Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:31198787

TROAP Promotes Breast Cancer Proliferation and Metastasis.

Kai Li · Ruo Zhang · Minjie Wei · Li Zhao · Yu Wang · Xinxin Feng · Yongheng Yang · Shucai Yang · Lei Zhang

BioMed research international · 2019 doi:10.1155/2019/6140951

Paper

complete

Experiment

complete

Data

partial

Analysis

partial

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:31198787
kind
science-record
content_hash
sha256:42ea5d863304daa87072d24a67f248d3db8a51d58d98e5099fbf22d3a30be6bc
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:46Z
updated_at
2026-11-01T22:00:37Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
TROAP Promotes Breast Cancer Proliferation and Metastasis.
doi
10.1155/2019/6140951
pmid
31198787
authors array · 9 items
[0]
Kai Li
[1]
Ruo Zhang
[2]
Minjie Wei
[3]
Li Zhao
[4]
Yu Wang
[5]
Xinxin Feng
[6]
Yongheng Yang
[7]
Shucai Yang
[8]
Lei Zhang
journal
BioMed research international
year
2019
abstract
Trophinin-associated protein (TROAP) is a cytoplasmic protein required for microtubular cytoskeleton regulation and spindle assembly, and its expression plays a critical role in the initiation and progression of various types of cancer. However, little is known about the role of TROAP in breast cancer (BC). TROAP mRNA expression levels and clinical data from Gene Expression Omnibus (GEO) datasets (GSE42568, 104 BC patients; GSE1456, 159 BC patients; and GSE21653, 266 BC patients) were analyzed by the R2: Genomics Analysis and Visualization Platform to estimate overall survival (OS). We also analyzed the genes correlated with TROAP by gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to predict potential relationships between TROAP and other genes in BC. Our study verified that both TROAP mRNA and protein expression levels were upregulated in human BC samples and cell lines. In vitro experiments demonstrated that TROAP knockdown significantly inhibited cell proliferation, the G1 to S phase transition, and the migration and invasion abilities of BC cells. The present study suggests that TROAP plays an important role in promoting the proliferation, invasion, and metastasis of BC.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Our study estimated survival with the Kaplan-Meier method based on data from three GEO datasets, evaluated TROAP mRNA levels in BC and noncancerous tissues, and analyzed the different molecular subtypes of BC in TCGA datasets.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:31198787
locator
sections[4] "2.2. Database Analysis" paragraph 2
quote
Our study estimated survival with the Kaplan-Meier method based on data from three GEO datasets, evaluated TROAP mRNA levels in BC and noncancerous tissues, and analyzed the different molecular subtypes of BC in TCGA datasets.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The data used to support the findings of this study are included within the article.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:31198787
locator
sections[23] "Data Availability" paragraph 2
quote
The data used to support the findings of this study are included within the article.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:31198787
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
complete
blocked_on
null
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE1456
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the published analysis
kind
analysis
state
complete
blocked_on
null
description
Apply the paper's statistical method to the resolved series and compare the result with the published target.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE1456
outputs array · 1 item
[0]
the replicated result and its comparison
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
state
partial
assets array · 4 items
[0] object · 15 fields
id
source:pmid:31198787
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1155/2019/6140951
sha256
sha256:2a6340db05fdbfbd3946eb2be9720fa40f249994821a401062e5a2a7f00a4d4c
bytes
22853
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1155/2019/6140951
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC6526557
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE1456
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1456
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE1456
version
null
note
The data used to support the findings of this study are included within the article.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data used to support the findings of this study are included within the article.
access_statement_kind
data_availability_statement
sample_accessions array · 318 items
[0]
GSM107072
[1]
GSM107073
[2]
GSM107074
[3]
GSM107075
[4]
GSM107076
[5]
GSM107077
[6]
GSM107078
[7]
GSM107079
[8]
GSM107080
[9]
GSM107081
[10]
GSM107082
[11]
GSM107083
[12]
GSM107084
[13]
GSM107085
[14]
GSM107086
[15]
GSM107087
[16]
GSM107088
[17]
GSM107089
[18]
GSM107090
[19]
GSM107091
[20]
GSM107092
[21]
GSM107093
[22]
GSM107094
[23]
GSM107095
[24]
GSM107096
[25]
GSM107097
[26]
GSM107098
[27]
GSM107099
[28]
GSM107100
[29]
GSM107101
[30]
GSM107102
[31]
GSM107103
[32]
GSM107104
[33]
GSM107105
[34]
GSM107106
[35]
GSM107107
[36]
GSM107108
[37]
GSM107109
[38]
GSM107110
[39]
GSM107111
[40]
GSM107112
[41]
GSM107113
[42]
GSM107114
[43]
GSM107115
[44]
GSM107117
[45]
GSM107118
[46]
GSM107119
[47]
GSM107120
[48]
GSM107121
[49]
GSM107122
[50]
GSM107123
[51]
GSM107124
[52]
GSM107125
[53]
GSM107126
[54]
GSM107127
[55]
GSM107128
[56]
GSM107129
[57]
GSM107130
[58]
GSM107131
[59]
GSM107132
[60]
GSM107133
[61]
GSM107134
[62]
GSM107135
[63]
GSM107136
[64]
GSM107137
[65]
GSM107138
[66]
GSM107139
[67]
GSM107140
[68]
GSM107141
[69]
GSM107142
[70]
GSM107143
[71]
GSM107144
[72]
GSM107145
[73]
GSM107146
[74]
GSM107147
[75]
GSM107148
[76]
GSM107149
[77]
GSM107150
[78]
GSM107151
[79]
GSM107152
[80]
GSM107153
[81]
GSM107154
[82]
GSM107155
[83]
GSM107156
[84]
GSM107157
[85]
GSM107158
[86]
GSM107159
[87]
GSM107160
[88]
GSM107161
[89]
GSM107162
[90]
GSM107163
[91]
GSM107164
[92]
GSM107165
[93]
GSM107166
[94]
GSM107167
[95]
GSM107168
[96]
GSM107169
[97]
GSM107170
[98]
GSM107171
[99]
GSM107172
[100]
GSM107173
[101]
GSM107174
[102]
GSM107175
[103]
GSM107176
[104]
GSM107177
[105]
GSM107178
[106]
GSM107179
[107]
GSM107180
[108]
GSM107181
[109]
GSM107182
[110]
GSM107183
[111]
GSM107184
[112]
GSM107185
[113]
GSM107186
[114]
GSM107187
[115]
GSM107188
[116]
GSM107189
[117]
GSM107190
[118]
GSM107191
[119]
GSM107192
[120]
GSM107193
[121]
GSM107194
[122]
GSM107195
[123]
GSM107196
[124]
GSM107197
[125]
GSM107198
[126]
GSM107199
[127]
GSM107200
[128]
GSM107201
[129]
GSM107202
[130]
GSM107203
[131]
GSM107204
[132]
GSM107205
[133]
GSM107206
[134]
GSM107207
[135]
GSM107208
[136]
GSM107209
[137]
GSM107210
[138]
GSM107211
[139]
GSM107212
[140]
GSM107213
[141]
GSM107214
[142]
GSM107215
[143]
GSM107216
[144]
GSM107217
[145]
GSM107218
[146]
GSM107219
[147]
GSM107220
[148]
GSM107221
[149]
GSM107222
[150]
GSM107223
[151]
GSM107224
[152]
GSM107225
[153]
GSM107226
[154]
GSM107227
[155]
GSM107228
[156]
GSM107229
[157]
GSM107230
[158]
GSM107231
[159]
GSM107232
[160]
GSM107233
[161]
GSM107234
[162]
GSM107235
[163]
GSM107236
[164]
GSM107237
[165]
GSM107238
[166]
GSM107239
[167]
GSM107240
[168]
GSM107241
[169]
GSM107242
[170]
GSM107243
[171]
GSM107244
[172]
GSM107245
[173]
GSM107246
[174]
GSM107247
[175]
GSM107248
[176]
GSM107249
[177]
GSM107250
[178]
GSM107251
[179]
GSM107252
[180]
GSM107253
[181]
GSM107254
[182]
GSM107255
[183]
GSM107256
[184]
GSM107257
[185]
GSM107258
[186]
GSM107259
[187]
GSM107260
[188]
GSM107261
[189]
GSM107262
[190]
GSM107263
[191]
GSM107264
[192]
GSM107265
[193]
GSM107266
[194]
GSM107267
[195]
GSM107268
[196]
GSM107269
[197]
GSM107270
[198]
GSM107271
[199]
GSM107272
[200]
GSM107273
[201]
GSM107274
[202]
GSM107275
[203]
GSM107276
[204]
GSM107277
[205]
GSM107278
[206]
GSM107279
[207]
GSM107280
[208]
GSM107281
[209]
GSM107282
[210]
GSM107283
[211]
GSM107284
[212]
GSM107285
[213]
GSM107286
[214]
GSM107287
[215]
GSM107288
[216]
GSM107289
[217]
GSM107290
[218]
GSM107291
[219]
GSM107292
[220]
GSM107293
[221]
GSM107294
[222]
GSM107295
[223]
GSM107296
[224]
GSM107297
[225]
GSM107298
[226]
GSM107299
[227]
GSM107300
[228]
GSM107301
[229]
GSM107302
[230]
GSM107303
[231]
GSM107304
[232]
GSM107305
[233]
GSM107306
[234]
GSM107307
[235]
GSM107308
[236]
GSM107309
[237]
GSM107310
[238]
GSM107311
[239]
GSM107312
[240]
GSM107313
[241]
GSM107314
[242]
GSM107315
[243]
GSM107316
[244]
GSM107317
[245]
GSM107318
[246]
GSM107319
[247]
GSM107320
[248]
GSM107321
[249]
GSM107322
[250]
GSM107323
[251]
GSM107324
[252]
GSM107325
[253]
GSM107326
[254]
GSM107327
[255]
GSM107328
[256]
GSM107329
[257]
GSM107330
[258]
GSM107331
[259]
GSM107332
[260]
GSM107333
[261]
GSM107334
[262]
GSM107335
[263]
GSM107336
[264]
GSM107337
[265]
GSM107338
[266]
GSM107339
[267]
GSM107340
[268]
GSM107341
[269]
GSM107342
[270]
GSM107343
[271]
GSM107344
[272]
GSM107345
[273]
GSM107346
[274]
GSM107347
[275]
GSM107348
[276]
GSM107349
[277]
GSM107350
[278]
GSM107351
[279]
GSM107352
[280]
GSM107353
[281]
GSM107354
[282]
GSM107355
[283]
GSM107356
[284]
GSM107357
[285]
GSM107358
[286]
GSM107359
[287]
GSM107360
[288]
GSM107361
[289]
GSM107362
[290]
GSM107363
[291]
GSM107364
[292]
GSM107365
[293]
GSM107366
[294]
GSM107367
[295]
GSM107368
[296]
GSM107369
[297]
GSM107370
[298]
GSM107371
[299]
GSM107372
[300]
GSM107373
[301]
GSM107374
[302]
GSM107375
[303]
GSM107376
[304]
GSM107377
[305]
GSM107378
[306]
GSM107379
[307]
GSM107380
[308]
GSM107381
[309]
GSM107382
[310]
GSM107383
[311]
GSM107384
[312]
GSM107385
[313]
GSM107386
[314]
GSM107387
[315]
GSM107388
[316]
GSM107389
[317]
GSM107390
sample_count
318
group_sizes
null
group_sizes_basis
null
platform
96;97
taxon
Homo sapiens
title
Gene expression of breast cancer tissue in a large population-based cohort of Swedish patients
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE21653
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21653
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE21653
version
null
note
The data used to support the findings of this study are included within the article.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data used to support the findings of this study are included within the article.
access_statement_kind
data_availability_statement
sample_accessions array · 266 items
[0]
GSM540108
[1]
GSM540109
[2]
GSM540110
[3]
GSM540111
[4]
GSM540112
[5]
GSM540113
[6]
GSM540114
[7]
GSM540115
[8]
GSM540116
[9]
GSM540117
[10]
GSM540118
[11]
GSM540119
[12]
GSM540120
[13]
GSM540121
[14]
GSM540122
[15]
GSM540123
[16]
GSM540124
[17]
GSM540125
[18]
GSM540126
[19]
GSM540127
[20]
GSM540128
[21]
GSM540129
[22]
GSM540130
[23]
GSM540131
[24]
GSM540132
[25]
GSM540133
[26]
GSM540134
[27]
GSM540135
[28]
GSM540136
[29]
GSM540137
[30]
GSM540138
[31]
GSM540139
[32]
GSM540140
[33]
GSM540141
[34]
GSM540142
[35]
GSM540143
[36]
GSM540144
[37]
GSM540145
[38]
GSM540146
[39]
GSM540147
[40]
GSM540148
[41]
GSM540149
[42]
GSM540150
[43]
GSM540151
[44]
GSM540152
[45]
GSM540153
[46]
GSM540154
[47]
GSM540155
[48]
GSM540156
[49]
GSM540157
[50]
GSM540158
[51]
GSM540159
[52]
GSM540160
[53]
GSM540161
[54]
GSM540162
[55]
GSM540163
[56]
GSM540164
[57]
GSM540165
[58]
GSM540166
[59]
GSM540167
[60]
GSM540168
[61]
GSM540169
[62]
GSM540170
[63]
GSM540171
[64]
GSM540172
[65]
GSM540173
[66]
GSM540174
[67]
GSM540175
[68]
GSM540176
[69]
GSM540177
[70]
GSM540178
[71]
GSM540179
[72]
GSM540180
[73]
GSM540181
[74]
GSM540182
[75]
GSM540183
[76]
GSM540184
[77]
GSM540185
[78]
GSM540186
[79]
GSM540187
[80]
GSM540188
[81]
GSM540189
[82]
GSM540190
[83]
GSM540191
[84]
GSM540192
[85]
GSM540193
[86]
GSM540194
[87]
GSM540195
[88]
GSM540196
[89]
GSM540197
[90]
GSM540198
[91]
GSM540199
[92]
GSM540200
[93]
GSM540201
[94]
GSM540202
[95]
GSM540203
[96]
GSM540204
[97]
GSM540205
[98]
GSM540206
[99]
GSM540207
[100]
GSM540208
[101]
GSM540209
[102]
GSM540210
[103]
GSM540211
[104]
GSM540212
[105]
GSM540213
[106]
GSM540214
[107]
GSM540215
[108]
GSM540216
[109]
GSM540217
[110]
GSM540218
[111]
GSM540219
[112]
GSM540220
[113]
GSM540221
[114]
GSM540222
[115]
GSM540223
[116]
GSM540224
[117]
GSM540225
[118]
GSM540226
[119]
GSM540227
[120]
GSM540228
[121]
GSM540229
[122]
GSM540230
[123]
GSM540231
[124]
GSM540232
[125]
GSM540233
[126]
GSM540234
[127]
GSM540235
[128]
GSM540236
[129]
GSM540237
[130]
GSM540238
[131]
GSM540239
[132]
GSM540240
[133]
GSM540241
[134]
GSM540242
[135]
GSM540243
[136]
GSM540244
[137]
GSM540245
[138]
GSM540246
[139]
GSM540247
[140]
GSM540248
[141]
GSM540249
[142]
GSM540250
[143]
GSM540251
[144]
GSM540252
[145]
GSM540253
[146]
GSM540254
[147]
GSM540255
[148]
GSM540256
[149]
GSM540257
[150]
GSM540258
[151]
GSM540259
[152]
GSM540260
[153]
GSM540261
[154]
GSM540262
[155]
GSM540263
[156]
GSM540264
[157]
GSM540265
[158]
GSM540266
[159]
GSM540267
[160]
GSM540268
[161]
GSM540269
[162]
GSM540270
[163]
GSM540271
[164]
GSM540272
[165]
GSM540273
[166]
GSM540274
[167]
GSM540275
[168]
GSM540276
[169]
GSM540277
[170]
GSM540278
[171]
GSM540279
[172]
GSM540280
[173]
GSM540281
[174]
GSM540282
[175]
GSM540283
[176]
GSM540284
[177]
GSM540285
[178]
GSM540286
[179]
GSM540287
[180]
GSM540288
[181]
GSM540289
[182]
GSM540290
[183]
GSM540291
[184]
GSM540292
[185]
GSM540293
[186]
GSM540294
[187]
GSM540295
[188]
GSM540296
[189]
GSM540297
[190]
GSM540298
[191]
GSM540299
[192]
GSM540300
[193]
GSM540301
[194]
GSM540302
[195]
GSM540303
[196]
GSM540304
[197]
GSM540305
[198]
GSM540306
[199]
GSM540307
[200]
GSM540308
[201]
GSM540309
[202]
GSM540310
[203]
GSM540311
[204]
GSM540312
[205]
GSM540313
[206]
GSM540314
[207]
GSM540315
[208]
GSM540316
[209]
GSM540317
[210]
GSM540318
[211]
GSM540319
[212]
GSM540320
[213]
GSM540321
[214]
GSM540322
[215]
GSM540323
[216]
GSM540324
[217]
GSM540325
[218]
GSM540326
[219]
GSM540327
[220]
GSM540328
[221]
GSM540329
[222]
GSM540330
[223]
GSM540331
[224]
GSM540332
[225]
GSM540333
[226]
GSM540334
[227]
GSM540335
[228]
GSM540336
[229]
GSM540337
[230]
GSM540338
[231]
GSM540339
[232]
GSM540340
[233]
GSM540341
[234]
GSM540342
[235]
GSM540343
[236]
GSM540344
[237]
GSM540345
[238]
GSM540346
[239]
GSM540347
[240]
GSM540348
[241]
GSM540349
[242]
GSM540350
[243]
GSM540351
[244]
GSM540352
[245]
GSM540353
[246]
GSM540354
[247]
GSM540355
[248]
GSM540356
[249]
GSM540357
[250]
GSM540358
[251]
GSM540359
[252]
GSM540360
[253]
GSM540361
[254]
GSM540362
[255]
GSM540363
[256]
GSM540364
[257]
GSM540365
[258]
GSM540366
[259]
GSM540367
[260]
GSM540368
[261]
GSM540369
[262]
GSM540370
[263]
GSM540371
[264]
GSM540372
[265]
GSM540373
sample_count
266
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
A gene expression signature identifies two prognostic subgroups of basal breast cancer
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 15 fields
id
data:geo:GSE42568
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE42568
version
null
note
The data used to support the findings of this study are included within the article.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data used to support the findings of this study are included within the article.
access_statement_kind
data_availability_statement
sample_accessions array · 121 items
[0]
GSM1045191
[1]
GSM1045192
[2]
GSM1045193
[3]
GSM1045194
[4]
GSM1045195
[5]
GSM1045196
[6]
GSM1045197
[7]
GSM1045198
[8]
GSM1045199
[9]
GSM1045200
[10]
GSM1045201
[11]
GSM1045202
[12]
GSM1045203
[13]
GSM1045204
[14]
GSM1045205
[15]
GSM1045206
[16]
GSM1045207
[17]
GSM1045208
[18]
GSM1045209
[19]
GSM1045210
[20]
GSM1045211
[21]
GSM1045212
[22]
GSM1045213
[23]
GSM1045214
[24]
GSM1045215
[25]
GSM1045216
[26]
GSM1045217
[27]
GSM1045218
[28]
GSM1045219
[29]
GSM1045220
[30]
GSM1045221
[31]
GSM1045222
[32]
GSM1045223
[33]
GSM1045224
[34]
GSM1045225
[35]
GSM1045226
[36]
GSM1045227
[37]
GSM1045228
[38]
GSM1045229
[39]
GSM1045230
[40]
GSM1045231
[41]
GSM1045232
[42]
GSM1045233
[43]
GSM1045234
[44]
GSM1045235
[45]
GSM1045236
[46]
GSM1045237
[47]
GSM1045238
[48]
GSM1045239
[49]
GSM1045240
[50]
GSM1045241
[51]
GSM1045242
[52]
GSM1045243
[53]
GSM1045244
[54]
GSM1045245
[55]
GSM1045246
[56]
GSM1045247
[57]
GSM1045248
[58]
GSM1045249
[59]
GSM1045250
[60]
GSM1045251
[61]
GSM1045252
[62]
GSM1045253
[63]
GSM1045254
[64]
GSM1045255
[65]
GSM1045256
[66]
GSM1045257
[67]
GSM1045258
[68]
GSM1045259
[69]
GSM1045260
[70]
GSM1045261
[71]
GSM1045262
[72]
GSM1045263
[73]
GSM1045264
[74]
GSM1045265
[75]
GSM1045266
[76]
GSM1045267
[77]
GSM1045268
[78]
GSM1045269
[79]
GSM1045270
[80]
GSM1045271
[81]
GSM1045272
[82]
GSM1045273
[83]
GSM1045274
[84]
GSM1045275
[85]
GSM1045276
[86]
GSM1045277
[87]
GSM1045278
[88]
GSM1045279
[89]
GSM1045280
[90]
GSM1045281
[91]
GSM1045282
[92]
GSM1045283
[93]
GSM1045284
[94]
GSM1045285
[95]
GSM1045286
[96]
GSM1045287
[97]
GSM1045288
[98]
GSM1045289
[99]
GSM1045290
[100]
GSM1045291
[101]
GSM1045292
[102]
GSM1045293
[103]
GSM1045294
[104]
GSM1045295
[105]
GSM1045296
[106]
GSM1045297
[107]
GSM1045298
[108]
GSM1045299
[109]
GSM1045300
[110]
GSM1045301
[111]
GSM1045302
[112]
GSM1045303
[113]
GSM1045304
[114]
GSM1045305
[115]
GSM1045306
[116]
GSM1045307
[117]
GSM1045308
[118]
GSM1045309
[119]
GSM1045310
[120]
GSM1045311
sample_count
121
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Breast Cancer Gene Expression Analysis
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 6 items
[0]
asset:data:geo:GSE1456 not downloaded
[1]
asset:data:geo:GSE1456 licence not read
[2]
asset:data:geo:GSE21653 not downloaded
[3]
asset:data:geo:GSE21653 licence not read
[4]
asset:data:geo:GSE42568 not downloaded
[5]
asset:data:geo:GSE42568 licence not read
analysis object · 4 fields
state
partial
methods array · 3 items
[0] object · 10 fields
id
method-1
family
survival_analysis
specific
kaplan_meier
label
Survival analysis
dsl_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
1
band
verbatim
quote
Our study estimated survival with the Kaplan-Meier method based on data from three GEO datasets, evaluated TROAP mRNA levels in BC and noncancerous tissues, and analyzed the different molecular subtypes of BC in TCGA datasets.
[1] object · 10 fields
id
method-2
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
analysis of variance
[2] object · 10 fields
id
method-3
family
correlation_analysis
specific
pearson
label
Correlation analysis
dsl_operations array · 1 item
[0]
pearson_r
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
paired_numeric_columns
evidence object · 3 fields
score
0.8
band
high
quote
Pearson's correlation
targets array · 0 items
gaps array · 1 item
[0]
method.reader_differs_from_extractor
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 3 items
[0]
GSE42568
[1]
GSE1456
[2]
GSE21653
resolved_accessions array · 3 items
[0]
GSE42568
[1]
GSE1456
[2]
GSE21653
statements array · 1 item
[0]
The data used to support the findings of this study are included within the article.
basis
The paper names GSE42568, GSE1456, GSE21653 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
survival_km
assets array · 2 items
[0]
source:pmid:31198787
[1]
data:geo:GSE1456
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE1456
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:15:01Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
18848
completion_tokens
1468
cached_tokens
640
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
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 · 3 items
[0] object · 3 fields
id
pmid:31198787
type
paper
label
pmid:31198787
[1] object · 3 fields
id
source:pmid:31198787
type
manuscript
label
PMID 31198787 full text
[2] object · 3 fields
id
data:geo:GSE1456
type
dataset
label
GEO GSE1456
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:31198787
type
paper
label
pmid:31198787
[1] object · 3 fields
id
source:pmid:31198787
type
manuscript
label
PMID 31198787 full text
[2] object · 3 fields
id
data:geo:GSE1456
type
dataset
label
GEO GSE1456
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-31198787
type
extraction
used array · 1 item
[0]
source:pmid:31198787
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE1456
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE1456
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:31198787
parent_hash
sha256:59718975625cf3994dbc3717cb5c0703beeb9f19bf22fcd74b4471242d140243
fork_of
null
gaps array · 11 items
[0]
asset:data:geo:GSE1456 licence not read
[1]
asset:data:geo:GSE1456 not downloaded
[2]
asset:data:geo:GSE21653 licence not read
[3]
asset:data:geo:GSE21653 not downloaded
[4]
asset:data:geo:GSE42568 licence not read
[5]
asset:data:geo:GSE42568 not downloaded
[6]
execution.not_run
[7]
method.reader_differs_from_extractor
[8]
review.human_critique
[9]
review.independent_reader
[10]
review.machine_critique
assays array · 4 items
[0] object · 11 fields
role
data_generation
definition_id
transfection
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.85
evidence array · 1 item
[0]
In vitro experiments demonstrated that TROAP knockdown significantly inhibited cell proliferation,
order_basis
paper_text_order:995
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
cell_culture
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
ty Cancer Hospital (Harbin, P.R. China). All cell lines were cultured at 37°C in a humidified atmosphere with 5% C
[1]
ied atmosphere with 5% CO2. MCF-7 cells were cultured in MEM; MDA-MB-231 and MDA-MB-468 cells were cu
[2]
in MEM; MDA-MB-231 and MDA-MB-468 cells were cultured in L-15 medium supplemented with 10% fetal bovi
[3]
ial amino acids (1%); and MCF-10A cells were cultured in DMEM/F12 medium supplemented with 5% horse s
order_basis
paper_text_order:1376
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
rna_seq
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
ssues and controls were evaluated by t-test. RNA-sequencing data were downloaded from the GEO database (
order_basis
paper_text_order:2419
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
survival_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
survival_km
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Our study estimated survival with the Kaplan-Meier method based on data from three GEO datasets, evaluated TROAP mRNA levels in BC and noncancerous tissues, and analyzed the different molecular subtypes of BC in TCGA datasets.
order_basis
consumes_earlier_output
id
assay:4
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31198787", "kind": "science-record", "revision": 7, "content_hash": "sha256:42ea5d863304daa87072d24a67f248d3db8a51d58d98e5099fbf22d3a30be6bc", "created_at": "2026-11-01T15:40:46Z", "updated_at": "2026-11-01T22:00:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "TROAP Promotes Breast Cancer Proliferation and Metastasis.", "doi": "10.1155/2019/6140951", "pmid": "31198787", "authors": ["Kai Li", "Ruo Zhang", "Minjie Wei", "Li Zhao", "Yu Wang", "Xinxin Feng", "Yongheng Yang", "Shucai Yang", "Lei Zhang"], "journal": "BioMed research international", "year": 2019, "abstract": "Trophinin-associated protein (TROAP) is a cytoplasmic protein required for microtubular cytoskeleton regulation and spindle assembly, and its expression plays a critical role in the initiation and progression of various types of cancer. However, little is known about the role of TROAP in breast cancer (BC). TROAP mRNA expression levels and clinical data from Gene Expression Omnibus (GEO) datasets (GSE42568, 104 BC patients; GSE1456, 159 BC patients; and GSE21653, 266 BC patients) were analyzed by the R2: Genomics Analysis and Visualization Platform to estimate overall survival (OS). We also analyzed the genes correlated with TROAP by gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to predict potential relationships between TROAP and other genes in BC. Our study verified that both TROAP mRNA and protein expression levels were upregulated in human BC samples and cell lines. In vitro experiments demonstrated that TROAP knockdown significantly inhibited cell proliferation, the G1 to S phase transition, and the migration and invasion abilities of BC cells. The present study suggests that TROAP plays an important role in promoting the proliferation, invasion, and metastasis of BC.", "claims": [{"id": "claim-method", "statement": "Our study estimated survival with the Kaplan-Meier method based on data from three GEO datasets, evaluated TROAP mRNA levels in BC and noncancerous tissues, and analyzed the different molecular subtypes of BC in TCGA datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31198787", "locator": "sections[4] \"2.2. Database Analysis\" paragraph 2", "quote": "Our study estimated survival with the Kaplan-Meier method based on data from three GEO datasets, evaluated TROAP mRNA levels in BC and noncancerous tissues, and analyzed the different molecular subtypes of BC in TCGA datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31198787", "locator": "sections[23] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included within the article."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31198787"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE1456"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE1456"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31198787", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2019/6140951", "sha256": "sha256:2a6340db05fdbfbd3946eb2be9720fa40f249994821a401062e5a2a7f00a4d4c", "bytes": 22853, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2019/6140951", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6526557", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE1456", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1456", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1456", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM107072", "GSM107073", "GSM107074", "GSM107075", "GSM107076", "GSM107077", "GSM107078", "GSM107079", "GSM107080", "GSM107081", "GSM107082", "GSM107083", "GSM107084", "GSM107085", "GSM107086", "GSM107087", "GSM107088", "GSM107089", "GSM107090", "GSM107091", "GSM107092", "GSM107093", "GSM107094", "GSM107095", "GSM107096", "GSM107097", "GSM107098", "GSM107099", "GSM107100", "GSM107101", "GSM107102", "GSM107103", "GSM107104", "GSM107105", "GSM107106", "GSM107107", "GSM107108", "GSM107109", "GSM107110", "GSM107111", "GSM107112", "GSM107113", "GSM107114", "GSM107115", "GSM107117", "GSM107118", "GSM107119", "GSM107120", "GSM107121", "GSM107122", "GSM107123", "GSM107124", "GSM107125", "GSM107126", "GSM107127", "GSM107128", "GSM107129", "GSM107130", "GSM107131", "GSM107132", "GSM107133", "GSM107134", "GSM107135", "GSM107136", "GSM107137", "GSM107138", "GSM107139", "GSM107140", "GSM107141", "GSM107142", "GSM107143", "GSM107144", "GSM107145", "GSM107146", "GSM107147", "GSM107148", "GSM107149", "GSM107150", "GSM107151", "GSM107152", "GSM107153", "GSM107154", "GSM107155", "GSM107156", "GSM107157", "GSM107158", "GSM107159", "GSM107160", "GSM107161", "GSM107162", "GSM107163", "GSM107164", "GSM107165", "GSM107166", "GSM107167", "GSM107168", "GSM107169", "GSM107170", "GSM107171", "GSM107172", "GSM107173", "GSM107174", "GSM107175", "GSM107176", "GSM107177", "GSM107178", "GSM107179", "GSM107180", "GSM107181", "GSM107182", "GSM107183", "GSM107184", "GSM107185", "GSM107186", "GSM107187", "GSM107188", "GSM107189", "GSM107190", "GSM107191", "GSM107192", "GSM107193", "GSM107194", "GSM107195", "GSM107196", "GSM107197", "GSM107198", "GSM107199", "GSM107200", "GSM107201", "GSM107202", "GSM107203", "GSM107204", "GSM107205", "GSM107206", "GSM107207", "GSM107208", "GSM107209", "GSM107210", "GSM107211", "GSM107212", "GSM107213", "GSM107214", "GSM107215", "GSM107216", "GSM107217", "GSM107218", "GSM107219", "GSM107220", "GSM107221", "GSM107222", "GSM107223", "GSM107224", "GSM107225", "GSM107226", "GSM107227", "GSM107228", "GSM107229", "GSM107230", "GSM107231", "GSM107232", "GSM107233", "GSM107234", "GSM107235", "GSM107236", "GSM107237", "GSM107238", "GSM107239", "GSM107240", "GSM107241", "GSM107242", "GSM107243", "GSM107244", "GSM107245", "GSM107246", "GSM107247", "GSM107248", "GSM107249", "GSM107250", "GSM107251", "GSM107252", "GSM107253", "GSM107254", "GSM107255", "GSM107256", "GSM107257", "GSM107258", "GSM107259", "GSM107260", "GSM107261", "GSM107262", "GSM107263", "GSM107264", "GSM107265", "GSM107266", "GSM107267", "GSM107268", "GSM107269", "GSM107270", "GSM107271", "GSM107272", "GSM107273", "GSM107274", "GSM107275", "GSM107276", "GSM107277", "GSM107278", "GSM107279", "GSM107280", "GSM107281", "GSM107282", "GSM107283", "GSM107284", "GSM107285", "GSM107286", "GSM107287", "GSM107288", "GSM107289", "GSM107290", "GSM107291", "GSM107292", "GSM107293", "GSM107294", "GSM107295", "GSM107296", "GSM107297", "GSM107298", "GSM107299", "GSM107300", "GSM107301", "GSM107302", "GSM107303", "GSM107304", "GSM107305", "GSM107306", "GSM107307", "GSM107308", "GSM107309", "GSM107310", "GSM107311", "GSM107312", "GSM107313", "GSM107314", "GSM107315", "GSM107316", "GSM107317", "GSM107318", "GSM107319", "GSM107320", "GSM107321", "GSM107322", "GSM107323", "GSM107324", "GSM107325", "GSM107326", "GSM107327", "GSM107328", "GSM107329", "GSM107330", "GSM107331", "GSM107332", "GSM107333", "GSM107334", "GSM107335", "GSM107336", "GSM107337", "GSM107338", "GSM107339", "GSM107340", "GSM107341", "GSM107342", "GSM107343", "GSM107344", "GSM107345", "GSM107346", "GSM107347", "GSM107348", "GSM107349", "GSM107350", "GSM107351", "GSM107352", "GSM107353", "GSM107354", "GSM107355", "GSM107356", "GSM107357", "GSM107358", "GSM107359", "GSM107360", "GSM107361", "GSM107362", "GSM107363", "GSM107364", "GSM107365", "GSM107366", "GSM107367", "GSM107368", "GSM107369", "GSM107370", "GSM107371", "GSM107372", "GSM107373", "GSM107374", "GSM107375", "GSM107376", "GSM107377", "GSM107378", "GSM107379", "GSM107380", "GSM107381", "GSM107382", "GSM107383", "GSM107384", "GSM107385", "GSM107386", "GSM107387", "GSM107388", "GSM107389", "GSM107390"], "sample_count": 318, "group_sizes": null, "group_sizes_basis": null, "platform": "96;97", "taxon": "Homo sapiens", "title": "Gene expression of breast cancer tissue in a large population-based cohort of Swedish patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE21653", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21653", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21653", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM540108", "GSM540109", "GSM540110", "GSM540111", "GSM540112", "GSM540113", "GSM540114", "GSM540115", "GSM540116", "GSM540117", "GSM540118", "GSM540119", "GSM540120", "GSM540121", "GSM540122", "GSM540123", "GSM540124", "GSM540125", "GSM540126", "GSM540127", "GSM540128", "GSM540129", "GSM540130", "GSM540131", "GSM540132", "GSM540133", "GSM540134", "GSM540135", "GSM540136", "GSM540137", "GSM540138", "GSM540139", "GSM540140", "GSM540141", "GSM540142", "GSM540143", "GSM540144", "GSM540145", "GSM540146", "GSM540147", "GSM540148", "GSM540149", "GSM540150", "GSM540151", "GSM540152", "GSM540153", "GSM540154", "GSM540155", "GSM540156", "GSM540157", "GSM540158", "GSM540159", "GSM540160", "GSM540161", "GSM540162", "GSM540163", "GSM540164", "GSM540165", "GSM540166", "GSM540167", "GSM540168", "GSM540169", "GSM540170", "GSM540171", "GSM540172", "GSM540173", "GSM540174", "GSM540175", "GSM540176", "GSM540177", "GSM540178", "GSM540179", "GSM540180", "GSM540181", "GSM540182", "GSM540183", "GSM540184", "GSM540185", "GSM540186", "GSM540187", "GSM540188", "GSM540189", "GSM540190", "GSM540191", "GSM540192", "GSM540193", "GSM540194", "GSM540195", "GSM540196", "GSM540197", "GSM540198", "GSM540199", "GSM540200", "GSM540201", "GSM540202", "GSM540203", "GSM540204", "GSM540205", "GSM540206", "GSM540207", "GSM540208", "GSM540209", "GSM540210", "GSM540211", "GSM540212", "GSM540213", "GSM540214", "GSM540215", "GSM540216", "GSM540217", "GSM540218", "GSM540219", "GSM540220", "GSM540221", "GSM540222", "GSM540223", "GSM540224", "GSM540225", "GSM540226", "GSM540227", "GSM540228", "GSM540229", "GSM540230", "GSM540231", "GSM540232", "GSM540233", "GSM540234", "GSM540235", "GSM540236", "GSM540237", "GSM540238", "GSM540239", "GSM540240", "GSM540241", "GSM540242", "GSM540243", "GSM540244", "GSM540245", "GSM540246", "GSM540247", "GSM540248", "GSM540249", "GSM540250", "GSM540251", "GSM540252", "GSM540253", "GSM540254", "GSM540255", "GSM540256", "GSM540257", "GSM540258", "GSM540259", "GSM540260", "GSM540261", "GSM540262", "GSM540263", "GSM540264", "GSM540265", "GSM540266", "GSM540267", "GSM540268", "GSM540269", "GSM540270", "GSM540271", "GSM540272", "GSM540273", "GSM540274", "GSM540275", "GSM540276", "GSM540277", "GSM540278", "GSM540279", "GSM540280", "GSM540281", "GSM540282", "GSM540283", "GSM540284", "GSM540285", "GSM540286", "GSM540287", "GSM540288", "GSM540289", "GSM540290", "GSM540291", "GSM540292", "GSM540293", "GSM540294", "GSM540295", "GSM540296", "GSM540297", "GSM540298", "GSM540299", "GSM540300", "GSM540301", "GSM540302", "GSM540303", "GSM540304", "GSM540305", "GSM540306", "GSM540307", "GSM540308", "GSM540309", "GSM540310", "GSM540311", "GSM540312", "GSM540313", "GSM540314", "GSM540315", "GSM540316", "GSM540317", "GSM540318", "GSM540319", "GSM540320", "GSM540321", "GSM540322", "GSM540323", "GSM540324", "GSM540325", "GSM540326", "GSM540327", "GSM540328", "GSM540329", "GSM540330", "GSM540331", "GSM540332", "GSM540333", "GSM540334", "GSM540335", "GSM540336", "GSM540337", "GSM540338", "GSM540339", "GSM540340", "GSM540341", "GSM540342", "GSM540343", "GSM540344", "GSM540345", "GSM540346", "GSM540347", "GSM540348", "GSM540349", "GSM540350", "GSM540351", "GSM540352", "GSM540353", "GSM540354", "GSM540355", "GSM540356", "GSM540357", "GSM540358", "GSM540359", "GSM540360", "GSM540361", "GSM540362", "GSM540363", "GSM540364", "GSM540365", "GSM540366", "GSM540367", "GSM540368", "GSM540369", "GSM540370", "GSM540371", "GSM540372", "GSM540373"], "sample_count": 266, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A gene expression signature identifies two prognostic subgroups of basal breast cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE42568", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42568", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1045191", "GSM1045192", "GSM1045193", "GSM1045194", "GSM1045195", "GSM1045196", "GSM1045197", "GSM1045198", "GSM1045199", "GSM1045200", "GSM1045201", "GSM1045202", "GSM1045203", "GSM1045204", "GSM1045205", "GSM1045206", "GSM1045207", "GSM1045208", "GSM1045209", "GSM1045210", "GSM1045211", "GSM1045212", "GSM1045213", "GSM1045214", "GSM1045215", "GSM1045216", "GSM1045217", "GSM1045218", "GSM1045219", "GSM1045220", "GSM1045221", "GSM1045222", "GSM1045223", "GSM1045224", "GSM1045225", "GSM1045226", "GSM1045227", "GSM1045228", "GSM1045229", "GSM1045230", "GSM1045231", "GSM1045232", "GSM1045233", "GSM1045234", "GSM1045235", "GSM1045236", "GSM1045237", "GSM1045238", "GSM1045239", "GSM1045240", "GSM1045241", "GSM1045242", "GSM1045243", "GSM1045244", "GSM1045245", "GSM1045246", "GSM1045247", "GSM1045248", "GSM1045249", "GSM1045250", "GSM1045251", "GSM1045252", "GSM1045253", "GSM1045254", "GSM1045255", "GSM1045256", "GSM1045257", "GSM1045258", "GSM1045259", "GSM1045260", "GSM1045261", "GSM1045262", "GSM1045263", "GSM1045264", "GSM1045265", "GSM1045266", "GSM1045267", "GSM1045268", "GSM1045269", "GSM1045270", "GSM1045271", "GSM1045272", "GSM1045273", "GSM1045274", "GSM1045275", "GSM1045276", "GSM1045277", "GSM1045278", "GSM1045279", "GSM1045280", "GSM1045281", "GSM1045282", "GSM1045283", "GSM1045284", "GSM1045285", "GSM1045286", "GSM1045287", "GSM1045288", "GSM1045289", "GSM1045290", "GSM1045291", "GSM1045292", "GSM1045293", "GSM1045294", "GSM1045295", "GSM1045296", "GSM1045297", "GSM1045298", "GSM1045299", "GSM1045300", "GSM1045301", "GSM1045302", "GSM1045303", "GSM1045304", "GSM1045305", "GSM1045306", "GSM1045307", "GSM1045308", "GSM1045309", "GSM1045310", "GSM1045311"], "sample_count": 121, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Breast Cancer Gene Expression Analysis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE1456 not downloaded", "asset:data:geo:GSE1456 licence not read", "asset:data:geo:GSE21653 not downloaded", "asset:data:geo:GSE21653 licence not read", "asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE42568 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Our study estimated survival with the Kaplan-Meier method based on data from three GEO datasets, evaluated TROAP mRNA levels in BC and noncancerous tissues, and analyzed the different molecular subtypes of BC in TCGA datasets."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson's correlation"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE42568", "GSE1456", "GSE21653"], "resolved_accessions": ["GSE42568", "GSE1456", "GSE21653"], "statements": ["The data used to support the findings of this study are included within the article."], "basis": "The paper names GSE42568, GSE1456, GSE21653 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:31198787", "data:geo:GSE1456"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE1456"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 18848, "completion_tokens": 1468, "cached_tokens": 640}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31198787", "type": "paper", "label": "pmid:31198787"}, {"id": "source:pmid:31198787", "type": "manuscript", "label": "PMID 31198787 full text"}, {"id": "data:geo:GSE1456", "type": "dataset", "label": "GEO GSE1456"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31198787", "type": "paper", "label": "pmid:31198787"}, {"id": "source:pmid:31198787", "type": "manuscript", "label": "PMID 31198787 full text"}, {"id": "data:geo:GSE1456", "type": "dataset", "label": "GEO GSE1456"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31198787", "type": "extraction", "used": ["source:pmid:31198787"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE1456", "type": "accession_resolution", "used": ["data:geo:GSE1456"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:31198787", "parent_hash": "sha256:59718975625cf3994dbc3717cb5c0703beeb9f19bf22fcd74b4471242d140243", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE1456 licence not read", "asset:data:geo:GSE1456 not downloaded", "asset:data:geo:GSE21653 licence not read", "asset:data:geo:GSE21653 not downloaded", "asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE42568 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["In vitro experiments demonstrated that TROAP knockdown significantly inhibited cell proliferation,"], "order_basis": "paper_text_order:995", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ty Cancer Hospital (Harbin, P.R. China). All cell lines were cultured at 37°C in a humidified atmosphere with 5% C", "ied atmosphere with 5% CO2. MCF-7 cells were cultured in MEM; MDA-MB-231 and MDA-MB-468 cells were cu", "in MEM; MDA-MB-231 and MDA-MB-468 cells were cultured in L-15 medium supplemented with 10% fetal bovi", "ial amino acids (1%); and MCF-10A cells were cultured in DMEM/F12 medium supplemented with 5% horse s"], "order_basis": "paper_text_order:1376", "id": "assay:2"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ssues and controls were evaluated by t-test. RNA-sequencing data were downloaded from the GEO database ("], "order_basis": "paper_text_order:2419", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Our study estimated survival with the Kaplan-Meier method based on data from three GEO datasets, evaluated TROAP mRNA levels in BC and noncancerous tissues, and analyzed the different molecular subtypes of BC in TCGA datasets."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}