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pmid:40524029

To reveal the key mechanism of Citri Reticulatae Pericarpium-Reynoutria japonica Houtt in the treatment of liver cancer and its correlation with lipid metabolism: synergetic effect with network pharmacology, molecular docking and bioinformatics.

Discover oncology · 2025 doi:10.1007/s12672-025-02708-8

Paper

partial

Experiment

partial

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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title
To reveal the key mechanism of Citri Reticulatae Pericarpium-Reynoutria japonica Houtt in the treatment of liver cancer and its correlation with lipid metabolism: synergetic effect with network pharmacology, molecular docking and bioinformatics.
doi
10.1007/s12672-025-02708-8
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40524029
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null
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Discover oncology
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2025
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Grid box centers and sizes for molecular docking of target genes
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Molecular docking validation and ADMET analysis
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Grid box centers and sizes for molecular docking of target genes
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The 123 common targets between active compound targets of CR and liver cancer disease targets
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Active components of CR and Potential targets in LC
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The 123 common targets between active compound targets of CR and liver cancer disease targets
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101
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121
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82
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102
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122
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83
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[7]
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95
[9]
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[13]
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76
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96
[9]
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[13]
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78
[7]
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98
[9]
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118
[11]
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[13]
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19
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[7]
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[9]
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[11]
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[13]
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20
[1]
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[3]
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[5]
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80
[7]
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100
[9]
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[11]
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Top 28 targets, ranked by degree in the compound–target–pathway network of liver cancer
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PMC12170481
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18
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PPI network construction and analysis
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Table 3
caption
Top 28 targets, ranked by degree in the compound–target–pathway network of liver cancer
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[0]
Gene name
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[3]
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[0]
TP53
[1]
96
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RELA
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32
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64
[2]
CASP3
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32
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56
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MDM2
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32
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50
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FOS
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28
[5] array · 4 items
[0]
TNF
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48
[2]
MAPK8
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28
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[0]
HSP90AA1
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46
[2]
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28
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[0]
ESR1
[1]
46
[2]
CXCL8
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26
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[0]
BCL2
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42
[2]
IFNG
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26
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[0]
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40
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26
[10] array · 4 items
[0]
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40
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26
[11] array · 4 items
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24
[12] array · 4 items
[0]
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38
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24
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[0]
EGFR
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34
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24
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Top 16 targets, ranked by degree in the compound–target–pathway network of liver cancer
structure object · 5 fields
pmcid
PMC12170481
section_index
20
section_title
Analysis of compound–target–pathway interactions and core target identification in liver cancer
row_count
9
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4
table object · 8 fields
label
Table 4
caption
Top 16 targets, ranked by degree in the compound–target–pathway network of liver cancer
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[0] array · 4 items
[0]
Gene name
[1]
Degree
[2]
Gene name
[3]
Degree
[1] array · 4 items
[0]
RB1
[1]
18
[2]
AR
[3]
5
[2] array · 4 items
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11
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GSTP1
[3]
4
[3] array · 4 items
[0]
HSP90AA1
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11
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IL10
[3]
4
[4] array · 4 items
[0]
TOP2A
[1]
9
[2]
DPP4
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4
[5] array · 4 items
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GSK3B
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8
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ESR1
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4
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JUN
[1]
7
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BCL2
[3]
4
[7] array · 4 items
[0]
PIK3CG
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7
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CASP9
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4
[8] array · 4 items
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PPARG
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CASP3
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4
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Details of the top 10 compounds in the compound–target–pathway network of liver cancer
structure object · 5 fields
pmcid
PMC12170481
section_index
20
section_title
Analysis of compound–target–pathway interactions and core target identification in liver cancer
row_count
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Table 5
caption
Details of the top 10 compounds in the compound–target–pathway network of liver cancer
rows array · 11 items
[0] array · 8 items
[0]
Rank
[1]
Component ID
[2]
Component name
[3]
Structure
[4]
CAS
[5]
Degree
[6]
OB(%)
[7]
DL
[1] array · 8 items
[0]
1
[1]
MOL000098
[2]
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[4]
117-39-5
[5]
97
[6]
46.43
[7]
0.28
[2] array · 8 items
[0]
2
[1]
MOL000006
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Luteolin
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[4]
491-70-3
[5]
45
[6]
36.16
[7]
0.25
[3] array · 8 items
[0]
3
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MOL004328
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Naringenin
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[4]
67604-48-2
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25
[6]
59.29
[7]
0.21
[4] array · 8 items
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4
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MOL005828
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[4]
478-01-3
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23
[6]
61.67
[7]
0.52
[5] array · 8 items
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5
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MOL000358
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Beta-sitosterol
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[4]
83-46-5
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13
[6]
36.91
[7]
0.75
[6] array · 8 items
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6
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MOL013287
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Physovenine
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[4]
6091-05-0
[5]
12
[6]
106.21
[7]
0.19
[7] array · 8 items
[0]
7
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MOL013281
[2]
6,8-Dihydroxy-7-methoxyxanthone
[3]
[4]
87339-74-0
[5]
9
[6]
35.83
[7]
0.21
[8] array · 8 items
[0]
8
[1]
MOL000492
[2]
(+)-catechin
[3]
[4]
154-23-4
[5]
6
[6]
54.83
[7]
0.24
[9] array · 8 items
[0]
9
[1]
MOL005100
[2]
5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chroman-4-one
[3]
[4]
520-33-2
[5]
5
[6]
47.74
[7]
0.27
[10] array · 8 items
[0]
10
[1]
MOL002268
[2]
Rhein
[3]
[4]
478-43-3
[5]
5
[6]
47.07
[7]
0.28
row_count
11
column_count
8
numeric_cells
62
header_rows
1
locator
section[20]/table-wrap[2]#Tab5
[6] object · 16 fields
id
asset:table:pmid:40524029:6
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table
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jats-table
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application/vnd.jats.table+json
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null
sha256
sha256:160ed912667ec177723cb3a6f72ef33a7d30d929c2a0a5e96e7615167b89c810
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section[22]/table-wrap[1]#Tab6
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Top 21 targets in the compound–target–pathway network of NAFLD-LMDs, ranked by degree
structure object · 5 fields
pmcid
PMC12170481
section_index
22
section_title
Analysis of shared pathways and core targets in NAFLD and DLM-related LC
row_count
12
column_count
4
table object · 8 fields
label
Table 6
caption
Top 21 targets in the compound–target–pathway network of NAFLD-LMDs, ranked by degree
rows array · 12 items
[0] array · 4 items
[0]
Gene name
[1]
Degree
[2]
Gene name
[3]
Degree
[1] array · 4 items
[0]
RB1
[1]
15
[2]
BCL2
[3]
4
[2] array · 4 items
[0]
PTGS2
[1]
11
[2]
CDKN1A
[3]
3
[3] array · 4 items
[0]
HSP90AA1
[1]
11
[2]
NOS3
[3]
3
[4] array · 4 items
[0]
JUN
[1]
9
[2]
RXRA
[3]
3
[5] array · 4 items
[0]
GSK3B
[1]
7
[2]
BAX
[3]
3
[6] array · 4 items
[0]
IL10
[1]
7
[2]
AKT1
[3]
3
[7] array · 4 items
[0]
PIK3CG
[1]
7
[2]
MMP9
[3]
3
[8] array · 4 items
[0]
PPARG
[1]
6
[2]
MAPK1
[3]
3
[9] array · 4 items
[0]
ADRB2
[1]
4
[2]
TP53
[3]
3
[10] array · 4 items
[0]
DPP4
[1]
4
[2]
GSTP1
[3]
3
[11] array · 4 items
[0]
ESR1
[1]
4
[2]
[3]
row_count
12
column_count
4
numeric_cells
24
header_rows
1
locator
section[22]/table-wrap[1]#Tab6
[7] object · 16 fields
id
asset:table:pmid:40524029:7
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table
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jats-table
media_type
application/vnd.jats.table+json
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null
sha256
sha256:5e1a227a403c5af25991dac5645aa8439222c2c0338fb25f3d2364047a986003
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1456
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read_table
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section[24]/table-wrap[1]#Tab7
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null
note
Molecular docking binding affinities (kcal/mol) between active compounds and target proteins
structure object · 5 fields
pmcid
PMC12170481
section_index
24
section_title
Molecular docking
row_count
11
column_count
10
table object · 8 fields
label
Table 7
caption
Molecular docking binding affinities (kcal/mol) between active compounds and target proteins
rows array · 11 items
[0] array · 10 items
[0]
ID
[1]
Compounds
[2]
AKT1(kcal/mol)
[3]
JUN(kcal/mol)
[4]
TP53(kcal/mol)
[5]
TNF(kcal/mol)
[6]
HSP90AA1(kcal/mol)
[7]
ESR1(kcal/mol)
[8]
BCL2(kcal/mol)
[9]
IL6(kcal/mol)
[1] array · 10 items
[0]
MOL000358
[1]
Beta-sitosterol
[2]
−7.0
[3]
−5.9
[4]
−6.1
[5]
−7.6
[6]
−7.9
[7]
−6.7
[8]
−7.7
[9]
−6.3
[2] array · 10 items
[0]
MOL013281
[1]
6,8-Dihydroxy-7-methoxyxanthone
[2]
−6.0
[3]
−6.1
[4]
−7.2
[5]
−7.1
[6]
−8.9
[7]
−7.4
[8]
−6.4
[9]
−6.0
[3] array · 10 items
[0]
MOL000492
[1]
(+)-catechin
[2]
−6.4
[3]
−5.9
[4]
−7.8
[5]
−8.9
[6]
−8.7
[7]
−7.3
[8]
−6.7
[9]
−6.4
[4] array · 10 items
[0]
MOL005100
[1]
5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chroman-4-one
[2]
−6.1
[3]
−6.4
[4]
−8.2
[5]
−8.8
[6]
−9.0
[7]
−7.5
[8]
−7.1
[9]
−6.8
[5] array · 10 items
[0]
MOL002268
[1]
rhein
[2]
−6.7
[3]
−6.7
[4]
−8.3
[5]
−8.9
[6]
−9.6
[7]
−8.6
[8]
−7.5
[9]
−6.9
[6] array · 10 items
[0]
MOL000006
[1]
luteolin
[2]
−6.1
[3]
−6.5
[4]
−8.0
[5]
−8.8
[6]
−9.3
[7]
−8.0
[8]
−6.9
[9]
−7.2
[7] array · 10 items
[0]
MOL004328
[1]
naringenin
[2]
−6.2
[3]
−6.2
[4]
−7.8
[5]
−8.4
[6]
−9.1
[7]
−8.6
[8]
−6.7
[9]
−6.6
[8] array · 10 items
[0]
MOL000098
[1]
quercetin
[2]
−6.0
[3]
−6.4
[4]
−7.9
[5]
−9.0
[6]
−9.1
[7]
−7.3
[8]
−6.9
[9]
−7.1
[9] array · 10 items
[0]
MOL005828
[1]
nobiletin
[2]
−5.7
[3]
−5.8
[4]
−6.9
[5]
−7.3
[6]
−8.3
[7]
−6.9
[8]
−6.2
[9]
−6.0
[10] array · 10 items
[0]
MOL013287
[1]
Physovenine
[2]
−6.0
[3]
−6.4
[4]
−6.8
[5]
−6.2
[6]
−7.5
[7]
−7.5
[8]
−6.8
[9]
−5.5
row_count
11
column_count
10
numeric_cells
94
header_rows
1
locator
section[24]/table-wrap[1]#Tab7
[8] object · 16 fields
id
asset:table:pmid:40524029:8
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table
format
jats-table
media_type
application/vnd.jats.table+json
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null
sha256
sha256:f7c255d5bc2acba3519bf9a9259b13ba4a75bc661612802cba716820e43bfbab
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1703
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read_table
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section[25]/table-wrap[1]#Tab8
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null
note
ADMET profiling of compounds
structure object · 5 fields
pmcid
PMC12170481
section_index
25
section_title
ADMET analysis
row_count
15
column_count
10
table object · 8 fields
label
Table 8
caption
ADMET profiling of compounds
rows array · 15 items
[0] array · 10 items
[0]
Compounds
[1]
Quercetin
[2]
Luteolin
[3]
Naringenin
[4]
Nobiletin
[5]
Physovenine
[6]
6,8-Dihydroxy-7-methoxyxanthone
[7]
(+)-catechin
[8]
5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chroman-4-one
[9]
Rhein
[1] array · 10 items
[0]
GIabsorption
[1]
High
[2]
High
[3]
High
[4]
High
[5]
High
[6]
High
[7]
High
[8]
High
[9]
High
[2] array · 10 items
[0]
BBBpermeant
[1]
No
[2]
No
[3]
No
[4]
No
[5]
Yes
[6]
No
[7]
No
[8]
No
[9]
No
[3] array · 10 items
[0]
Pgpsubstrate
[1]
No
[2]
No
[3]
Yes
[4]
No
[5]
Yes
[6]
No
[7]
Yes
[8]
Yes
[9]
No
[4] array · 10 items
[0]
CYP1A2 inhibitor
[1]
Yes
[2]
Yes
[3]
Yes
[4]
No
[5]
No
[6]
Yes
[7]
No
[8]
Yes
[9]
No
[5] array · 10 items
[0]
CYP2C19 inhibitor
[1]
No
[2]
No
[3]
No
[4]
No
[5]
No
[6]
No
[7]
No
[8]
No
[9]
No
[6] array · 10 items
[0]
CYP2C9 inhibitor
[1]
No
[2]
No
[3]
No
[4]
Yes
[5]
No
[6]
No
[7]
No
[8]
No
[9]
No
[7] array · 10 items
[0]
CYP2D6 inhibitor
[1]
Yes
[2]
Yes
[3]
No
[4]
No
[5]
Yes
[6]
Yes
[7]
No
[8]
No
[9]
No
[8] array · 10 items
[0]
CYP3A4 inhibitor
[1]
Yes
[2]
Yes
[3]
Yes
[4]
Yes
[5]
No
[6]
Yes
[7]
No
[8]
Yes
[9]
No
[9] array · 10 items
[0]
PredictedLD50
[1]
159 mg/kg
[2]
3919 mg/kg
[3]
2000 mg/kg
[4]
5000 mg/kg
[5]
2 mg/kg
[6]
3800 mg/kg
[7]
10,000 mg/kg
[8]
2000 mg/kg
[9]
5000 mg/kg
[10] array · 10 items
[0]
ToxicityReversemutationAmestest
[1]
Non-Toxic
[2]
Non-Toxic
[3]
Non-Toxic
[4]
Non-Toxic
[5]
Non-Toxic
[6]
Non-Toxic
[7]
Non-Toxic
[8]
Non-Toxic
[9]
Non-Toxic
[11] array · 10 items
[0]
Hepatotoxicity
[1]
Inactive
[2]
Inactive
[3]
Inactive
[4]
Inactive
[5]
Inactive
[6]
Inactive
[7]
Inactive
[8]
Inactive
[9]
Inactive
[12] array · 10 items
[0]
Carcinogenicity
[1]
Active (0.68)
[2]
Active (0.68)
[3]
Inactive
[4]
Inactive
[5]
Inactive
[6]
Inactive
[7]
Inactive
[8]
Inactive
[9]
Inactive
[13] array · 10 items
[0]
Mutagenicity
[1]
Active (0.51)
[2]
Active (0.51)
[3]
Inactive
[4]
Inactive
[5]
Inactive
[6]
Inactive
[7]
Inactive
[8]
Inactive
[9]
Active (0.76)
[14] array · 10 items
[0]
Cytotoxicity
[1]
Inactive
[2]
Inactive
[3]
Active (0.59)
[4]
Inactive
[5]
Inactive
[6]
Inactive
[7]
Inactive
[8]
Inactive
[9]
Inactive
row_count
15
column_count
10
numeric_cells
19
header_rows
1
locator
section[25]/table-wrap[1]#Tab8
[9] object · 16 fields
id
asset:table:pmid:40524029:9
role
table
format
jats-table
media_type
application/vnd.jats.table+json
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null
sha256
sha256:780323f332689b4e2c1e2a4ad71b057acef6e810429dd9973506db572e1c4a0b
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5241
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reader_status
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identifier
section[36]/table-wrap[1]#Tab9
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null
note
Overview of data sets/tools/figures/tables
structure object · 5 fields
pmcid
PMC12170481
section_index
36
section_title
Molecular docking and pharmacokinetic properties
row_count
42
column_count
4
table object · 8 fields
label
Table 9
caption
Overview of data sets/tools/figures/tables
rows array · 42 items
[0] array · 4 items
[0]
Label
[1]
Name of data file/data set
[2]
File types(file extension)
[3]
Data repository and identifier (DOI or accession number)
[1] array · 4 items
[0]
Data set 1
[1]
TCMSP database
[2]
Database
[3]
https://old.tcmsp-e.com/tcmsp.php
[2] array · 4 items
[0]
Data set 2
[1]
SwissTargetPrediction database
[2]
Database
[3]
http://www.swisstargetprediction.ch/
[3] array · 4 items
[0]
Data set 3
[1]
PharmMapper database
[2]
Database
[3]
https://www.lilab-ecust.cn/pharmmapper/index.html
[4] array · 4 items
[0]
Data set 4
[1]
The UniProt database
[2]
Database
[3]
https://www.uniprot.org/
[5] array · 4 items
[0]
Data set 5
[1]
GeneCards database
[2]
Database
[3]
http://www.genecards.org/
[6] array · 4 items
[0]
Data set 6
[1]
Therapeutic Target Database(TTD)
[2]
Database
[3]
http://db.idrblab.net/ttd
[7] array · 4 items
[0]
Data set 7
[1]
the Online Mendelian Inheritance in Man (OMIM) database
[2]
Database
[3]
https://omim.org/
[8] array · 4 items
[0]
Data set 8
[1]
The STRING v3.11.1 database
[2]
Database
[3]
https://string-db.org
[9] array · 4 items
[0]
Data set 9
[1]
The Gene Expression Omnibus (GEO) database
[2]
Database
[3]
https://www.ncbi.nlm.nih.gov/geo
[10] array · 4 items
[0]
Data set 10
[1]
DAVID database
[2]
Database
[3]
https://david.ncifcrf.gov/
[11] array · 4 items
[0]
Data set 11
[1]
BioGPS database
[2]
Database
[3]
https://biogps.org
[12] array · 4 items
[0]
Data set 12
[1]
The PubChem database
[2]
Database
[3]
https://pubchem.ncbi.nlm.nih.gov
[13] array · 4 items
[0]
Tool 1
[1]
VENNY 2.1.0
[2]
Web-based tool
[3]
https://bioinfogp.cnb.csic.es/tools/venny/index.html
[14] array · 4 items
[0]
Tool 2
[1]
The Bioinformatics platform
[2]
Web-based tool
[3]
https://bioinformatics.com.cn
[15] array · 4 items
[0]
Tool 3
[1]
PyMOL version 2.5.0
[2]
Web-based tool
[3]
https://pymol.org/2/
[16] array · 4 items
[0]
Tool 4
[1]
The RCSB Protein Data Bank
[2]
Web-based tool
[3]
https://www.pdb.org/
[17] array · 4 items
[0]
Tool 5
[1]
The AutoDock Tools 1.5.7
[2]
Web-based tool
[3]
https://ccsb.scripps.edu/mgltools/downloads/
[18] array · 4 items
[0]
Tool 6
[1]
AutoDock Vina Version 1.1.2
[2]
Web-based tool
[3]
https://vina.scripps.edu
[19] array · 4 items
[0]
Tool 7
[1]
SwissADME online server
[2]
Web-based tool
[3]
http://www.swissadme.ch/
[20] array · 4 items
[0]
Tool 8
[1]
ProToxII
[2]
Web-based tool
[3]
https://tox.charite.de/protox3/
[21] array · 4 items
[0]
Tool 9
[1]
GEPIA2
[2]
Web-based tool
[3]
http://gepia2.cancer-pku.cn/
[22] array · 4 items
[0]
Figure 1
[1]
A detailed workflow of the network pharmacological investigation strategy for CR in the treatment of LC
[2]
Image (.png)
[3]
Uploaded via journal submission system
[23] array · 4 items
[0]
Figure 2
[1]
A LC and CR target Venn diagram. B Herb–compound–target network
[2]
Image (.png)
[3]
Uploaded via journal submission system
[24] array · 4 items
[0]
Figure 3
[1]
A PPI analysis. B top 28 core targets. C Bar chart. D PPI network based on cluster analysis
[2]
Image (.png)
[3]
Uploaded via journal submission system
[25] array · 4 items
[0]
Figure 4
[1]
A KEGG enrichment analysis. B Sankey diagram of the KEGG pathway. C GO functional enrichment analysis. D GO enrichmentanalysis, exhibit BP, CC and MF respectively
[2]
Image (.png)
[3]
Uploaded via journal submission system
[26] array · 4 items
[0]
Figure5
[1]
A Compound-target-pathway network. B LC-PPI and Drug–Target–Path analysis Venn diagram. C Target-organ network
[2]
Image (.png)
[3]
Uploaded via journal submission system
[27] array · 4 items
[0]
Figure6
[1]
A PPI analysis. B Bar chart of the top 5 core targets. C Compound–target–pathway network.D NAFLD+DLM PPI and Drug-Target-Path analysis Venn diagram
[2]
Image (.png)
[3]
Uploaded via journal submission system
[28] array · 4 items
[0]
Figure 7
[1]
Heatmap of LC molecular docking scores
[2]
Image (.png)
[3]
Uploaded via journal submission system
[29] array · 4 items
[0]
Figure 8
[1]
Docking patterns of core targets and active compounds of Liver Cancer.
[2]
Image (.png)
[3]
Uploaded via journal submission system
[30] array · 4 items
[0]
Figure 9
[1]
Volcano and Heatmap plot. A GSE76427, B GSE87630, C GSE112790 datasets
[2]
Image (.png)
[3]
Uploaded via journal submission system
[31] array · 4 items
[0]
Figure 10
[1]
Pearson’s coefficient analysis A HSP90 AA1, B ESR1. Core targets’s Expression in LIHC. C HSP90 AA1, D ESR1E Survival map of Hazardous Ratio
[2]
Image (.png)
[3]
Uploaded via journal submission system
[32] array · 4 items
[0]
Table 1
[1]
Grid Box Centers and Sizes for Molecular Docking of Target Genes
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[33] array · 4 items
[0]
Table 2
[1]
The 123 common targets between active compound targets of CR and Liver Cancer disease targets
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[34] array · 4 items
[0]
Table 3
[1]
Top 28 targets, ranked by degree in the compound–target–pathway network of liver cancer
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[35] array · 4 items
[0]
Table 4
[1]
Top 16 targets, ranked by degree in the compound–target–pathway network of Liver Cancer
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[36] array · 4 items
[0]
Table 5
[1]
Details of the top 10 compounds in the compound–target–pathway network of Liver Cancer.
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[37] array · 4 items
[0]
Table 6
[1]
Top 21 targets in the compound-target-pathway network of NAFLD-LMDs, ranked by degree
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[38] array · 4 items
[0]
Table 7
[1]
ADMET profiling of compounds
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[39] array · 4 items
[0]
Table 8
[1]
Molecular docking binding affinities (kcal/mol) between active compounds and target proteins.
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[40] array · 4 items
[0]
Table 9
[1]
Overview of data sets/Tools/Figures/Tables
[2]
Table (.docx)
[3]
Uploaded via journal submission system
[41] array · 4 items
[0]
Table 10
[1]
Abbreviations
[2]
Table (.docx)
[3]
Uploaded via journal submission system
row_count
42
column_count
4
numeric_cells
54
header_rows
1
locator
section[36]/table-wrap[1]#Tab9
[10] object · 16 fields
id
asset:table:pmid:40524029:10
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table
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jats-table
media_type
application/vnd.jats.table+json
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null
sha256
sha256:329b71a5536e1125872648e18e251fb29d1c4395a81c0688e226da7b99108f74
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verified
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reader_status
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identifier
section[36]/table-wrap[2]#Tab10
version
null
note
Abbreviations
structure object · 5 fields
pmcid
PMC12170481
section_index
36
section_title
Molecular docking and pharmacokinetic properties
row_count
25
column_count
2
table object · 8 fields
label
Table10
caption
Abbreviations
rows array · 25 items
[0] array · 2 items
[0]
Full name
[1]
Abbreviations
[1] array · 2 items
[0]
Absorption, distribution, metabolism, and excretion
[1]
ADME
[2] array · 2 items
[0]
betweenness centrality
[1]
BC
[3] array · 2 items
[0]
Citri Reticulatae Pericarpium
[1]
CRP
[4] array · 2 items
[0]
Citri Reticulatae Pericarpium-Reynoutria japonica
[1]
CR
[5] array · 2 items
[0]
Closeness centrality
[1]
CC
[6] array · 2 items
[0]
Degree centrality
[1]
DC
[7] array · 2 items
[0]
Drug likeness
[1]
DL
[8] array · 2 items
[0]
Gene Ontology
[1]
GO
[9] array · 2 items
[0]
Hepatocellular carcinoma
[1]
HCC
[10] array · 2 items
[0]
Kyoto Encyclopedia of Genes and Genomes
[1]
KEGG
[11] array · 2 items
[0]
Liver cancer
[1]
LC
[12] array · 2 items
[0]
Metabolic Lipid Disorders
[1]
DLM
[13] array · 2 items
[0]
Non-alcoholic fatty liver disease
[1]
NAFLD
[14] array · 2 items
[0]
Oral bioavailability
[1]
OB
[15] array · 2 items
[0]
Protein–protein interaction
[1]
PPI
[16] array · 2 items
[0]
Reynoutria japonica Houtt
[1]
RJ
[17] array · 2 items
[0]
The differentially expressed genes
[1]
DEGs
[18] array · 2 items
[0]
The Gene Expression Omnibus
[1]
GEO
[19] array · 2 items
[0]
The Molecular Complex Detection
[1]
MCODE
[20] array · 2 items
[0]
The Online Mendelian Inheritance in Man
[1]
OMIM
[21] array · 2 items
[0]
Therapeutic Target Database
[1]
TTD
[22] array · 2 items
[0]
Traditional Chinese Medicine
[1]
TCM
[23] array · 2 items
[0]
Traditional Chinese Medicine Systems Pharmacology
[1]
TCMSP
[24] array · 2 items
[0]
Tumour necrosis factor-alpha
[1]
TNF-α
row_count
25
column_count
2
numeric_cells
0
header_rows
1
locator
section[36]/table-wrap[2]#Tab10
gaps array · 1 item
[0]
asset:source:pmid:40524029 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
blocking_axis
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 11 items
[0]
source:pmid:40524029
[1]
asset:table:pmid:40524029:1
[2]
asset:table:pmid:40524029:2
[3]
asset:table:pmid:40524029:3
[4]
asset:table:pmid:40524029:4
[5]
asset:table:pmid:40524029:5
[6]
asset:table:pmid:40524029:6
[7]
asset:table:pmid:40524029:7
[8]
asset:table:pmid:40524029:8
[9]
asset:table:pmid:40524029:9
[10]
asset:table:pmid:40524029:10
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:40524029
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:cd40e1bc2e8f5f15c97edeb13eeeb362efd35198d3a42ed6f521cc575c24df0a
type
sep_package
label
SEP v1 package for pmid:40524029
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40524029
type
conversion
used array · 1 item
[0]
package:cd40e1bc2e8f5f15c97edeb13eeeb362efd35198d3a42ed6f521cc575c24df0a
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:40524029
parent_hash
sha256:6ea68431cf4c5e61761be4dfc238971ec479a763f11de2a44ec6a738b63063c7
fork_of
null
generation
2
gaps array · 14 items
[0]
abstract
[1]
asset:source:pmid:40524029 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:40524029' 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:40524029", "kind": "science-record", "revision": 2, "content_hash": "sha256:a90f32ecd4d974479335b998f7d5234506a4746b0820f70efd6c5b0f37ef10ed", "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": "To reveal the key mechanism of Citri Reticulatae Pericarpium-Reynoutria japonica Houtt in the treatment of liver cancer and its correlation with lipid metabolism: synergetic effect with network pharmacology, molecular docking and bioinformatics.", "doi": "10.1007/s12672-025-02708-8", "pmid": "40524029", "authors": null, "journal": "Discover oncology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": 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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:40524029", "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 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"section[13]/table-wrap[1]#Tab1", "version": null, "note": "Grid box centers and sizes for molecular docking of target genes", "structure": {"pmcid": "PMC12170481", "section_index": 13, "section_title": "Molecular docking validation and ADMET analysis", "row_count": 9, "column_count": 3}, "table": {"label": "Table 1", "caption": "Grid box centers and sizes for molecular docking of target genes", "rows": [["Gene name", "Grid box center", "Grid box size"], ["TP53", "x = 122.593, y = 97.379, z = −41.654", "x = 24 Å, y = 26 Å, z = 28 Å"], ["ESR1", "x = 26.6, y = −12.807, z = 16.742", "x = 32 Å, y = 26 Å, z = 34 Å"], ["BCL2", "x = −0.141, y = −5.997, z = 5.575", "x = 28 Å, y = 22 Å, z = 20 Å"], ["JUN", "x = 23.99, y = −20.976, z = −4.06", "x = 30 Å, y = 24 Å, z = 26 Å"], ["TNF", "x = 16.05, y = 15.494, z = 114.301", "x = 30 Å, y = 28 Å, z = 34 Å"], ["HSP90 AA1", "x = −43.634, y = 15.277, z = −18.917", "x = 18 Å, y = 24 Å, z = 36 Å"], ["AKT1", "x = 19.901, y = 18.534, z = 15.857", "x = 24 Å, y = 18 Å, z = 26 Å"], ["IL-6", "x = 8.185, y = −25.073, z = −0.568", "x = 28 Å, y = 26 Å, z = 16 Å"]], "row_count": 9, "column_count": 3, "numeric_cells": 19, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:40524029:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3c5346064fb94cfbb6275d5a04fd7ab61743c174e72046e36723b51e4414df7d", "bytes": 2052, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab2", "version": null, "note": "The 123 common targets between active compound targets of CR and liver cancer disease targets", "structure": {"pmcid": "PMC12170481", "section_index": 17, "section_title": "Active components of CR and Potential targets in LC", "row_count": 21, "column_count": 14}, "table": {"label": "Table 2", "caption": "The 123 common targets between active compound targets of CR and liver cancer disease targets", "rows": [["No.", "Target", "No.", "Target", "No.", "Target", "No.", "Target", "No.", "Target", "No.", "Target", "No.", "Target"], ["1", "AKT1", "21", "CDK4", "41", "RXRA", "61", "ADIPOQ", "81", "INSR", "101", "CYP1B1", "121", "GJA1"], ["2", "APOB", "22", "MYC", "42", "IL10", "62", "CYP19A1", "82", "ESR2", "102", "HSPB1", "122", "CAT"], ["3", "CASP8", "23", "MAPK1", "43", "GSTM1", "63", "PPARA", "83", "SPP1", "103", "CCNA2", "123", "ODC1"], ["4", "CCND1", "24", "NFE2L2", "44", "CDK2", "64", "STAT1", "84", "E2 F1", "104", "F3", "", ""], ["5", "CDKN2A", "25", "IL6", "45", "EGF", "65", "MAPK8", "85", "RASSF1", "105", "CCNB1", "", ""], ["6", "EGFR", "26", "TNF", "46", "PIK3CG", "66", "IGFBP3", "86", "NOS2", "106", "PRKCA", "", ""], ["7", "EPHB2", "27", "PPARG", "47", "CDKN1A", "67", "CCL2", "87", "HMOX1", "107", "CREB1", "", ""], ["8", "ERBB2", "28", "TGFB1", "48", "GSTP1", "68", "PGR", "88", "MAPK3", "108", "CTSD", "", ""], ["9", "ESR1", "29", "ERBB3", "49", "ICAM1", "69", "FASN", "89", "CASP9", "109", "NOS3", "", ""], ["10", "IL1B", "30", "VEGFA", "50", "CXCL8", "70", "CAV1", "90", "IL4", "110", "HMGCR", "", ""], ["11", "IRF1", "31", "JUN", "51", "PTGS2", "71", "ABCC1", "91", "NFKBIA", "111", "SOD1", "", ""], ["12", "MPO", "32", "BAX", "52", "CYP1A1", "72", "PARP1", "92", "IL1A", "112", "CD40LG", "", ""], ["13", "NQO1", "33", "IGF2", "53", "IFNG", "73", "CRP", "93", "RELA", "113", "CHUK", "", ""], ["14", "PTEN", "34", "MDM2", "54", "MMP9", "74", "SERPINE1", "94", "GSK3B", "114", "TOP1", "", ""], ["15", "RB1", "35", "IL2", "55", "UGT1A1", "75", "MMP1", "95", "MAPK14", "115", "MMP3", "", ""], ["16", "TP53", "36", "HIF1A", "56", "MMP2", "76", "TIMP1", "96", "NR1I2", "116", "DPP4", "", ""], ["17", "TOP2A", "37", "RAF1", "57", "CASP3", "77", "BCL2L1", "97", "MCL1", "117", "ACACA", "", ""], ["18", "CHEK2", "38", "CYP3A4", "58", "CYP1A2", "78", "PLAU", "98", "CHEK1", "118", "VCAM1", "", ""], ["19", "MET", "39", "BCL2", "59", "BIRC5", "79", "PCNA", "99", "SREBF1", "119", "AHR", "", ""], ["20", "AR", "40", "HSP90AA1", "60", "ABCG2", "80", "FOS", "100", "HSPA5", "120", "BAD", "", ""]], "row_count": 21, "column_count": 14, "numeric_cells": 129, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:40524029:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:03b3bb347fa6b9ec5613593dfb2aacd94e0b7b24ca22104e8308b457596eecbf", "bytes": 664, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#Tab3", "version": null, "note": "Top 28 targets, ranked by degree in the compound–target–pathway network of liver cancer", "structure": {"pmcid": "PMC12170481", "section_index": 18, "section_title": "PPI network construction and analysis", "row_count": 15, "column_count": 4}, "table": {"label": "Table 3", "caption": "Top 28 targets, ranked by degree in the compound–target–pathway network of liver cancer", "rows": [["Gene name", "Degree", "Gene name", "Degree"], ["TP53", "96", "RELA", "32"], ["AKT1", "64", "CASP3", "32"], ["JUN", "56", "MDM2", "32"], ["IL6", "50", "FOS", "28"], ["TNF", "48", "MAPK8", "28"], ["HSP90AA1", "46", "CDKN1A", "28"], ["ESR1", "46", "CXCL8", "26"], ["BCL2", "42", "IFNG", "26"], ["MAPK3", "40", "CCL2", "26"], ["CCND1", "40", "HIF1A", "26"], ["MAPK1", "40", "CDKN2A", "24"], ["MYC", "38", "CDK4", "24"], ["EGFR", "34", "BCL2L1", "24"], ["IL1B", "34", "MAPK14", "24"]], "row_count": 15, "column_count": 4, "numeric_cells": 31, "header_rows": 1, "locator": "section[18]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:40524029:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:68583bcdc03805f201d73f318d0b33665d68c70012f0e6968c429791dfcbe47a", "bytes": 489, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#Tab4", "version": null, "note": "Top 16 targets, ranked by degree in the compound–target–pathway network of liver cancer", "structure": {"pmcid": "PMC12170481", "section_index": 20, "section_title": "Analysis of compound–target–pathway interactions and core target identification in liver cancer", "row_count": 9, "column_count": 4}, "table": {"label": "Table 4", "caption": "Top 16 targets, ranked by degree in the compound–target–pathway network of liver cancer", "rows": [["Gene name", "Degree", "Gene name", "Degree"], ["RB1", "18", "AR", "5"], ["PTGS2", "11", "GSTP1", "4"], ["HSP90AA1", "11", "IL10", "4"], ["TOP2A", "9", "DPP4", "4"], ["GSK3B", "8", "ESR1", "4"], ["JUN", "7", "BCL2", "4"], ["PIK3CG", "7", "CASP9", "4"], ["PPARG", "6", "CASP3", "4"]], "row_count": 9, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[20]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:40524029:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:aaa5212de3ca038e686980458f8e2ff2a6679896726baaf0473f12c028ad5acb", "bytes": 1040, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[2]#Tab5", "version": null, "note": "Details of the top 10 compounds in the compound–target–pathway network of liver cancer", "structure": {"pmcid": "PMC12170481", "section_index": 20, "section_title": "Analysis of compound–target–pathway interactions and core target identification in liver cancer", "row_count": 11, "column_count": 8}, "table": {"label": "Table 5", "caption": "Details of the top 10 compounds in the compound–target–pathway network of liver cancer", "rows": [["Rank", "Component ID", "Component name", "Structure", "CAS", "Degree", "OB(%)", "DL"], ["1", "MOL000098", "Quercetin", "", "117-39-5", "97", "46.43", "0.28"], ["2", "MOL000006", "Luteolin", "", "491-70-3", "45", "36.16", 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C Compound–target–pathway network.D NAFLD+DLM PPI and Drug-Target-Path analysis Venn diagram", "Image (.png)", "Uploaded via journal submission system"], ["Figure 7", "Heatmap of LC molecular docking scores", "Image (.png)", "Uploaded via journal submission system"], ["Figure 8", "Docking patterns of core targets and active compounds of Liver Cancer.", "Image (.png)", "Uploaded via journal submission system"], ["Figure 9", "Volcano and Heatmap plot. A GSE76427, B GSE87630, C GSE112790 datasets", "Image (.png)", "Uploaded via journal submission system"], ["Figure 10", "Pearson’s coefficient analysis A HSP90 AA1, B ESR1. Core targets’s Expression in LIHC. 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