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pmid:41354084

TMEM106A as a Macrophage-Associated Biomarker of Prognosis in IDH-Wildtype Glioma: Integrative Multi-Omics and Spatial Analyses.

Cancer medicine · 2025 doi:10.1002/cam4.71454

Paper

partial

Experiment

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Data

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Analysis

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:41354084
kind
science-record
content_hash
sha256:cbaf9d3a3da1537d263dd25555b595d3f15f7a6f4c1fd43d84713e588c292965
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:54Z
updated_at
2026-11-01T14:01:52Z
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corpus-assay-engine
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sep_to_sci_v1
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urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
TMEM106A as a Macrophage-Associated Biomarker of Prognosis in IDH-Wildtype Glioma: Integrative Multi-Omics and Spatial Analyses.
doi
10.1002/cam4.71454
pmid
41354084
authors
null
journal
Cancer medicine
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
id
claim-1
statement
the headline numerical result the paper states for its main finding
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qualitative
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blocked
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null
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null
tolerance
null
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null
evidence array · 0 items
gaps array · 2 items
[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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:41354084
outputs array · 1 item
[0]
the published estimate, its unit and its interval
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[1] object · 13 fields
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obtain_source_data
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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.
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the source data with its provenance
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run_analysis
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Run the analysis programme
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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:41354084
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
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the registered result
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id
source:pmid:41354084
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xml
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https://doi.org/10.1002/cam4.71454
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sha256:a69e8a8ca91714476c771095efdc061349a21ca03e7193222f18ef7dd7ca2b24
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10.1002/cam4.71454
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null
note
Source read by the package builder: full_text.
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[1] object · 16 fields
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Correlation between TMEM106A and 12 principal cell compartments in glioma subtypes.
structure object · 5 fields
pmcid
PMC12682394
section_index
9
section_title
Figure–Data Source Map
row_count
27
column_count
9
table object · 8 fields
label
TABLE 1
caption
Correlation between TMEM106A and 12 principal cell compartments in glioma subtypes.
rows array · 27 items
[0] array · 6 items
[0]
[1]
[2]
[3]
IDH wildtype astrocytoma
[4]
IDH mutant astrocytoma
[5]
Oligodendroglioma
[1] array · 8 items
[0]
TMEM106A
[1]
Datasets
[2]
TCGA
[3]
CGGA
[4]
TCGA
[5]
CGGA
[6]
TCGA
[7]
CGGA
[2] array · 8 items
[0]
[1]
Number (N)
[2]
233
[3]
447
[4]
247
[5]
352
[6]
182
[7]
214
[3] array · 9 items
[0]
Tumor
[1]
Stemcell_tumor
[2]
Correlation
[3]
−0.270**
[4]
−0.337****
[5]
−0.199**
[6]
−0.324***
[7]
−0.358***
[8]
−0.373***
[4] array · 7 items
[0]
p
[1]
< 0.001
[2]
< 0.001
[3]
0.002
[4]
< 0.001
[5]
< 0.001
[6]
< 0.001
[5] array · 8 items
[0]
Prolif_stemcell_tumor
[1]
Correlation
[2]
−0.076
[3]
−0.117*
[4]
−0.113
[5]
−0.158**
[6]
0.266***
[7]
−0.105
[6] array · 7 items
[0]
p
[1]
0.249
[2]
0.013
[3]
0.076
[4]
0.003
[5]
< 0.001
[6]
0.126
[7] array · 8 items
[0]
Differentiated_tumor
[1]
Correlation
[2]
−0.268***
[3]
−0.146**
[4]
−0.049
[5]
0.118*
[6]
0.226**
[7]
0.248***
[8] array · 7 items
[0]
p
[1]
< 0.001
[2]
0.002
[3]
0.442
[4]
0.027
[5]
0.002
[6]
< 0.001
[9] array · 9 items
[0]
Stroma
[1]
Oligodendrocyte
[2]
Correlation
[3]
−0.119
[4]
−0.070
[5]
−0.039
[6]
0.127*
[7]
0.096
[8]
0.285***
[10] array · 7 items
[0]
p
[1]
0.070
[2]
0.140
[3]
0.543
[4]
0.017
[5]
0.197
[6]
< 0.001
[11] array · 8 items
[0]
Pericyte
[1]
Correlation
[2]
−0.008
[3]
0.107*
[4]
−0.185**
[5]
0.109*
[6]
0.012
[7]
0.061
[12] array · 7 items
[0]
p
[1]
0.899
[2]
0.023
[3]
0.003
[4]
0.041
[5]
0.872
[6]
0.376
[13] array · 8 items
[0]
Endothelial
[1]
Correlation
[2]
−0.131*
[3]
−0.278***
[4]
−0.153*
[5]
−0.159**
[6]
−0.055
[7]
0.027
[14] array · 7 items
[0]
p
[1]
0.045
[2]
< 0.001
[3]
0.016
[4]
0.003
[5]
0.457
[6]
0.692
[15] array · 8 items
[0]
Fibroblast
[1]
Correlation
[2]
0.373***
[3]
0.362***
[4]
0.122
[5]
0.201***
[6]
0.257***
[7]
0.215**
[16] array · 7 items
[0]
p
[1]
< 0.001
[2]
< 0.001
[3]
0.055
[4]
< 0.001
[5]
< 0.001
[6]
0.002
[17] array · 9 items
[0]
Immune
[1]
Myeloid
[2]
Correlation
[3]
0.792***
[4]
0.702***
[5]
0.776***
[6]
0.639***
[7]
0.782***
[8]
0.542***
[18] array · 7 items
[0]
p
[1]
< 0 .001
[2]
< 0.001
[3]
< 0.001
[4]
< 0.001
[5]
< 0.001
[6]
< 0.001
[19] array · 8 items
[0]
Dendritic_cell
[1]
Correlation
[2]
−0.092
[3]
−0.320***
[4]
−0.297***
[5]
−0.301***
[6]
−0.144
[7]
−0.213**
[20] array · 7 items
[0]
p
[1]
0.160
[2]
< 0.001
[3]
< 0.001
[4]
< 0.001
[5]
0.052
[6]
0.002
[21] array · 8 items
[0]
T_cell
[1]
Correlation
[2]
0.129*
[3]
0.186***
[4]
−0.065
[5]
0.171**
[6]
−0.242**
[7]
0.332***
[22] array · 7 items
[0]
p
[1]
0.049
[2]
< 0.001
[3]
0.306
[4]
0.001
[5]
0.001
[6]
< 0.001
[23] array · 8 items
[0]
B_cell
[1]
Correlation
[2]
−0.078
[3]
0.028
[4]
.c
[5]
.b
[6]
.c
[7]
−0.088
[24] array · 7 items
[0]
p
[1]
0.233
[2]
0.552
[3]
[4]
[5]
[6]
0.199
[25] array · 8 items
[0]
Granulocyte
[1]
Correlation
[2]
0.575***
[3]
0.418***
[4]
0.399***
[5]
0.254***
[6]
0.335***
[7]
0.181**
[26] array · 7 items
[0]
p
[1]
< 0.001
[2]
< 0.001
[3]
< 0.001
[4]
< 0.001
[5]
< 0.001
[6]
0.008
locator
section[9]/table-wrap[1]#cam471454-tbl-0001
[2] object · 16 fields
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asset:table:pmid:41354084:2
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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:bb2cb6f76310f769a6d0ee3b447bae767942b9ee73dbed1cf62919b083188d10
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3662
access
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state
verified
reader
read_table
reader_status
available
identifier
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version
null
note
Correlation of TMEM106A expression with 22 immune cell types across glioma subtypes.
structure object · 5 fields
pmcid
PMC12682394
section_index
9
section_title
Figure–Data Source Map
row_count
47
column_count
8
table object · 8 fields
label
TABLE 2
caption
Correlation of TMEM106A expression with 22 immune cell types across glioma subtypes.
rows array · 47 items
[0] array · 5 items
[0]
TMEM106A
[1]
n
[2]
IDH wildtype astrocytoma
[3]
IDH mutant astrocytoma
[4]
Oligodendroglioma
[1] array · 6 items
[0]
TCGA
[1]
CGGA
[2]
TCGA
[3]
CGGA
[4]
TCGA
[5]
CGGA
[2] array · 6 items
[0]
49
[1]
112
[2]
86
[3]
136
[4]
14
[5]
24
[3] array · 8 items
[0]
B_cells_naive
[1]
Correlation
[2]
−0.014
[3]
0.151
[4]
−0.091
[5]
0.157
[6]
−0.459
[7]
.c
[4] array · 7 items
[0]
p
[1]
0.926
[2]
0.111
[3]
0.404
[4]
0.068
[5]
0.099
[6]
[5] array · 8 items
[0]
B_cells_memory
[1]
Correlation
[2]
−0.203
[3]
−0.317**
[4]
−0.027
[5]
−0.325***
[6]
0.066
[7]
−0.461*
[6] array · 7 items
[0]
p
[1]
0.162
[2]
0.001
[3]
0.806
[4]
< 0.001
[5]
0.822
[6]
0.027
[7] array · 8 items
[0]
Plasma_cells
[1]
Correlation
[2]
−0.193
[3]
−0.127
[4]
−0.034
[5]
−0.166
[6]
0.202
[7]
0.117
[8] array · 7 items
[0]
p
[1]
0.184
[2]
0.184
[3]
0.756
[4]
0.053
[5]
0.489
[6]
0.595
[9] array · 8 items
[0]
T_cells_CD8
[1]
Correlation
[2]
0.293*
[3]
0.078
[4]
0.010
[5]
0.035
[6]
0.016
[7]
0.155
[10] array · 7 items
[0]
p
[1]
0.041
[2]
0.415
[3]
0.927
[4]
0.688
[5]
0.957
[6]
0.480
[11] array · 8 items
[0]
T_cells_CD4_naive
[1]
Correlation
[2]
.c
[3]
−0.002
[4]
−0.035
[5]
−0.226**
[6]
.c
[7]
0.051
[12] array · 7 items
[0]
p
[1]
[2]
0.985
[3]
0.751
[4]
0.008
[5]
[6]
0.816
[13] array · 8 items
[0]
T_cells_CD4_memory_resting
[1]
Correlation
[2]
−0.139
[3]
0.028
[4]
−0.053
[5]
0.062
[6]
0.238
[7]
0.192
[14] array · 7 items
[0]
p
[1]
0.341
[2]
0.773
[3]
0.628
[4]
0.474
[5]
0.413
[6]
0.380
[15] array · 8 items
[0]
T_cells_CD4_memory_activated
[1]
Correlation
[2]
0.001
[3]
−0.054
[4]
0.251*
[5]
−0.126
[6]
0.204
[7]
0.159
[16] array · 7 items
[0]
p
[1]
0.993
[2]
0.573
[3]
0.020
[4]
0.145
[5]
0.485
[6]
0.468
[17] array · 8 items
[0]
T_cells_follicular_helper
[1]
Correlation
[2]
0.058
[3]
−0.221*
[4]
−0.171
[5]
−0.273**
[6]
−0.507
[7]
−0.528**
[18] array · 7 items
[0]
p
[1]
0.690
[2]
0.019
[3]
0.115
[4]
0.001
[5]
0.064
[6]
0.010
[19] array · 8 items
[0]
T_cells_regulatory_Tregs
[1]
Correlation
[2]
−0.197
[3]
−0.146
[4]
−0.048
[5]
0.095
[6]
−0.180
[7]
0.190
[20] array · 7 items
[0]
p
[1]
0.175
[2]
0.126
[3]
0.658
[4]
0.271
[5]
0.538
[6]
0.385
[21] array · 8 items
[0]
T_cells_gamma_delta
[1]
Correlation
[2]
0.246
[3]
−0.165
[4]
−0.108
[5]
−0.004
[6]
−0.035
[7]
0.071
[22] array · 7 items
[0]
p
[1]
0.088
[2]
0.082
[3]
0.321
[4]
0.959
[5]
0.906
[6]
0.747
[23] array · 8 items
[0]
NK_cells_resting
[1]
Correlation
[2]
−0.205
[3]
−0.166
[4]
−0.012
[5]
−0.091
[6]
−0.070
[7]
0.069
[24] array · 8 items
[0]
[1]
p
[2]
0.157
[3]
0.081
[4]
0.916
[5]
0.293
[6]
0.811
[7]
0.753
[25] array · 8 items
[0]
NK_cells_activated
[1]
Correlation
[2]
0.085
[3]
−0.061
[4]
−0.062
[5]
−0.182*
[6]
−0.140
[7]
0.001
[26] array · 7 items
[0]
p
[1]
0.560
[2]
0.521
[3]
0.569
[4]
0.034
[5]
0.634
[6]
0.996
[27] array · 8 items
[0]
Monocytes
[1]
Correlation
[2]
0.250
[3]
0.095
[4]
0.113
[5]
0.161
[6]
−0.466
[7]
−0.046
[28] array · 7 items
[0]
p
[1]
0.083
[2]
0.319
[3]
0.300
[4]
0.061
[5]
0.093
[6]
0.834
[29] array · 8 items
[0]
Macrophages_M0
[1]
Correlation
[2]
−0.373**
[3]
−0.216*
[4]
−0.028
[5]
−0.183*
[6]
0.420
[7]
−0.110
[30] array · 7 items
[0]
p
[1]
0.008
[2]
0.022
[3]
0.801
[4]
0.033
[5]
0.135
[6]
0.616
[31] array · 8 items
[0]
Macrophages_M1
[1]
Correlation
[2]
0.362*
[3]
0.136
[4]
0.266*
[5]
0.125
[6]
0.145
[7]
0.029
[32] array · 7 items
[0]
p
[1]
0.011
[2]
0.153
[3]
0.013
[4]
0.148
[5]
0.621
[6]
0.897
[33] array · 8 items
[0]
Macrophages_M2
[1]
Correlation
[2]
0.298*
[3]
0.280**
[4]
0.098
[5]
0.356***
[6]
0.315
[7]
0.200
[34] array · 7 items
[0]
p
[1]
0.037
[2]
0.003
[3]
0.369
[4]
< 0.001
[5]
0.272
[6]
0.360
[35] array · 8 items
[0]
Dendritic_cells_resting
[1]
Correlation
[2]
0.200
[3]
0.069
[4]
−0.036
[5]
0.127
[6]
0.020
[7]
−0.291
[36] array · 7 items
[0]
p
[1]
0.169
[2]
0.472
[3]
0.743
[4]
0.141
[5]
0.945
[6]
0.177
[37] array · 8 items
[0]
Dendritic_cells_activated
[1]
Correlation
[2]
−0.142
[3]
−0.059
[4]
0.037
[5]
−0.146
[6]
.c
[7]
0.042
[38] array · 7 items
[0]
p
[1]
0.330
[2]
0.537
[3]
0.735
[4]
0.090
[5]
[6]
0.849
[39] array · 8 items
[0]
Mast_cells_resting
[1]
Correlation
[2]
−0.078
[3]
−0.060
[4]
0.156
[5]
−0.054
[6]
0.427
[7]
0.063
[40] array · 7 items
[0]
p
[1]
0.593
[2]
0.530
[3]
0.152
[4]
0.535
[5]
0.127
[6]
0.774
[41] array · 8 items
[0]
Mast_cells_activated
[1]
Correlation
[2]
0.072
[3]
0.037
[4]
−0.160
[5]
−0.188*
[6]
−0.229
[7]
−0.064
[42] array · 7 items
[0]
p
[1]
0.622
[2]
0.702
[3]
0.142
[4]
0.028
[5]
0.431
[6]
0.773
[43] array · 8 items
[0]
Eosinophils
[1]
Correlation
[2]
−0.016
[3]
0.305**
[4]
−0.182
[5]
0.008
[6]
−0.291
[7]
−0.017
[44] array · 7 items
[0]
p
[1]
0.913
[2]
0.001
[3]
0.093
[4]
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Neutrophils
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Correlation
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0.106
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0.725
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Known mechanistic roles of TMEM106A in other cancers.
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34
section_title
TMEM106A as an Independent Prognostic Marker in Glioma: Context‐Dependent Biology Divergent From Other Cancers
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TABLE 3
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Known mechanistic roles of TMEM106A in other cancers.
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[0] array · 4 items
[0]
Cancer type
[1]
Experimental Findings (Mechanistic Insights)
[2]
Functional
[3]
Ref
[1] array · 4 items
[0]
Non–Small Cell Lung Cancer (NSCLC)
[1]
TMEM106A is downregulated in NSCLC. Overexpression reduces proliferation, migration, invasion, and induces apoptosis. TMEM106A also reverses EMT (↑E‐cadherin, ↓N‐cadherin, and vimentin) and inhibits the PI3K–Akt–NFκB pathway.
[2]
Tumor suppressor (inhibits growth and EMT)
[3]
[29]
[2] array · 4 items
[0]
Gastric cancer
[1]
Silencing via promoter hypermethylation renders TMEM106A absent or low in tumors. Restoring TMEM106A suppresses growth, induces apoptosis, and slows the expansion of xenograft tumors. Re‐expression triggers the activation of caspase‐2, −9, and −3, as well as BID cleavage, leading to PARP inactivation. Approximately 89% of GCs exhibit TMEM106A methylation, which correlates with metastasis.
[2]
Tumor suppressor (pro‐apoptotic, epigenetically silenced)
[3]
[30]
[3] array · 4 items
[0]
Renal cell carcinoma (RCC)
[1]
TMEM106A is downregulated in RCC. Overexpression slows proliferation and migration while inducing caspase–3–dependent apoptosis. Knockdown in normal cells boosts colony formation. TMEM106A thus acts as a tumor suppressor in RCC.
[2]
Tumor suppressor (restricts proliferation & survival)
[3]
[31]
[4] array · 4 items
[0]
Hepatocellular carcinoma (HCC)
[1]
TMEM106A is markedly downregulated (often via promoter methylation). Highly metastatic HCC cells exhibit lower TMEM106A levels, and these low levels predict poor postoperative survival. Re‐expression inhibits migration, invasion, and lung metastases, functioning as an anti‐metastatic suppressor.
[2]
Tumor suppressor
[3]
[32]
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section[34]/table-wrap[1]#cam471454-tbl-0003
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Overexpression reduces proliferation, migration, invasion, and induces apoptosis. TMEM106A also reverses EMT (↑E‐cadherin, ↓N‐cadherin, and vimentin) and inhibits the PI3K–Akt–NFκB pathway.", "Tumor suppressor (inhibits growth and EMT)", "[29]"], ["Gastric cancer", "Silencing via promoter hypermethylation renders TMEM106A absent or low in tumors. Restoring TMEM106A suppresses growth, induces apoptosis, and slows the expansion of xenograft tumors. Re‐expression triggers the activation of caspase‐2, −9, and −3, as well as BID cleavage, leading to PARP inactivation. Approximately 89% of GCs exhibit TMEM106A methylation, which correlates with metastasis.", "Tumor suppressor (pro‐apoptotic, epigenetically silenced)", "[30]"], ["Renal cell carcinoma (RCC)", "TMEM106A is downregulated in RCC. Overexpression slows proliferation and migration while inducing caspase–3–dependent apoptosis. Knockdown in normal cells boosts colony formation. TMEM106A thus acts as a tumor suppressor in RCC.", "Tumor suppressor (restricts proliferation & survival)", "[31]"], ["Hepatocellular carcinoma (HCC)", "TMEM106A is markedly downregulated (often via promoter methylation). Highly metastatic HCC cells exhibit lower TMEM106A levels, and these low levels predict poor postoperative survival. Re‐expression inhibits migration, invasion, and lung metastases, functioning as an anti‐metastatic suppressor.", "Tumor suppressor", "[32]"]], "row_count": 5, "column_count": 4, "numeric_cells": 8, "header_rows": 1, "locator": "section[34]/table-wrap[1]#cam471454-tbl-0003"}}], "gaps": ["asset:source:pmid:41354084 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41354084", "asset:table:pmid:41354084:1", "asset:table:pmid:41354084:2", "asset:table:pmid:41354084:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41354084"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:3c1b1d9adad17e270c93286d7a8f27b04dd4e96752ead8d1711a82ae503f011d", "type": "sep_package", "label": "SEP v1 package for pmid:41354084"}], "activities": [{"id": "activity:conversion:pmid:41354084", "type": "conversion", "used": ["package:3c1b1d9adad17e270c93286d7a8f27b04dd4e96752ead8d1711a82ae503f011d"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41354084", "parent_hash": "sha256:b4da7963f57f005eca0117b25c6d619549e3f21b97774d2f15778763d27bbe01", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:41354084 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "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:41354084' does not resolve to a declared asset", "targets"]}