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pmid:40353950

Combination of RNA-sequencing data analysis, network pharmacology, molecular docking techniques to investigate the mechanism of Prunella vulgaris L. in the treatment of non-small cell lung cancer.

Discover oncology · 2025 doi:10.1007/s12672-025-02563-7

Paper

partial

Experiment

partial

Data

partial

Analysis

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Execution

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:40353950
kind
science-record
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sha256:3cd349479822ccb4943169ba4e994a273d533c59e393b24f68d9e351cb90cdd3
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:50Z
updated_at
2026-11-01T14:01:40Z
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corpus-assay-engine
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sep_to_sci_v1
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paper object · 10 fields
state
partial
title
Combination of RNA-sequencing data analysis, network pharmacology, molecular docking techniques to investigate the mechanism of Prunella vulgaris L. in the treatment of non-small cell lung cancer.
doi
10.1007/s12672-025-02563-7
pmid
40353950
authors
null
journal
Discover oncology
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
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the headline numerical result the paper states for its main finding
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qualitative
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null
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null
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null
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null
evidence array · 0 items
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[0]
abstract
[1]
authors
experiment object · 8 fields
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partial
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the headline numerical result the paper states for its main finding
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read_published_estimate
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Read the published estimate and its interval from the source
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other
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complete
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The number a replication must land on, and the sentence it came from.
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[0]
source:pmid:40353950
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[0]
the published estimate, its unit and its interval
instruments array · 0 items
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[1] object · 13 fields
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obtain_source_data
order
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Obtain the source data behind the published result
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data-preparation
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The published result cannot be recomputed without the data the paper analysed.
parameters object · 0 fields
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[0]
the source data with its provenance
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Run the analysis programme
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no owned computational capability is bound to this experiment
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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:40353950
parameters object · 0 fields
inputs array · 0 items
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the registered result
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step:obtain_source_data blocked on data:not_downloaded
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step:run_analysis blocked on no owned computational capability is bound to this experiment
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step:run_analysis input 'materials:the source data behind the published result in pmid:40353950' does not resolve to a declared asset
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source:pmid:40353950
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xml
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null
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Sequences for qRT-PCR primers
structure object · 5 fields
pmcid
PMC12069211
section_index
13
section_title
Quantitative real-time polymerase chain reaction (qRT-PCR)
row_count
15
column_count
2
table object · 8 fields
label
Table 1
caption
Sequences for qRT-PCR primers
rows array · 15 items
[0] array · 2 items
[0]
Name
[1]
Primer sequences
[1] array · 2 items
[0]
AKT1
[1]
Forward: 5′-CCCAGGAGGTTTTTGGGCTT-3′
[2] array · 1 item
[0]
Reverse: 5′-AAGGTGCGTTCGATGACAGT-3′
[3] array · 2 items
[0]
MMP9
[1]
Forward: 5′-TCCCTGGAGACCTGAGAACC-3′
[4] array · 1 item
[0]
Reverse: 5′-CCACCCGAGTGTAACCATAGC-3′
[5] array · 2 items
[0]
ESR1
[1]
Forward: 5′-CTGCCAAGGAGACTCGCTAC-3′
[6] array · 1 item
[0]
Reverse: 5′-GCAACTCTTCCTCCGGTTCT-3′
[7] array · 2 items
[0]
XDH
[1]
Forward: 5′-CAGAAGCTGGGCCAAGAGAA-3′
[8] array · 1 item
[0]
Reverse: 5′-AGCTCTCTGTGTGTGTTCCG-3′
[9] array · 2 items
[0]
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[1]
Forward: 5′-CACCGTTTTCCGCGAATTC-3′
[10] array · 1 item
[0]
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[11] array · 2 items
[0]
HIF-1α
[1]
Forward: 5′-AGAGGTTGAGGGACGGAGAT-3′
[12] array · 1 item
[0]
Reverse: 5′-CTCCGACATTGGGAGCTCAT-3′
[13] array · 2 items
[0]
GAPDH
[1]
Forward: 5′-AATGGGCAGCCGTTAGGAAA-3′
[14] array · 1 item
[0]
Reverse: 5′-GCGCCCAATACGACCAAATC-3′
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null
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Details of active compounds in Prunella vulgaris L
structure object · 5 fields
pmcid
PMC12069211
section_index
17
section_title
Screening of PVL’s active ingredients and their targets
row_count
12
column_count
8
table object · 8 fields
label
Table 2
caption
Details of active compounds in Prunella vulgaris L
rows array · 12 items
[0] array · 8 items
[0]
No
[1]
Mol ID
[2]
Molecule name
[3]
OB (%)
[4]
DL
[5]
PubChem CID
[6]
SMILES
[7]
Interaction
[1] array · 8 items
[0]
1
[1]
MOL000358
[2]
Beta-sitosterol
[3]
36.91
[4]
0.75
[5]
222284
[6]
CCC(CCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C)C(C)C
[7]
44
[2] array · 8 items
[0]
2
[1]
MOL000422
[2]
Kaempferol
[3]
41.88
[4]
0.24
[5]
5280863
[6]
C1=CC(=CC=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O
[7]
104
[3] array · 8 items
[0]
3
[1]
MOL004355
[2]
Spinasterol
[3]
42.98
[4]
0.76
[5]
5281331
[6]
CCC(C=CC(C)C1CCC2C1(CCC3C2=CCC4C3(CCC(C4)O)C)C)C(C)C
[7]
58
[4] array · 8 items
[0]
4
[1]
MOL000449
[2]
Stigmasterol
[3]
43.83
[4]
0.76
[5]
5280794
[6]
CCC(C=CC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C)C(C)C
[7]
41
[5] array · 8 items
[0]
5
[1]
MOL004798
[2]
Delphinidin
[3]
40.63
[4]
0.28
[5]
128853
[6]
C1=C(C=C(C(=C1O)O)O)C2=[O+]C3=CC(=CC(=C3C=C2O)O)O
[7]
104
[6] array · 8 items
[0]
6
[1]
MOL000006
[2]
Luteolin
[3]
36.16
[4]
0.25
[5]
5280445
[6]
C1=CC(=C(C=C1C2=CC(=O)C3=C(C=C(C=C3O2)O)O)O)O
[7]
104
[7] array · 8 items
[0]
7
[1]
MOL006767
[2]
Vulgaxanthin-I
[3]
56.14
[4]
0.26
[5]
5281217
[6]
C1C(N=C(C=C1C=CNC(CCC(=O)N)C(=O)O)C(=O)O)C(=O)O
[7]
1
[8] array · 8 items
[0]
8
[1]
MOL006772
[2]
Poriferasterol monoglucoside_qt
[3]
43.83
[4]
0.76
[5]
N/A
[6]
CC[C@H](C=C[C@@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C)C(C)C
[7]
48
[9] array · 8 items
[0]
9
[1]
MOL006774
[2]
Stigmast-7-enol
[3]
37.42
[4]
0.75
[5]
12315384
[6]
CCC(CCC(C)C1CCC2C1(CCC3C2=CCC4C3(CCC(C4)O)C)C)C(C)C
[7]
56
[10] array · 8 items
[0]
10
[1]
MOL000737
[2]
Morin
[3]
46.23
[4]
0.27
[5]
5281670
[6]
C1=CC(=C(C=C1O)O)C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O
[7]
104
[11] array · 8 items
[0]
11
[1]
MOL000098
[2]
Quercetin
[3]
46.43
[4]
0.28
[5]
5280343
[6]
C1=CC(=C(C=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O)O
[7]
104
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[3] object · 16 fields
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note
Potential candidate targets of Prunella vulgaris L. for treating non-small cell lung cancer
structure object · 5 fields
pmcid
PMC12069211
section_index
17
section_title
Screening of PVL’s active ingredients and their targets
row_count
21
column_count
8
table object · 8 fields
label
Table 3
caption
Potential candidate targets of Prunella vulgaris L. for treating non-small cell lung cancer
rows array · 21 items
[0] array · 8 items
[0]
No
[1]
Gene symbol
[2]
P value
[3]
logFC
[4]
No
[5]
Gene symbol
[6]
P value
[7]
log FC
[1] array · 8 items
[0]
1
[1]
AKR1B10
[2]
0.0000866
[3]
2.3932595
[4]
21
[5]
ACHE
[6]
0.0415
[7]
3.5809483
[2] array · 8 items
[0]
2
[1]
ADORA3
[2]
0.000332
[3]
1.5149787
[4]
22
[5]
NOS2
[6]
0.00000115
[7]
−2.9362951
[3] array · 8 items
[0]
3
[1]
SERPINA6
[2]
0.000388
[3]
1.6530115
[4]
23
[5]
PDE4D
[6]
0.00000708
[7]
−1.8826387
[4] array · 8 items
[0]
4
[1]
GCGR
[2]
0.000427
[3]
1.079908
[4]
24
[5]
CA4
[6]
0.0000316
[7]
−4.677416
[5] array · 8 items
[0]
5
[1]
CYP1B1
[2]
0.00129
[3]
2.353458
[4]
25
[5]
CHRM2
[6]
0.000517
[7]
−1.0184839
[6] array · 8 items
[0]
6
[1]
MMP12
[2]
0.00129
[3]
4.3452597
[4]
26
[5]
ABCB1
[6]
0.000757
[7]
−3.130854
[7] array · 8 items
[0]
7
[1]
CAMK2B
[2]
0.00175
[3]
1.5617937
[4]
27
[5]
CDK6
[6]
0.00093
[7]
−1.4464042
[8] array · 8 items
[0]
8
[1]
HSD17B2
[2]
0.00207
[3]
1.3030574
[4]
28
[5]
ABCG2
[6]
0.00117
[7]
−1.2862328
[9] array · 8 items
[0]
9
[1]
NEK6
[2]
0.00293
[3]
1.1406784
[4]
29
[5]
AKR1C1
[6]
0.00167
[7]
−1.6951737
[10] array · 8 items
[0]
10
[1]
TOP2A
[2]
0.00341
[3]
1.8746864
[4]
30
[5]
FABP5
[6]
0.00281
[7]
−1.3844588
[11] array · 8 items
[0]
11
[1]
XDH
[2]
0.00345
[3]
2.4103457
[4]
31
[5]
ALOX5
[6]
0.00753
[7]
−1.0923645
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[0]
12
[1]
AKT1
[2]
0.00364
[3]
1.3787715
[4]
32
[5]
SLC6A4
[6]
0.00958
[7]
−1.6490666
[13] array · 8 items
[0]
13
[1]
MMP13
[2]
0.00748
[3]
3.2412005
[4]
33
[5]
CA2
[6]
0.0117
[7]
−1.2531044
[14] array · 8 items
[0]
14
[1]
PTGES
[2]
0.00781
[3]
1.1341809
[4]
34
[5]
BCHE
[6]
0.0123
[7]
−1.5660594
[15] array · 8 items
[0]
15
[1]
CA13
[2]
0.00982
[3]
1.4324762
[4]
35
[5]
HSD11B1
[6]
0.0125
[7]
−1.3634651
[16] array · 8 items
[0]
16
[1]
MMP9
[2]
0.0114
[3]
1.9071978
[4]
36
[5]
PFKFB3
[6]
0.013
[7]
−2.3139196
[17] array · 8 items
[0]
17
[1]
MAPT
[2]
0.0163
[3]
1.2303265
[4]
37
[5]
AKR1C4
[6]
0.0138
[7]
−1.0646393
[18] array · 8 items
[0]
18
[1]
CCNB2
[2]
0.0163
[3]
1.1197655
[4]
38
[5]
ESR1
[6]
0.0213
[7]
−1.1750729
[19] array · 8 items
[0]
19
[1]
PTPRF
[2]
0.0253
[3]
1.1681767
[4]
39
[5]
AR
[6]
0.0267
[7]
−1.0753623
[20] array · 8 items
[0]
20
[1]
SHBG
[2]
0.0398
[3]
1.1883309
[4]
[5]
[6]
[7]
locator
section[17]/table-wrap[2]#Tab3
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asset:table:pmid:40353950:4
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read_table
reader_status
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section[24]/table-wrap[1]#Tab4
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null
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Docking center and binding pocket of compounds and targets
structure object · 5 fields
pmcid
PMC12069211
section_index
24
section_title
Results of molecular docking
row_count
7
column_count
4
table object · 8 fields
label
Table 4
caption
Docking center and binding pocket of compounds and targets
rows array · 7 items
[0] array · 4 items
[0]
Targets (PDB ID)
[1]
Compounds
[2]
Docking center (x, y, z)
[3]
Docking pocket (x, y, z)
[1] array · 4 items
[0]
AKT1 (3O96)
[1]
Morin, Luteolin, Delphinidin, Kaempferol and Quercetin
[2]
x = 6.782, y = −11.138, z = 20.57
[3]
x = 54.25, y = 62.0, z = 63.55
[2] array · 4 items
[0]
MMP9 (1L6J)
[1]
Morin, Luteolin, Delphinidin, Kaempferol and Quercetin
[2]
x = 38.538, y = 35.802, z = 34.594
[3]
x = 49.6166666667, y = 78.8777777778, z = 67.4277777778
[3] array · 4 items
[0]
ESR1 (6PSJ)
[1]
Morin, Luteolin, Delphinidin, Kaempferol and Quercetin
[2]
x = 5.414, y = −19.865, z = 19.855
[3]
x = 52.4444444444, y = 49.1666666667, z = 54.0833333333
[4] array · 4 items
[0]
XDH (3AX7)
[1]
Morin, Luteolin, Delphinidin, Kaempferol and Quercetin
[2]
x = 14.333, y = −0.128, z = 26.623
[3]
x = 104.0, y = 88.0, z = 82.0
[5] array · 4 items
[0]
MAPT (5MP5)
[1]
Morin, Luteolin, Delphinidin, Kaempferol and Quercetin
[2]
x = 10.834, y = −23.535, z = −40.736
[3]
x = 15.0, y = 15.0, z = 15.0
[6] array · 4 items
[0]
CYP1B1 (3PM0)
[1]
Morin, Luteolin, Delphinidin, Kaempferol and Quercetin
[2]
x = −18.657, y = 17.823, z = −11.837
[3]
x = 69.25, y = 52.3222222222, z = 69.25
locator
section[24]/table-wrap[1]#Tab4
gaps array · 1 item
[0]
asset:source:pmid:40353950 not verified
analysis object · 4 fields
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[1]
targets
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partial
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source:pmid:40353950
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asset:table:pmid:40353950:2
[3]
asset:table:pmid:40353950:3
[4]
asset:table:pmid:40353950:4
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read_published_estimate
must_build object · 5 fields
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xml
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source:pmid:40353950
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review object · 5 fields
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partial
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policy
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decisive_fields array · 4 items
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work_type
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number_stated
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parent_value
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target_materials
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independent_readings
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The independent readings are incomplete or disagree; the source evidence must resolve the difference.
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minimax
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HTTP Error 429: Too Many Requests
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provider
minimax_alt
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HTTP Error 429: Too Many Requests
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[2] object · 4 fields
provider
minimax
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HTTP Error 429: Too Many Requests
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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:637b9141a61ed32412b71ea2beb19f674ff96a43ca8ef7ec675b34e8e172fca0
type
sep_package
label
SEP v1 package for pmid:40353950
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40353950
type
conversion
used array · 1 item
[0]
package:637b9141a61ed32412b71ea2beb19f674ff96a43ca8ef7ec675b34e8e172fca0
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:40353950
parent_hash
sha256:9811bd2284180d4aa1e1acbe04c7c94b65d99c9728fcc5ea2790f050776d51e9
fork_of
null
gaps array · 14 items
[0]
abstract
[1]
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[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:40353950' does not resolve to a declared asset
[13]
targets
Complete file
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