1]
4.954
[2]
4.978
[3]
0.002422395
[4]
0.00043884
[5]
−0.028950786
[6]
PMID: 39023605
[48] array · 7 items
[0]
RO.3306
[1]
4.803
[2]
4.885
[3]
0.001404402
[4]
0.000244244
[5]
−0.099624065
[6]
[49] array · 7 items
[0]
Epothilone.B
[1]
−4.903
[2]
−5.04
[3]
0.001241353
[4]
0.000206892
[5]
0.148448881
[6]
[50] array · 7 items
[0]
GSK269962A
[1]
3.635
[2]
3.755
[3]
0.001241353
[4]
0.00020276
[5]
−0.18013549
[6]
[51] array · 7 items
[0]
AZD.0530
[1]
4.053
[2]
4.181
[3]
0.000977892
[4]
0.00014881
[5]
−0.147212978
[6]
[52] array · 7 items
[0]
JNK.Inhibitor.VIII
[1]
5.833
[2]
5.886
[3]
6.28E−05
[4]
6.37E−06
[5]
−0.054132883
[6]
[53] array · 7 items
[0]
Vinorelbine
[1]
−3.475
[2]
−3.62
[3]
0.000415296
[4]
6.02E−05
[5]
0.146138882
[6]
PMID: 39776939
[54] array · 7 items
[0]
WO2009093972
[1]
2.971
[2]
3.128
[3]
6.18E−05
[4]
5.82E−06
[5]
−0.167943832
[6]
[55] array · 7 items
[0]
PD.0325901
[1]
0.22
[2]
0.01011
[3]
0.000411263
[4]
5.66E−05
[5]
0.170290237
[6]
[56] array · 7 items
[0]
Shikonin
[1]
0.1304
[2]
0.3193
[3]
8.96E−06
[4]
5.19E−07
[5]
−0.171613126
[6]
[57] array · 7 items
[0]
Pazopanib
[1]
4.534
[2]
4.644
[3]
5.18E−05
[4]
4.51E−06
[5]
−0.135988084
[6]
PMID: 36877187
[58] array · 7 items
[0]
Temsirolimus
[1]
−1.091
[2]
−1.049
[3]
0.000333998
[4]
4.36E−05
[5]
−0.06551927
[6]
PMID: 22861825
[59] array · 7 items
[0]
CMK
[1]
3.639
[2]
3.663
[3]
0.000333998
[4]
4.13E−05
[5]
−0.022727652
[6]
[60] array · 7 items
[0]
BMS.708163
[1]
4.986
[2]
4.938
[3]
4.99E−05
[4]
3.98E−06
[5]
0.049136545
[6]
[61] array · 7 items
[0]
Elesclomol
[1]
−2.976
[2]
−2.739
[3]
4.99E−05
[4]
3.82E−06
[5]
−0.257894071
[6]
[62] array · 7 items
[0]
GDC0941
[1]
2.169
[2]
2.222
[3]
4.99E−05
[4]
3.57E−06
[5]
−0.055258206
[6]
[63] array · 7 items
[0]
FTI.277
[1]
3.699
[2]
3.757
[3]
0.000298753
[4]
3.46E−05
[5]
−0.061556158
[6]
[64] array · 7 items
[0]
BIBW2992
[1]
2.279
[2]
2.206
[3]
3.09E−09
[4]
2.24E−11
[5]
0.076788254
[6]
PMID: 39894491
[65] array · 7 items
[0]
X681640
[1]
2.668
[2]
2.531
[3]
4.28E−06
[4]
2.17E−07
[5]
0.16932215
[6]
[66] array · 7 items
[0]
CI.1040
[1]
2.62
[2]
2.595
[3]
0.000163328
[4]
1.78E−05
[5]
0.022405468
[6]
[67] array · 7 items
[0]
GNF.2
[1]
4.505
[2]
4.575
[3]
3.91E−06
[4]
1.70E−07
[5]
−0.083372586
[6]
[68] array · 7 items
[0]
AMG.706
[1]
4.112
[2]
4.193
[3]
7.28E−09
[4]
1.58E−10
[5]
−0.104445814
[6]
[69] array · 7 items
[0]
AG.014699
[1]
4.157
[2]
4.187
[3]
4.37E−08
[4]
1.27E−09
[5]
−0.040279378
[6]
PMID: 30830551
[70] array · 7 items
[0]
LFM.A13
[1]
6.142
[2]
6.205
[3]
2.83E−07
[4]
1.02E−08
[5]
−0.065518629
[6]
[71] array · 7 items
[0]
CCT007093
[1]
5.597
[2]
5.626
[3]
7.03E−09
[4]
1.02E−10
[5]
−0.024293532
[6]
locator
section[27]/table-wrap[1]#table-5
gaps array · 1 item
[0]
asset:source:pmid:40547309 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 · 6 items
[0]
source:pmid:40547309
[1]
asset:table:pmid:40547309:1
[2]
asset:table:pmid:40547309:2
[3]
asset:table:pmid:40547309:3
[4]
asset:table:pmid:40547309:4
[5]
asset:table:pmid:40547309:5
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:40547309
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 0 items
target_providers array · 0 items
agreement
false
disagreements array · 0 items
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 · 4 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
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[3] 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 · 3 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
[2]
review.machine_critique.providers
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:b5db1246b72a2639411a3cc3304c5662b2257d4bcd7fc03f9b3b87201b184c3b
type
sep_package
label
SEP v1 package for pmid:40547309
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40547309
type
conversion
used array · 1 item
[0]
package:b5db1246b72a2639411a3cc3304c5662b2257d4bcd7fc03f9b3b87201b184c3b
agent
agent:corpus-assay-engine
agents array · 1 item
[0] 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:40547309
parent_hash
sha256:ea0e3d027cad337e8bf37b3e13c11eed043883fa87910ff5688a82f913585c2d
fork_of
null
gaps array · 14 items
[0]
abstract
[1]
asset:source:pmid:40547309 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]
review.machine_critique.providers
[10]
step:obtain_source_data blocked on data:not_downloaded
[11]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[12]
step:run_analysis input 'materials:the source data behind the published result in pmid:40547309' does not resolve to a declared asset
[13]
targets
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40547309", "kind": "science-record", "revision": 2, "content_hash": "sha256:00368366a914518d28bb233532ea82d8ad8881565d7249d2dcf4eb49e828f508", "created_at": "2026-11-01T10:25:51Z", "updated_at": "2026-11-01T14:01:42Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Mito-fission gene prognostic model for colorectal cancer.", "doi": "10.7717/peerj.19522", "pmid": "40547309", "authors": null, "journal": "PeerJ", "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:40547309"], "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:40547309", "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:40547309' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40547309", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.19522", "sha256": "sha256:606748f8ce65e4dfc14015fe44aab8973f3e133749e05d0f2db6828f2e788f71", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.19522", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40547309:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8bad0916f06cf63e39507665afa48fef1da1aabfbde06d8dda93838fe91fb032", "bytes": 778, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#table-1", "version": null, "note": "List of 40 MFRGs.", "structure": {"pmcid": "PMC12182055", "section_index": 3, "section_title": "Data extraction", "row_count": 41, "column_count": 2}, "table": {"label": "Table 1", "caption": "List of 40 MFRGs.", "rows": [["Number", "Symbol"], ["1", "DNM1L"], ["2", "RALBP1"], ["3", "MTFR2"], ["4", "LRRK2"], ["5", "MIEF2"], ["6", "COX10"], ["7", "C11orf65"], ["8", "DCN"], ["9", "PGAM5"], ["10", "DDHD2"], ["11", "KDR"], ["12", "MAPT"], ["13", "OPA1"], ["14", "PRKN"], ["15", "FIS1"], ["16", "MTFP1"], ["17", "CYRIB"], ["18", "GDAP1"], ["19", "MIEF1"], ["20", "PPARG"], ["21", "MARCHF5"], ["22", "VPS35"], ["23", "MTFR1L"], ["24", "SPIRE1"], ["25", "MFF"], ["26", "RALA"], ["27", "INF2"], ["28", "PINK1"], ["29", "TMEM135"], ["30", "BNIP3"], ["31", "STAT2"], ["32", "AURKA"], ["33", "UCP2"], ["34", "MUL1"], ["35", "MYO19"], ["36", "DDHD1"], ["37", "AP3B1"], ["38", "MCU"], ["39", "SLC25A46"], ["40", "MTFR1"]], "row_count": 41, "column_count": 2, "numeric_cells": 46, "header_rows": 1, "locator": "section[3]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:40547309:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:91e7f050fbfce752b7c82466bca358b3a8ca17e54cabfcb4a4e72e4067ecf96a", "bytes": 543, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#table-2", "version": null, "note": "Primer sequence information for RT-qPCR.", "structure": {"pmcid": "PMC12182055", "section_index": 15, "section_title": "RNA isolation and quantitative real-time polymerase chain reaction (qRT-PCR)", "row_count": 9, "column_count": 2}, "table": {"label": "Table 2", "caption": "Primer sequence information for RT-qPCR.", "rows": [["Primer", "Sequence"], ["CCDC68 F", "TGCCTTGTATGAGTCTACGTCC"], ["CCDC68 R", "AGCCCTGTTGAAGGTTTCCAC"], ["FAM151A F", "CTGAATGTGGAGTGGCTGGT"], ["FAM151A R", "TTCTGTGTCTGGGAGGGTCA"], ["MC1R F", "GTGTCGAAATGTCCTGGGGA"], ["MC1R R", "GACACCTCCTGGCATCTACC"], ["Internal reference-GAPDH F", "CGAAGGTGGAGTCAACGGATTT"], ["Internal reference-GAPDH R", "ATGGGTGGAATCATATTGGAAC"]], "row_count": 9, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[15]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:40547309:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bac1b2df95558ae0015ea4f98bcd8822ae545f6ec3e41ffa4a9cdce741a30d38", "bytes": 2347, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[1]#table-3", "version": null, "note": "List of functional information for ten genes from univariate Cox analysis.", "structure": {"pmcid": "PMC12182055", "section_index": 23, "section_title": "Identification of hub gene and risk model construction", "row_count": 11, "column_count": 5}, "table": {"label": "Table 3", "caption": "List of functional information for ten genes from univariate Cox analysis.", "rows": [["", "Full name", "Function", "Correlation with cancer", "Correlation with mitochondrial dysregulation"], ["HIGD1A", "HIG1 Hypoxia Inducible Domain Family Member 1A", "Regulating polyamine metabolism, inhibited tumor growth and metastasis", "colon cancer (PMID: 37479180)", "Mitochondrial inner membrane protein, regulating metabolic homeostasis (PMID: 37492734)"], ["DIAPH3", "Diaphanous Related Formin 3", "Involved in actin remodeling and regulate cell movement and adhesion, promote migration and invasion of CRC cells", "colorectal cancer (PMID: 39843730)", "NA"], ["CCDC68", "Coiled-Coil Domain Containing 68", "Involved in microtubule anchoring at centrosome and protein localization", "colorectal cancer (PMID: 35557589)", "NA"], ["FAM151A", "Family With Sequence Similarity 151 Member A", "Highly expressed in the intestine, kidney and spleen (PMID: 31949211)", "NA", "NA"], ["KRTAP5.1", "Keratin Associated Protein 5-1", "Essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins (PMID: 37014946)", "NA", "NA"], ["HSF4", "Heat Shock Transcription Factor 4", "Promotes the proliferation and metastasis of CRC by regulating EMT-related signalling pathways", "colorectal cancer (PMID: 39881364)", "NA"], ["MC1R", "Melanocortin 1 Receptor", "Regulates T regulatory cell differentiation through metabolic reprogramming to promote colon cancer", "colorectal cancer (PMID: 38917522)", "Suppressing the oxidative stress, apoptosis, and mitochondrial fission through the AMPK/SIRT1/PGC-1α signaling pathway (PMID: 33391490)"], ["ZNF692", "Zinc Finger Protein 692", "Promotes the progression of colorectal cancer by regulating HSF4 expression", "colorectal cancer (PMID: 38435777)", "NA"], ["LIME1", "Lck Interacting Transmembrane Adaptor 1", "Docking protein to recruit signaling molecules, and involved in inflammatory pathways", "bladder cancer (PMID: 39429662)", "NA"], ["TTYH3", "Tweety Family Member 3", "Plays a role in tissue formation, embryonic development, and immune response to pathogen related 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"caption": "Table of relevant information on 71 discrepant drugs.", "rows": [["drugs", "high_group_res", "low_group_res", "padj", "pvalue", "log2FoldChange", "References"], ["Mitomycin.C", "−1.011", "−1.029", "0.09352216", "0.048116473", "0.028560435", "PMID: 39531120"], ["Sorafenib", "3.844", "3.826", "0.083005791", "0.042104387", "0.014156188", "PMID: 39577235"], ["VX.680", "2.478", "2.364", "0.075511125", "0.037755563", "0.039769178", ""], ["X17.AAG", "−0.9516", "−0.8502", "0.072798168", "0.035871561", "−0.144174664", ""], ["Methotrexate", "0.9782", "0.953", "0.064334946", "0.031235082", "0.021896508", "PMID: 363377"], ["AZD.2281", "4.856", "4.915", "0.059041856", "0.028237409", "−0.090080215", "PMID: 36082969"], ["GSK.650394", "4.256", "4.187", "0.055894746", "0.026327236", "0.05820392", ""], ["CGP.082996", "4.036", "4.07", "0.04924791", "0.022839611", "−0.033324433", ""], ["ABT.263", "2.787", "2.855", "0.042698772", "0.019492918", "−0.066165992", ""], ["MK.2206", "2.807", "2.837", 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