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pmid:40707667

Shared blood gene signature in lung adenocarcinoma and microbial lung infections: a bioinformatic analysis and in silico validation.

Discover oncology · 2025 doi:10.1007/s12672-025-03272-x

Paper

partial

Experiment

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Data

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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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2026-11-01T10:25:51Z
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paper object · 10 fields
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title
Shared blood gene signature in lung adenocarcinoma and microbial lung infections: a bioinformatic analysis and in silico validation.
doi
10.1007/s12672-025-03272-x
pmid
40707667
authors
null
journal
Discover oncology
year
2025
abstract
null
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the headline numerical result the paper states for its main finding
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quantitative
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complete
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7
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genes
tolerance
null
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chars 2091-2363 of source sha256 900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265
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chars 2091-2363 of source sha256 900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265
quote
This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections, associated with immunosuppressive microenvironment features, suggesting a potential link between infection-driven inflammation and tumor-promoting immune modulation.
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abstract
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authors
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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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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:40707667
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the registered result
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step:obtain_source_data blocked on data:not_downloaded
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Summary of the test and validation datasets included in the study
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PMC12290164
section_index
3
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Dataset selection
row_count
11
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Table 1
caption
Summary of the test and validation datasets included in the study
rows array · 11 items
[0] array · 7 items
[0]
Dataset
[1]
Platform
[2]
Country
[3]
Pathology
[4]
Sample type
[5]
Sample size
[6]
Analyzed samples
[1] array · 3 items
[0]
Case
[1]
Control
[2]
Total
[2] array · 11 items
[0]
Test
[1]
Lung infection
[2]
GSE40012
[3]
GPL6947
[4]
Australia
[5]
Bacterial pneumonia
[6]
Peripheral blood
[7]
190
[8]
61
[9]
36
[10]
97
[3] array · 9 items
[0]
GSE65682
[1]
GPL13667
[2]
The Netherlands
[3]
Bacterial pneumonia (CAP, HAP)
[4]
Peripheral blood
[5]
802
[6]
145
[7]
42
[8]
187
[4] array · 9 items
[0]
GSE103119
[1]
GPL10558
[2]
US
[3]
Bacterial pneumonia (CAP)
[4]
Peripheral blood
[5]
172
[6]
29
[7]
16
[8]
45
[5] array · 10 items
[0]
Lung cancer
[1]
GSE39345
[2]
GPL6104
[3]
China
[4]
LUAD
[5]
Peripheral blood
[6]
69
[7]
35
[8]
20
[9]
55
[6] array · 9 items
[0]
GSE103527
[1]
GPL10558
[2]
The Netherlands
[3]
LUAD
[4]
Peripheral blood
[5]
19
[6]
13
[7]
6
[8]
19
[7] array · 11 items
[0]
Validation
[1]
Lung infection
[2]
GSE42826
[3]
GPL10558
[4]
UK
[5]
Bacterial pneumonia
[6]
Peripheral blood
[7]
102
[8]
6
[9]
52
[10]
58
[8] array · 5 items
[0]
GSE42830
[1]
95
[2]
8
[3]
38
[4]
46
[9] array · 7 items
[0]
Lung cancer
[1]
GSE42826
[2]
LUAD
[3]
102
[4]
8
[5]
52
[6]
60
[10] array · 5 items
[0]
GSE42830
[1]
95
[2]
8
[3]
38
[4]
46
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11
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11
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51
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section[3]/table-wrap[1]#Tab1
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Overall summary of test dataset analysis
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pmcid
PMC12290164
section_index
13
section_title
Analysis of test and validation datasets
row_count
53
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11
table object · 8 fields
label
Table 2
caption
Overall summary of test dataset analysis
rows array · 53 items
[0] array · 3 items
[0]
Test dataset
[1]
Total DEG count
[2]
Top 10 DEGs
[1] array · 5 items
[0]
Upregulated
[1]
Downregulated
[2]
Total
[3]
Upregulated
[4]
Downregulated
[2] array · 6 items
[0]
DEG
[1]
|log2FC|
[2]
Adj. P value
[3]
DEG
[4]
|log2FC|
[5]
Adj. P value
[3] array · 11 items
[0]
Lung infection
[1]
GSE40012
[2]
191
[3]
197
[4]
388
[5]
MCEMP1
[6]
3.38
[7]
< 0.001
[8]
GNLY
[9]
2.38
[10]
< 0.001
[4] array · 6 items
[0]
ARG1
[1]
2.69
[2]
< 0.001
[3]
IL2RB
[4]
2.28
[5]
< 0.001
[5] array · 6 items
[0]
S100A12
[1]
2.68
[2]
< 0.001
[3]
SPOCK2
[4]
2.19
[5]
< 0.001
[6] array · 6 items
[0]
SLPI
[1]
2.66
[2]
< 0.001
[3]
SERPINA13P
[4]
2.17
[5]
< 0.001
[7] array · 6 items
[0]
ZDHHC19
[1]
2.56
[2]
< 0.001
[3]
CD8A
[4]
2.11
[5]
< 0.001
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[0]
S100P
[1]
2.54
[2]
< 0.001
[3]
ETS1
[4]
2.10
[5]
< 0.001
[9] array · 6 items
[0]
RETN
[1]
2.41
[2]
< 0.001
[3]
CD247
[4]
2.09
[5]
< 0.001
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[0]
HP
[1]
2.38
[2]
< 0.001
[3]
MATK
[4]
1.97
[5]
< 0.001
[11] array · 6 items
[0]
RNASE2
[1]
2.35
[2]
< 0.001
[3]
RUNX3
[4]
1.95
[5]
< 0.001
[12] array · 6 items
[0]
MMP9
[1]
2.17
[2]
< 0.001
[3]
GZMB
[4]
1.93
[5]
< 0.001
[13] array · 10 items
[0]
GSE65682
[1]
739
[2]
989
[3]
1728
[4]
CD177
[5]
6.51
[6]
< 0.001
[7]
LEF1
[8]
3.55
[9]
< 0.001
[14] array · 6 items
[0]
MMP8
[1]
5.69
[2]
< 0.001
[3]
CCR3
[4]
3.50
[5]
< 0.001
[15] array · 6 items
[0]
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[1]
5.51
[2]
< 0.001
[3]
FCER1A
[4]
3.47
[5]
< 0.001
[16] array · 6 items
[0]
HP
[1]
5.35
[2]
< 0.001
[3]
TCF7
[4]
3.41
[5]
< 0.001
[17] array · 6 items
[0]
CLEC4D
[1]
4.60
[2]
< 0.001
[3]
BCL11B
[4]
3.37
[5]
< 0.001
[18] array · 6 items
[0]
OLFM4
[1]
4.55
[2]
< 0.001
[3]
IL2RB
[4]
3.32
[5]
< 0.001
[19] array · 6 items
[0]
RETN
[1]
4.51
[2]
< 0.001
[3]
TCF7
[4]
3.15
[5]
< 0.001
[20] array · 6 items
[0]
GPR84
[1]
4.39
[2]
< 0.001
[3]
LRRN3
[4]
3.09
[5]
< 0.001
[21] array · 6 items
[0]
ANXA3
[1]
4.32
[2]
< 0.001
[3]
CD3D
[4]
3.08
[5]
< 0.001
[22] array · 6 items
[0]
RETN
[1]
4.31
[2]
< 0.001
[3]
IL7R
[4]
3.06
[5]
< 0.001
[23] array · 10 items
[0]
GSE103119
[1]
294
[2]
180
[3]
474
[4]
HP
[5]
3.45
[6]
< 0.001
[7]
HLA-A
[8]
3.18
[9]
0.025
[24] array · 6 items
[0]
IFI27
[1]
2.99
[2]
0.002
[3]
HLA-DRB6
[4]
2.40
[5]
0.033
[25] array · 6 items
[0]
GPR84
[1]
2.66
[2]
< 0.001
[3]
HEMGN
[4]
2.28
[5]
< 0.001
[26] array · 6 items
[0]
DEFA4
[1]
2.64
[2]
< 0.001
[3]
MS4A1
[4]
2.25
[5]
0.001
[27] array · 6 items
[0]
LTF
[1]
2.62
[2]
< 0.001
[3]
FCER1A
[4]
2.13
[5]
< 0.001
[28] array · 6 items
[0]
NAIP
[1]
2.54
[2]
< 0.001
[3]
PRSS23
[4]
2.12
[5]
0.004
[29] array · 6 items
[0]
SLC26A8
[1]
2.51
[2]
< 0.001
[3]
MYBL1
[4]
2.12
[5]
< 0.001
[30] array · 6 items
[0]
VNN1
[1]
2.50
[2]
< 0.001
[3]
HEMGN
[4]
2.09
[5]
< 0.001
[31] array · 6 items
[0]
ZDHHC19
[1]
2.49
[2]
< 0.001
[3]
FCRL3
[4]
1.99
[5]
< 0.001
[32] array · 6 items
[0]
FCGR1A
[1]
2.44
[2]
< 0.001
[3]
SNORD13
[4]
1.86
[5]
< 0.001
[33] array · 11 items
[0]
Lung cancer
[1]
GSE39345
[2]
584
[3]
379
[4]
963
[5]
IFNB1
[6]
4.95
[7]
< 0.001
[8]
MARCHF3
[9]
3.03
[10]
< 0.001
[34] array · 6 items
[0]
CERKL
[1]
3.80
[2]
< 0.001
[3]
ZNF660
[4]
2.56
[5]
< 0.001
[35] array · 6 items
[0]
YAP1
[1]
3.44
[2]
< 0.001
[3]
CTAG1B
[4]
2.15
[5]
< 0.001
[36] array · 6 items
[0]
GAGE7
[1]
3.40
[2]
< 0.001
[3]
CBFA2T2
[4]
2.11
[5]
< 0.001
[37] array · 6 items
[0]
MANBAL
[1]
3.39
[2]
0.005
[3]
RPL13
[4]
2.11
[5]
0.002
[38] array · 6 items
[0]
NOX4
[1]
3.29
[2]
< 0.001
[3]
SLC25A10
[4]
2.08
[5]
0.002
[39] array · 6 items
[0]
FAM150A
[1]
3.13
[2]
< 0.001
[3]
CCDC144B
[4]
2.06
[5]
0.003
[40] array · 6 items
[0]
KIT
[1]
3.13
[2]
< 0.001
[3]
UBL7
[4]
2.05
[5]
0.005
[41] array · 6 items
[0]
IMPACT
[1]
3.10
[2]
< 0.001
[3]
TRAPPC2
[4]
2.04
[5]
< 0.001
[42] array · 6 items
[0]
DRC3
[1]
3.09
[2]
< 0.001
[3]
SPRY1
[4]
2.02
[5]
0.001
[43] array · 10 items
[0]
GSE103527
[1]
1054
[2]
971
[3]
2025
[4]
SFTPA1
[5]
5.64
[6]
< 0.001
[7]
MAL
[8]
4.18
[9]
< 0.001
[44] array · 6 items
[0]
LMNA
[1]
5.31
[2]
< 0.001
[3]
TCEA3
[4]
3.69
[5]
< 0.001
[45] array · 6 items
[0]
CXCR6
[1]
5.25
[2]
< 0.001
[3]
TCF7
[4]
3.45
[5]
< 0.001
[46] array · 6 items
[0]
METRNL
[1]
4.90
[2]
< 0.001
[3]
SELL
[4]
3.44
[5]
0.015
[47] array · 6 items
[0]
SFTPC
[1]
4.89
[2]
< 0.001
[3]
SNORD13
[4]
3.41
[5]
< 0.001
[48] array · 6 items
[0]
LMNA
[1]
4.65
[2]
< 0.001
[3]
HBB
[4]
3.32
[5]
< 0.001
[49] array · 6 items
[0]
CCL4L1
[1]
4.53
[2]
< 0.001
[3]
SNORD3D
[4]
3.32
[5]
< 0.001
[50] array · 6 items
[0]
C1QB
[1]
4.42
[2]
< 0.001
[3]
SNORD3C
[4]
3.28
[5]
< 0.001
[51] array · 6 items
[0]
PARD6G
[1]
4.29
[2]
< 0.001
[3]
TCF7
[4]
3.24
[5]
< 0.001
[52] array · 6 items
[0]
BATF
[1]
4.07
[2]
< 0.001
[3]
TMEM107
[4]
3.19
[5]
< 0.001
row_count
53
column_count
11
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242
header_rows
3
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section[13]/table-wrap[1]#Tab2
[3] object · 16 fields
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asset:table:pmid:40707667:3
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Quantitative summary of the expression of hub genes shared between lung infection and lung cancer in test and validation datasets
structure object · 5 fields
pmcid
PMC12290164
section_index
15
section_title
PPI network analysis
row_count
21
column_count
14
table object · 8 fields
label
Table 3
caption
Quantitative summary of the expression of hub genes shared between lung infection and lung cancer in test and validation datasets
rows array · 21 items
[0] array · 2 items
[0]
Dataset
[1]
Shared hub genes
[1] array · 10 items
[0]
BCL6
[1]
CD163
[2]
IL1RN
[3]
MMP9
[4]
S100A12
[5]
FLT3LG
[6]
RPL13
[7]
RPL14
[8]
RPL22
[9]
RPS4X
[2] array · 14 items
[0]
Test
[1]
Lung infection
[2]
GSE40012
[3]
log2FC
[4]
1.19
[5]
1.25
[6]
0.78
[7]
2.17
[8]
2.68
[9]
−0.83
[10]
−0.65
[11]
−1.29
[12]
−1.05
[13]
−1.48
[3] array · 11 items
[0]
P
[1]
< 0.001
[2]
< 0.001
[3]
< 0.001
[4]
< 0.001
[5]
< 0.001
[6]
< 0.001
[7]
< 0.001
[8]
< 0.001
[9]
< 0.001
[10]
< 0.001
[4] array · 12 items
[0]
GSE65682
[1]
log2FC
[2]
1.27
[3]
1.84
[4]
1.27
[5]
2.98
[6]
3.35
[7]
−1.45
[8]
−0.72
[9]
−1.23
[10]
−1.18
[11]
−1.35
[5] array · 11 items
[0]
P
[1]
< 0.001
[2]
< 0.001
[3]
< 0.001
[4]
< 0.001
[5]
< 0.001
[6]
< 0.001
[7]
< 0.001
[8]
< 0.001
[9]
< 0.001
[10]
< 0.001
[6] array · 12 items
[0]
GSE103119
[1]
log2FC
[2]
1.20
[3]
0.90
[4]
1.12
[5]
1.93
[6]
1.23
[7]
−0.75
[8]
−0.82
[9]
−1.33
[10]
−0.78
[11]
−0.72
[7] array · 11 items
[0]
P
[1]
< 0.001
[2]
0.003
[3]
< 0.001
[4]
< 0.001
[5]
0.007
[6]
0.010
[7]
< 0.001
[8]
< 0.001
[9]
< 0.001
[10]
< 0.001
[8] array · 13 items
[0]
Lung cancer
[1]
GSE39345
[2]
log2FC
[3]
1.78
[4]
0.88
[5]
1.31
[6]
0.99
[7]
1.41
[8]
−0.62
[9]
−2.11
[10]
−0.83
[11]
−0.79
[12]
−0.68
[9] array · 11 items
[0]
P
[1]
< 0.001
[2]
0.015
[3]
0.004
[4]
0.026
[5]
0.002
[6]
0.003
[7]
0.002
[8]
0.018
[9]
0.009
[10]
0.018
[10] array · 12 items
[0]
GSE103527
[1]
log2FC
[2]
1.39
[3]
1.08
[4]
1.17
[5]
1.44
[6]
0.96
[7]
−1.63
[8]
−1.03
[9]
−1.39
[10]
−1.42
[11]
−1.14
[11] array · 11 items
[0]
P
[1]
< 0.001
[2]
< 0.001
[3]
0.007
[4]
0.018
[5]
0.027
[6]
< 0.001
[7]
< 0.001
[8]
< 0.001
[9]
< 0.001
[10]
< 0.001
[12] array · 14 items
[0]
Validation
[1]
Lung infection
[2]
GSE42826
[3]
log2FC
[4]
1.05
[5]
1.19
[6]
0.92
[7]
1.81
[8]
1.53
[9]
−0.90
[10]
−0.75
[11]
−0.83
[12]
− 0.77
[13]
−0.75
[13] array · 11 items
[0]
P
[1]
< 0.001
[2]
0.008
[3]
< 0.001
[4]
< 0.001
[5]
< 0.001
[6]
0.005
[7]
0.005
[8]
0.010
[9]
< 0.001
[10]
< 0.001
[14] array · 12 items
[0]
GSE42830
[1]
log2FC
[2]
1.22
[3]
0.96
[4]
1.14
[5]
2.36
[6]
1.73
[7]
−1.36
[8]
−0.89
[9]
− 1.47
[10]
−0.80
[11]
−1.00
[15] array · 11 items
[0]
P
[1]
< 0.001
[2]
0.020
[3]
< 0.001
[4]
< 0.001
[5]
< 0.001
[6]
< 0.001
[7]
< 0.001
[8]
< 0.001
[9]
< 0.001
[10]
< 0.001
[16] array · 13 items
[0]
Lung cancer
[1]
GSE42826
[2]
log2FC
[3]
1.07
[4]
1.16
[5]
0.86
[6]
1.67
[7]
1.28
[8]
−0.83
[9]
−0.89
[10]
−1.62
[11]
−0.65
[12]
−0.68
[17] array · 11 items
[0]
P
[1]
< 0.001
[2]
0.001
[3]
< 0.001
[4]
< 0.001
[5]
< 0.001
[6]
0.003
[7]
< 0.001
[8]
0.010
[9]
< 0.001
[10]
< 0.001
[18] array · 12 items
[0]
GSE42830
[1]
log2FC
[2]
0.99
[3]
1.25
[4]
0.91
[5]
1.66
[6]
1.26
[7]
−0.83
[8]
−0.69
[9]
−0.91
[10]
−0.62
[11]
−0.59
[19] array · 11 items
[0]
P
[1]
< 0.001
[2]
0.001
[3]
< 0.001
[4]
0.018
[5]
0.008
[6]
0.005
[7]
0.002
[8]
0.005
[9]
0.002
[10]
0.002
[20] array · 11 items
[0]
Overall change
[1]
↑
[2]
↑
[3]
↑
[4]
↑
[5]
↑
[6]
↓
[7]
↓
[8]
↓
[9]
↓
[10]
↓
row_count
21
column_count
14
numeric_cells
194
header_rows
2
locator
section[15]/table-wrap[1]#Tab3
gaps array · 1 item
[0]
asset:source:pmid:40707667 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 · 4 items
[0]
source:pmid:40707667
[1]
asset:table:pmid:40707667:1
[2]
asset:table:pmid:40707667:2
[3]
asset:table:pmid:40707667:3
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:40707667
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 2 items
[0] object · 7 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
full-text-reading-v1
prompt_hash
e525d403fcf0dedbc758827f61ea2b3abf1a83eb77fb8fecb66cd606e91348ea
source_hash
900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265
raw_response_sha256
sha256:604a0965ed0a4e9f95617781652a6d155310627b184e1e43ea597d598b73d46f
raw_response_chars
9069
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
7fed0d2429769e20c79bdbae78942146db7f3674ab459f9e58d58a34ee8694d8
source_hash
900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265
raw_response_sha256
sha256:4c22d3cad7a93380eaf1f1f409f7fc668a1f22e8bf587cd0f0793c336b88ae6b
raw_response_chars
77930
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
6b19348755b33355a314b437c24b76bf2abf707bc44f9908ac30f21a5e0c4745
source_hash
900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265
raw_response
{"parent_value":7,"unit":"genes","evidence":"This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections, associated with immunosuppressive microenvironment features, suggesting a potential link between infection-driven inflammation and tumor-promoting immune modulation.","target_result":"A blood-based 7-gene signature shared between lung adenocarcinoma and microbial lung infections.","number_stated":true}
reading object · 6 fields
parent_value
7
unit
genes
evidence
This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections, associated with immunosuppressive microenvironment features, suggesting a potential link between infection-driven inflammation and tumor-promoting immune modulation.
target_result
A blood-based 7-gene signature shared between lung adenocarcinoma and microbial lung infections.
number_stated
true
source_locator
chars 2091-2363 of source sha256 900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265
recorded_at
2026-10-31T15:22:42.518192+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
a092cd2da55e4280c9e69f6db942591a843d7819a2484c2db897e9dde7217c47
source_hash
900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265
raw_response
<think>We need answer JSON only. Need identify single numerical result replication registered target headline numerical result main finding. Likely 7-gene signature. Need value 7, unit perhaps "genes" or "gene signature" printed unit? User says unit must be unit paper prints. Exact contiguous quotation contains number. Source says "This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections..." Headline number 7, unit perhaps "genes". Need quote whole clause so attribution. Evidence exact contiguous quote perhaps "This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections, associated with immunosuppressive microenvironment features, suggesting a potential link between infection-driven inflammation and tumor-promoting immune modulation." Parent_value 7, unit "genes" (paper prints 7-gene). target_result "A 7-gene blood-based signature..." Must avoid calculated. number_stated true. Question wording: "find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed." Registered target = headline numerical result paper states for main finding. Main conclusion 7-gene signature. Unit likely genes. Evidence exact contiguous quote contains number. Use quote. JSON valid.</think> {"parent_value":7,"unit":"genes","evidence":"This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections, associated with immunosuppressive microenvironment features, suggesting a potential link between infection-driven inflammation and tumor-promoting immune modulation.","target_result":"A blood-based 7-gene signature shared between LUAD and microbial lung infections.","number_stated":true}
reading object · 6 fields
parent_value
7
unit
genes
evidence
This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections, associated with immunosuppressive microenvironment features, suggesting a potential link between infection-driven inflammation and tumor-promoting immune modulation.
target_result
A blood-based 7-gene signature shared between LUAD and microbial lung infections.
number_stated
true
source_locator
chars 2091-2363 of source sha256 900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265
recorded_at
2026-10-31T15:23:03.236221+00:00
agreement
false
disagreements object · 3 fields
target_result object · 3 fields
minimax
A blood-based 7-gene signature shared between lung adenocarcinoma and microbial lung infections, comprising BCL6, S100A12, FLT3LG, RPL13, RPL14, RPL22, and RPS4X.
minimax_alt
A blood-based 7-gene signature shared between LUAD and microbial lung infections, comprising BCL6, S100A12, FLT3LG, RPL13, RPL14, RPL22, and RPS4X.
decisive
false
analysis_methods object · 3 fields
minimax array · 18 items
[0]
GEO2R
[1]
limma package
[2]
Benjamini-Hochberg false discovery rate correction
[3]
VennPainter
[4]
UpSetR
[5]
KEGG enrichment analysis
[6]
Gene Ontology enrichment analysis
[7]
clusterProfiler
[8]
STRING protein-protein interaction analysis
[9]
Cytoscape
[10]
CytoHubba
[11]
Shapiro-Wilk test
[12]
independent t-test
[13]
Wilcoxon rank-sum test
[14]
linear regression
[15]
F-test
[16]
Pearson correlation
[17]
xCell deconvolution algorithm
minimax_alt array · 8 items
[0]
GEO2R with the Limma package v3.52.4, including background correction, force-normalization, and Benjamini-Hochberg FDR correction
[1]
Test-set DEG selection using |log2FC| >1 and adjusted P-value <0.05, and validation-set DEG selection using |log2FC| >0.58 and adjusted P-value <0.05
[2]
Shared-DEG identification and intersection visualization using VennPainter v1.2.0 and UpSetR v1.4.0
[3]
KEGG and GO enrichment analysis using clusterProfiler v4.6.2, org.Hs.eg.db v3.16.0, enrichplot v1.11.1, and ggplot2 v3.5.2
[4]
PPI-network construction using STRING 12.0 and Cytoscape v3.10.2, with hub-gene identification using CytoHubba MCC, degree, betweenness, and closeness centrality
[5]
Quantile normalization using preprocessCore v1.58.0, followed by Shapiro-Wilk normality assessment, independent t-tests, and Wilcoxon rank-sum tests for hub-gene comparisons
[6]
Linear regression with F-test for co-regulation and Pearson correlation with Benjamini-Hochberg correction for defining the shared gene signature
[7]
xCell deconvolution using 64 immune and stromal cell types
decisive
false
statistical_method object · 3 fields
minimax
Linear regression for co-regulation assessment, with Pearson correlation for inter-gene relationships.
minimax_alt
Linear regression with an F-test for co-regulation, followed by Pearson correlation with Benjamini-Hochberg correction; genes satisfying both criteria were defined as the shared signature.
decisive
true
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 0 items
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 2 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 1 item
[0] object · 3 fields
id
package:f59ae9c8f7005c6be3b3beca5698ac9dfb18e885363301ef34dd5ea06d43e5c1
type
sep_package
label
SEP v1 package for pmid:40707667
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40707667
type
conversion
used array · 1 item
[0]
package:f59ae9c8f7005c6be3b3beca5698ac9dfb18e885363301ef34dd5ea06d43e5c1
agent
agent:corpus-assay-engine
agents array · 3 items
[0] object · 3 fields
id
agent:minimax
type
model
label
minimax
[1] object · 3 fields
id
agent:minimax_alt
type
model
label
minimax_alt
[2] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
source_run_id
run-20261023T122449232913
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:40707667
parent_hash
sha256:071e64a4913c2ffa9d065d1641b44a63b8dc3902cf766b0c623a98cd3a9f53f9
fork_of
null
generation
2
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40707667 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
step:obtain_source_data blocked on data:not_downloaded
[10]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[11]
step:run_analysis input 'materials:the source data behind the published result in pmid:40707667' does not resolve to a declared asset
[12]
targets
Complete file 
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40707667", "kind": "science-record", "revision": 2, "content_hash": "sha256:cadee325ae1d8cd7f028b981433b6cccaf43c74202c80cb1d574eb888227498f", "created_at": "2026-11-01T10:25:51Z", "updated_at": "2026-11-01T14:01:44Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Shared blood gene signature in lung adenocarcinoma and microbial lung infections: a bioinformatic analysis and in silico validation.", "doi": "10.1007/s12672-025-03272-x", "pmid": "40707667", "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": "quantitative", "state": "complete", "target": {"value": 7.0, "unit": "genes", "tolerance": null, "source": "chars 2091-2363 of source sha256 900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265"}, "evidence": [{"asset": "source:pmid:40707667", "locator": "chars 2091-2363 of source sha256 900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265", "quote": "This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections, associated with immunosuppressive microenvironment features, suggesting a potential link between infection-driven inflammation and tumor-promoting immune modulation."}]}], "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:40707667"], "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:40707667", "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:40707667' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40707667", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-025-03272-x", "sha256": "sha256:900f9ccda994ac60b61e715507ef49657d9ff452d55f428da617554be3fd3265", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-025-03272-x", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40707667:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0504c3739dcf0249f802a0d05d006fafd3c6da4bcc103ef5aee0c44b0916759d", "bytes": 1088, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Summary of the test and validation datasets included in the study", "structure": {"pmcid": "PMC12290164", "section_index": 3, "section_title": "Dataset selection", "row_count": 11, "column_count": 11}, "table": {"label": "Table 1", "caption": "Summary of the test and validation datasets included in the study", "rows": [["Dataset", "Platform", "Country", "Pathology", "Sample type", "Sample size", "Analyzed samples"], ["Case", "Control", "Total"], ["Test", "Lung infection", "GSE40012", "GPL6947", "Australia", "Bacterial pneumonia", "Peripheral blood", "190", "61", "36", "97"], ["GSE65682", "GPL13667", "The Netherlands", "Bacterial pneumonia (CAP, HAP)", "Peripheral blood", "802", "145", "42", "187"], ["GSE103119", "GPL10558", "US", "Bacterial pneumonia (CAP)", "Peripheral blood", "172", "29", "16", "45"], ["Lung cancer", "GSE39345", "GPL6104", "China", "LUAD", "Peripheral blood", "69", "35", "20", "55"], ["GSE103527", "GPL10558", "The Netherlands", "LUAD", "Peripheral blood", "19", "13", "6", "19"], ["Validation", "Lung infection", "GSE42826", "GPL10558", "UK", "Bacterial pneumonia", "Peripheral blood", "102", "6", "52", "58"], ["GSE42830", "95", "8", "38", "46"], ["Lung cancer", "GSE42826", "LUAD", "102", "8", "52", "60"], ["GSE42830", "95", "8", "38", "46"]], "row_count": 11, "column_count": 11, "numeric_cells": 51, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:40707667:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:52fd1a937033565d5e007a41ab2176e7f30c6f5a6ab3a6062226f53ab79873fa", "bytes": 3143, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab2", "version": null, "note": "Overall summary of test dataset analysis", "structure": {"pmcid": "PMC12290164", "section_index": 13, "section_title": "Analysis of test and validation datasets", "row_count": 53, "column_count": 11}, "table": {"label": "Table 2", "caption": "Overall summary of test dataset analysis", "rows": [["Test dataset", "Total DEG count", "Top 10 DEGs"], ["Upregulated", "Downregulated", "Total", "Upregulated", "Downregulated"], ["DEG", "|log2FC|", "Adj. P value", "DEG", "|log2FC|", "Adj. 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Need identify single numerical result replication registered target headline numerical result main finding. Likely 7-gene signature. Need value 7, unit perhaps \"genes\" or \"gene signature\" printed unit? User says unit must be unit paper prints. Exact contiguous quotation contains number. Source says \"This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections...\" Headline number 7, unit perhaps \"genes\". Need quote whole clause so attribution. Evidence exact contiguous quote perhaps \"This analysis identified a blood-based 7-gene signature shared between LUAD and microbial lung infections, associated with immunosuppressive microenvironment features, suggesting a potential link between infection-driven inflammation and tumor-promoting immune modulation.\" Parent_value 7, unit \"genes\" (paper prints 7-gene). target_result \"A 7-gene blood-based signature...\" Must avoid calculated. number_stated true.\n\nQuestion wording: \"find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed.\" Registered target = headline numerical result paper states for main finding. Main conclusion 7-gene signature. Unit likely genes. Evidence exact contiguous quote contains number. Use quote. 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