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pmid:39434164

Comprehensive multi-omics integration uncovers mitochondrial gene signatures for prognosis and personalized therapy in lung adenocarcinoma.

Wenjia Zhang · Lei Zhao · Tiansheng Zheng · Lihong Fan · Kai Wang · Guoshu Li

Journal of translational medicine · 2024 doi:10.1186/s12967-024-05754-y

Paper

complete

Experiment

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Data

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Comprehensive multi-omics integration uncovers mitochondrial gene signatures for prognosis and personalized therapy in lung adenocarcinoma.
doi
10.1186/s12967-024-05754-y
pmid
39434164
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Wenjia Zhang
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Lei Zhao
[2]
Tiansheng Zheng
[3]
Lihong Fan
[4]
Kai Wang
[5]
Guoshu Li
journal
Journal of translational medicine
year
2024
abstract
The therapeutic efficacy of lung adenocarcinoma (LUAD), the most prevalent histological subtype of primary lung cancer, remains inadequate, with accurate prognostic assessment posing significant challenges. This study sought to elucidate the prognostic significance of mitochondrial-related genes in LUAD through an integrative multi-omics approach, aimed at developing personalized therapeutic strategies. Utilizing transcriptomic and single-cell RNA sequencing (scRNA-seq) data, alongside clinical information from publicly available databases, we first applied dimensionality reduction and clustering techniques to the LUAD single-cell dataset, focusing on the subclassification of fibroblasts, epithelial cells, and T cells. Mitochondrial-related prognostic genes were subsequently identified using TCGA-LUAD data, and LUAD cases were stratified into distinct molecular subtypes through consensus clustering, allowing for the exploration of gene expression profiles and clinical feature distributions across subtypes. By leveraging an ensemble of machine learning algorithms, we developed an Artificial Intelligence-Derived Prognostic Signature (AIDPS) model based on mitochondrial-related genes and validated its prognostic accuracy across multiple independent datasets. The AIDPS model demonstrated robust predictive power for LUAD patient outcomes, revealing significant differences in responses to immunotherapy and chemotherapy, as well as survival outcomes between risk groups. Furthermore, we conducted comprehensive analyses of tumor mutation burden (TMB), immune microenvironment characteristics, and genome-wide association study (GWAS) data, providing additional insights into the mechanistic roles of mitochondrial-related genes in LUAD pathogenesis. This study not only offers a novel approach to improving prognostic assessments in LUAD but also establishes a strong foundation for the development of personalized therapeutic interventions.
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Receiver Operating Characteristic (ROC) analysis was applied to evaluate the predictive performance of the Artificial Intelligence-Derived Prognostic Signature (AIDPS) across 12 datasets and a meta-cohort combining all samples.
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sections[18] "Evaluation of AIDPS model" paragraph 2
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Receiver Operating Characteristic (ROC) analysis was applied to evaluate the predictive performance of the Artificial Intelligence-Derived Prognostic Signature (AIDPS) across 12 datasets and a meta-cohort combining all samples.
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sections[38] "Data Availability Statement" paragraphs 1-3
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All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
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The AIDPS model, selected as Enet[a = 0.2], achieved the highest average C-index of 0.655 and showed superior performance across all validation datasets.
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The optimal model, Enet[a = 0.2], with a highest average C-index (0.655), exhibited superior performance across all validation datasets (Fig. 5A).
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identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[4] object · 15 fields
id
data:geo:GSE30219
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=GSE30219
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE30219
version
null
note
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
access_statement_kind
data_availability_statement
sample_accessions array · 307 items
[0]
GSM1465989
[1]
GSM1465990
[2]
GSM1465991
[3]
GSM1465992
[4]
GSM1465993
[5]
GSM1465994
[6]
GSM1465995
[7]
GSM1465996
[8]
GSM1465997
[9]
GSM1465998
[10]
GSM1465999
[11]
GSM748053
[12]
GSM748054
[13]
GSM748055
[14]
GSM748056
[15]
GSM748057
[16]
GSM748058
[17]
GSM748059
[18]
GSM748060
[19]
GSM748061
[20]
GSM748062
[21]
GSM748063
[22]
GSM748064
[23]
GSM748065
[24]
GSM748066
[25]
GSM748067
[26]
GSM748068
[27]
GSM748069
[28]
GSM748070
[29]
GSM748071
[30]
GSM748072
[31]
GSM748073
[32]
GSM748074
[33]
GSM748075
[34]
GSM748076
[35]
GSM748077
[36]
GSM748078
[37]
GSM748079
[38]
GSM748080
[39]
GSM748081
[40]
GSM748083
[41]
GSM748084
[42]
GSM748085
[43]
GSM748086
[44]
GSM748087
[45]
GSM748088
[46]
GSM748089
[47]
GSM748090
[48]
GSM748091
[49]
GSM748092
[50]
GSM748093
[51]
GSM748094
[52]
GSM748095
[53]
GSM748096
[54]
GSM748097
[55]
GSM748098
[56]
GSM748099
[57]
GSM748100
[58]
GSM748101
[59]
GSM748102
[60]
GSM748103
[61]
GSM748104
[62]
GSM748105
[63]
GSM748106
[64]
GSM748107
[65]
GSM748108
[66]
GSM748109
[67]
GSM748110
[68]
GSM748111
[69]
GSM748112
[70]
GSM748113
[71]
GSM748115
[72]
GSM748116
[73]
GSM748117
[74]
GSM748118
[75]
GSM748119
[76]
GSM748120
[77]
GSM748121
[78]
GSM748122
[79]
GSM748123
[80]
GSM748124
[81]
GSM748125
[82]
GSM748126
[83]
GSM748127
[84]
GSM748128
[85]
GSM748129
[86]
GSM748130
[87]
GSM748131
[88]
GSM748132
[89]
GSM748133
[90]
GSM748134
[91]
GSM748135
[92]
GSM748136
[93]
GSM748137
[94]
GSM748138
[95]
GSM748139
[96]
GSM748140
[97]
GSM748141
[98]
GSM748142
[99]
GSM748143
[100]
GSM748144
[101]
GSM748145
[102]
GSM748146
[103]
GSM748147
[104]
GSM748148
[105]
GSM748149
[106]
GSM748150
[107]
GSM748151
[108]
GSM748152
[109]
GSM748153
[110]
GSM748154
[111]
GSM748155
[112]
GSM748156
[113]
GSM748157
[114]
GSM748158
[115]
GSM748159
[116]
GSM748160
[117]
GSM748161
[118]
GSM748162
[119]
GSM748163
[120]
GSM748164
[121]
GSM748165
[122]
GSM748166
[123]
GSM748167
[124]
GSM748168
[125]
GSM748169
[126]
GSM748170
[127]
GSM748171
[128]
GSM748172
[129]
GSM748173
[130]
GSM748174
[131]
GSM748175
[132]
GSM748176
[133]
GSM748177
[134]
GSM748178
[135]
GSM748179
[136]
GSM748180
[137]
GSM748181
[138]
GSM748182
[139]
GSM748183
[140]
GSM748184
[141]
GSM748185
[142]
GSM748186
[143]
GSM748187
[144]
GSM748188
[145]
GSM748189
[146]
GSM748191
[147]
GSM748192
[148]
GSM748193
[149]
GSM748195
[150]
GSM748196
[151]
GSM748197
[152]
GSM748198
[153]
GSM748199
[154]
GSM748200
[155]
GSM748201
[156]
GSM748202
[157]
GSM748203
[158]
GSM748206
[159]
GSM748207
[160]
GSM748209
[161]
GSM748210
[162]
GSM748211
[163]
GSM748212
[164]
GSM748213
[165]
GSM748214
[166]
GSM748215
[167]
GSM748216
[168]
GSM748217
[169]
GSM748218
[170]
GSM748219
[171]
GSM748220
[172]
GSM748221
[173]
GSM748222
[174]
GSM748223
[175]
GSM748224
[176]
GSM748225
[177]
GSM748226
[178]
GSM748227
[179]
GSM748228
[180]
GSM748229
[181]
GSM748232
[182]
GSM748233
[183]
GSM748234
[184]
GSM748235
[185]
GSM748239
[186]
GSM748240
[187]
GSM748242
[188]
GSM748243
[189]
GSM748244
[190]
GSM748245
[191]
GSM748246
[192]
GSM748247
[193]
GSM748248
[194]
GSM748249
[195]
GSM748250
[196]
GSM748251
[197]
GSM748252
[198]
GSM748253
[199]
GSM748254
[200]
GSM748255
[201]
GSM748256
[202]
GSM748257
[203]
GSM748258
[204]
GSM748259
[205]
GSM748260
[206]
GSM748261
[207]
GSM748262
[208]
GSM748263
[209]
GSM748264
[210]
GSM748265
[211]
GSM748266
[212]
GSM748267
[213]
GSM748268
[214]
GSM748269
[215]
GSM748270
[216]
GSM748271
[217]
GSM748272
[218]
GSM748273
[219]
GSM748274
[220]
GSM748275
[221]
GSM748276
[222]
GSM748277
[223]
GSM748278
[224]
GSM748279
[225]
GSM748280
[226]
GSM748281
[227]
GSM748282
[228]
GSM748283
[229]
GSM748284
[230]
GSM748285
[231]
GSM748286
[232]
GSM748287
[233]
GSM748288
[234]
GSM748291
[235]
GSM748292
[236]
GSM748294
[237]
GSM748295
[238]
GSM748296
[239]
GSM748297
[240]
GSM748298
[241]
GSM748299
[242]
GSM748300
[243]
GSM748301
[244]
GSM748302
[245]
GSM748303
[246]
GSM748304
[247]
GSM748305
[248]
GSM748306
[249]
GSM748307
[250]
GSM748308
[251]
GSM748309
[252]
GSM748310
[253]
GSM748311
[254]
GSM748312
[255]
GSM748313
[256]
GSM748314
[257]
GSM748315
[258]
GSM748316
[259]
GSM748317
[260]
GSM748318
[261]
GSM748319
[262]
GSM748320
[263]
GSM748321
[264]
GSM748323
[265]
GSM748324
[266]
GSM748325
[267]
GSM748326
[268]
GSM748327
[269]
GSM748328
[270]
GSM748329
[271]
GSM748330
[272]
GSM748331
[273]
GSM748332
[274]
GSM748333
[275]
GSM748334
[276]
GSM748335
[277]
GSM748336
[278]
GSM748337
[279]
GSM748338
[280]
GSM748339
[281]
GSM748341
[282]
GSM748342
[283]
GSM748343
[284]
GSM748344
[285]
GSM748345
[286]
GSM748346
[287]
GSM748347
[288]
GSM748348
[289]
GSM748349
[290]
GSM748350
[291]
GSM748351
[292]
GSM748352
[293]
GSM748353
[294]
GSM748354
[295]
GSM748355
[296]
GSM748356
[297]
GSM748357
[298]
GSM748358
[299]
GSM748359
[300]
GSM748360
[301]
GSM748361
[302]
GSM748362
[303]
GSM748363
[304]
GSM748364
[305]
GSM748365
[306]
GSM748366
sample_count
307
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
"Off-context" gene expression in lung cancer identifies a group of metastatic-prone tumors
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[5] object · 15 fields
id
data:geo:GSE31210
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=GSE31210
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE31210
version
null
note
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
access_statement_kind
data_availability_statement
sample_accessions array · 246 items
[0]
GSM773540
[1]
GSM773541
[2]
GSM773542
[3]
GSM773543
[4]
GSM773544
[5]
GSM773545
[6]
GSM773546
[7]
GSM773547
[8]
GSM773548
[9]
GSM773549
[10]
GSM773550
[11]
GSM773551
[12]
GSM773552
[13]
GSM773553
[14]
GSM773554
[15]
GSM773555
[16]
GSM773556
[17]
GSM773557
[18]
GSM773558
[19]
GSM773559
[20]
GSM773560
[21]
GSM773561
[22]
GSM773562
[23]
GSM773563
[24]
GSM773564
[25]
GSM773565
[26]
GSM773566
[27]
GSM773567
[28]
GSM773568
[29]
GSM773569
[30]
GSM773570
[31]
GSM773571
[32]
GSM773572
[33]
GSM773573
[34]
GSM773574
[35]
GSM773575
[36]
GSM773576
[37]
GSM773577
[38]
GSM773578
[39]
GSM773579
[40]
GSM773580
[41]
GSM773581
[42]
GSM773582
[43]
GSM773583
[44]
GSM773584
[45]
GSM773585
[46]
GSM773586
[47]
GSM773587
[48]
GSM773588
[49]
GSM773589
[50]
GSM773590
[51]
GSM773591
[52]
GSM773592
[53]
GSM773593
[54]
GSM773594
[55]
GSM773595
[56]
GSM773596
[57]
GSM773597
[58]
GSM773598
[59]
GSM773599
[60]
GSM773600
[61]
GSM773601
[62]
GSM773602
[63]
GSM773603
[64]
GSM773604
[65]
GSM773605
[66]
GSM773606
[67]
GSM773607
[68]
GSM773608
[69]
GSM773609
[70]
GSM773610
[71]
GSM773611
[72]
GSM773612
[73]
GSM773613
[74]
GSM773614
[75]
GSM773615
[76]
GSM773616
[77]
GSM773617
[78]
GSM773618
[79]
GSM773619
[80]
GSM773620
[81]
GSM773621
[82]
GSM773622
[83]
GSM773623
[84]
GSM773624
[85]
GSM773625
[86]
GSM773626
[87]
GSM773627
[88]
GSM773628
[89]
GSM773629
[90]
GSM773630
[91]
GSM773631
[92]
GSM773632
[93]
GSM773633
[94]
GSM773634
[95]
GSM773635
[96]
GSM773636
[97]
GSM773637
[98]
GSM773638
[99]
GSM773639
[100]
GSM773640
[101]
GSM773641
[102]
GSM773642
[103]
GSM773643
[104]
GSM773644
[105]
GSM773645
[106]
GSM773646
[107]
GSM773647
[108]
GSM773648
[109]
GSM773649
[110]
GSM773650
[111]
GSM773651
[112]
GSM773652
[113]
GSM773653
[114]
GSM773654
[115]
GSM773655
[116]
GSM773656
[117]
GSM773657
[118]
GSM773658
[119]
GSM773659
[120]
GSM773660
[121]
GSM773661
[122]
GSM773662
[123]
GSM773663
[124]
GSM773664
[125]
GSM773665
[126]
GSM773666
[127]
GSM773667
[128]
GSM773668
[129]
GSM773669
[130]
GSM773670
[131]
GSM773671
[132]
GSM773672
[133]
GSM773673
[134]
GSM773674
[135]
GSM773675
[136]
GSM773676
[137]
GSM773677
[138]
GSM773678
[139]
GSM773679
[140]
GSM773680
[141]
GSM773681
[142]
GSM773682
[143]
GSM773683
[144]
GSM773684
[145]
GSM773685
[146]
GSM773686
[147]
GSM773687
[148]
GSM773688
[149]
GSM773689
[150]
GSM773690
[151]
GSM773691
[152]
GSM773692
[153]
GSM773693
[154]
GSM773694
[155]
GSM773695
[156]
GSM773696
[157]
GSM773697
[158]
GSM773698
[159]
GSM773699
[160]
GSM773700
[161]
GSM773701
[162]
GSM773702
[163]
GSM773703
[164]
GSM773704
[165]
GSM773705
[166]
GSM773706
[167]
GSM773707
[168]
GSM773708
[169]
GSM773709
[170]
GSM773710
[171]
GSM773711
[172]
GSM773712
[173]
GSM773713
[174]
GSM773714
[175]
GSM773715
[176]
GSM773716
[177]
GSM773717
[178]
GSM773718
[179]
GSM773719
[180]
GSM773720
[181]
GSM773721
[182]
GSM773722
[183]
GSM773723
[184]
GSM773724
[185]
GSM773725
[186]
GSM773726
[187]
GSM773727
[188]
GSM773728
[189]
GSM773729
[190]
GSM773730
[191]
GSM773731
[192]
GSM773732
[193]
GSM773733
[194]
GSM773734
[195]
GSM773735
[196]
GSM773736
[197]
GSM773737
[198]
GSM773738
[199]
GSM773739
[200]
GSM773740
[201]
GSM773741
[202]
GSM773742
[203]
GSM773743
[204]
GSM773744
[205]
GSM773745
[206]
GSM773746
[207]
GSM773747
[208]
GSM773748
[209]
GSM773749
[210]
GSM773750
[211]
GSM773751
[212]
GSM773752
[213]
GSM773753
[214]
GSM773754
[215]
GSM773755
[216]
GSM773756
[217]
GSM773757
[218]
GSM773758
[219]
GSM773759
[220]
GSM773760
[221]
GSM773761
[222]
GSM773762
[223]
GSM773763
[224]
GSM773764
[225]
GSM773765
[226]
GSM773766
[227]
GSM773767
[228]
GSM773768
[229]
GSM773769
[230]
GSM773770
[231]
GSM773771
[232]
GSM773772
[233]
GSM773773
[234]
GSM773774
[235]
GSM773775
[236]
GSM773776
[237]
GSM773777
[238]
GSM773778
[239]
GSM773779
[240]
GSM773780
[241]
GSM773781
[242]
GSM773782
[243]
GSM773783
[244]
GSM773784
[245]
GSM773785
sample_count
246
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Gene expression data for pathological stage I-II lung adenocarcinomas
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[6] object · 15 fields
id
data:geo:GSE37745
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=GSE37745
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE37745
version
null
note
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
access_statement_kind
data_availability_statement
sample_accessions array · 196 items
[0]
GSM1019138
[1]
GSM1019139
[2]
GSM1019140
[3]
GSM1019141
[4]
GSM1019142
[5]
GSM1019143
[6]
GSM1019144
[7]
GSM1019145
[8]
GSM1019146
[9]
GSM1019147
[10]
GSM1019148
[11]
GSM1019149
[12]
GSM1019150
[13]
GSM1019151
[14]
GSM1019152
[15]
GSM1019153
[16]
GSM1019154
[17]
GSM1019155
[18]
GSM1019156
[19]
GSM1019157
[20]
GSM1019158
[21]
GSM1019159
[22]
GSM1019160
[23]
GSM1019161
[24]
GSM1019162
[25]
GSM1019163
[26]
GSM1019164
[27]
GSM1019165
[28]
GSM1019166
[29]
GSM1019167
[30]
GSM1019168
[31]
GSM1019169
[32]
GSM1019170
[33]
GSM1019171
[34]
GSM1019172
[35]
GSM1019173
[36]
GSM1019174
[37]
GSM1019175
[38]
GSM1019176
[39]
GSM1019177
[40]
GSM1019178
[41]
GSM1019179
[42]
GSM1019180
[43]
GSM1019181
[44]
GSM1019182
[45]
GSM1019183
[46]
GSM1019184
[47]
GSM1019185
[48]
GSM1019186
[49]
GSM1019187
[50]
GSM1019188
[51]
GSM1019189
[52]
GSM1019190
[53]
GSM1019191
[54]
GSM1019192
[55]
GSM1019193
[56]
GSM1019194
[57]
GSM1019195
[58]
GSM1019196
[59]
GSM1019197
[60]
GSM1019198
[61]
GSM1019199
[62]
GSM1019200
[63]
GSM1019201
[64]
GSM1019202
[65]
GSM1019203
[66]
GSM1019204
[67]
GSM1019205
[68]
GSM1019206
[69]
GSM1019207
[70]
GSM1019208
[71]
GSM1019209
[72]
GSM1019210
[73]
GSM1019211
[74]
GSM1019212
[75]
GSM1019213
[76]
GSM1019214
[77]
GSM1019215
[78]
GSM1019216
[79]
GSM1019217
[80]
GSM1019218
[81]
GSM1019219
[82]
GSM1019220
[83]
GSM1019221
[84]
GSM1019222
[85]
GSM1019223
[86]
GSM1019224
[87]
GSM1019225
[88]
GSM1019226
[89]
GSM1019227
[90]
GSM1019228
[91]
GSM1019229
[92]
GSM1019230
[93]
GSM1019231
[94]
GSM1019232
[95]
GSM1019233
[96]
GSM1019234
[97]
GSM1019235
[98]
GSM1019236
[99]
GSM1019237
[100]
GSM1019238
[101]
GSM1019239
[102]
GSM1019240
[103]
GSM1019241
[104]
GSM1019242
[105]
GSM1019243
[106]
GSM1019244
[107]
GSM1019245
[108]
GSM1019246
[109]
GSM1019247
[110]
GSM1019248
[111]
GSM1019249
[112]
GSM1019250
[113]
GSM1019251
[114]
GSM1019252
[115]
GSM1019253
[116]
GSM1019254
[117]
GSM1019255
[118]
GSM1019256
[119]
GSM1019257
[120]
GSM1019258
[121]
GSM1019259
[122]
GSM1019260
[123]
GSM1019261
[124]
GSM1019262
[125]
GSM1019263
[126]
GSM1019264
[127]
GSM1019265
[128]
GSM1019266
[129]
GSM1019267
[130]
GSM1019268
[131]
GSM1019269
[132]
GSM1019270
[133]
GSM1019271
[134]
GSM1019272
[135]
GSM1019273
[136]
GSM1019274
[137]
GSM1019275
[138]
GSM1019276
[139]
GSM1019277
[140]
GSM1019278
[141]
GSM1019279
[142]
GSM1019280
[143]
GSM1019281
[144]
GSM1019282
[145]
GSM1019283
[146]
GSM1019284
[147]
GSM1019285
[148]
GSM1019286
[149]
GSM1019287
[150]
GSM1019288
[151]
GSM1019289
[152]
GSM1019290
[153]
GSM1019291
[154]
GSM1019292
[155]
GSM1019293
[156]
GSM1019294
[157]
GSM1019295
[158]
GSM1019296
[159]
GSM1019297
[160]
GSM1019298
[161]
GSM1019299
[162]
GSM1019300
[163]
GSM1019301
[164]
GSM1019302
[165]
GSM1019303
[166]
GSM1019304
[167]
GSM1019305
[168]
GSM1019306
[169]
GSM1019307
[170]
GSM1019308
[171]
GSM1019309
[172]
GSM1019310
[173]
GSM1019311
[174]
GSM1019312
[175]
GSM1019313
[176]
GSM1019314
[177]
GSM1019315
[178]
GSM1019316
[179]
GSM1019317
[180]
GSM1019318
[181]
GSM1019319
[182]
GSM1019320
[183]
GSM1019321
[184]
GSM1019322
[185]
GSM1019323
[186]
GSM1019324
[187]
GSM1019325
[188]
GSM1019326
[189]
GSM1019327
[190]
GSM1019328
[191]
GSM1019329
[192]
GSM1019330
[193]
GSM1019331
[194]
GSM1019332
[195]
GSM1019333
sample_count
196
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis and tissue microarray validation
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[7] object · 15 fields
id
data:geo:GSE42127
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=GSE42127
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE42127
version
null
note
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
access_statement_kind
data_availability_statement
sample_accessions array · 176 items
[0]
GSM1032881
[1]
GSM1032882
[2]
GSM1032883
[3]
GSM1032884
[4]
GSM1032885
[5]
GSM1032886
[6]
GSM1032887
[7]
GSM1032888
[8]
GSM1032889
[9]
GSM1032890
[10]
GSM1032891
[11]
GSM1032892
[12]
GSM1032893
[13]
GSM1032894
[14]
GSM1032895
[15]
GSM1032896
[16]
GSM1032897
[17]
GSM1032898
[18]
GSM1032899
[19]
GSM1032900
[20]
GSM1032901
[21]
GSM1032902
[22]
GSM1032903
[23]
GSM1032904
[24]
GSM1032905
[25]
GSM1032906
[26]
GSM1032907
[27]
GSM1032908
[28]
GSM1032909
[29]
GSM1032910
[30]
GSM1032911
[31]
GSM1032912
[32]
GSM1032913
[33]
GSM1032914
[34]
GSM1032915
[35]
GSM1032916
[36]
GSM1032917
[37]
GSM1032918
[38]
GSM1032919
[39]
GSM1032920
[40]
GSM1032921
[41]
GSM1032922
[42]
GSM1032923
[43]
GSM1032924
[44]
GSM1032925
[45]
GSM1032926
[46]
GSM1032927
[47]
GSM1032928
[48]
GSM1032929
[49]
GSM1032930
[50]
GSM1032931
[51]
GSM1032932
[52]
GSM1032933
[53]
GSM1032934
[54]
GSM1032935
[55]
GSM1032936
[56]
GSM1032937
[57]
GSM1032938
[58]
GSM1032939
[59]
GSM1032940
[60]
GSM1032941
[61]
GSM1032942
[62]
GSM1032943
[63]
GSM1032944
[64]
GSM1032945
[65]
GSM1032946
[66]
GSM1032947
[67]
GSM1032948
[68]
GSM1032949
[69]
GSM1032950
[70]
GSM1032951
[71]
GSM1032952
[72]
GSM1032953
[73]
GSM1032954
[74]
GSM1032955
[75]
GSM1032956
[76]
GSM1032957
[77]
GSM1032958
[78]
GSM1032959
[79]
GSM1032960
[80]
GSM1032961
[81]
GSM1032962
[82]
GSM1032963
[83]
GSM1032964
[84]
GSM1032965
[85]
GSM1032966
[86]
GSM1032967
[87]
GSM1032968
[88]
GSM1032969
[89]
GSM1032970
[90]
GSM1032971
[91]
GSM1032972
[92]
GSM1032973
[93]
GSM1032974
[94]
GSM1032975
[95]
GSM1032976
[96]
GSM1032977
[97]
GSM1032978
[98]
GSM1032979
[99]
GSM1032980
[100]
GSM1032981
[101]
GSM1032982
[102]
GSM1032983
[103]
GSM1032984
[104]
GSM1032985
[105]
GSM1032986
[106]
GSM1032987
[107]
GSM1032988
[108]
GSM1032989
[109]
GSM1032990
[110]
GSM1032991
[111]
GSM1032992
[112]
GSM1032993
[113]
GSM1032994
[114]
GSM1032995
[115]
GSM1032996
[116]
GSM1032997
[117]
GSM1032998
[118]
GSM1032999
[119]
GSM1033000
[120]
GSM1033001
[121]
GSM1033002
[122]
GSM1033003
[123]
GSM1033004
[124]
GSM1033005
[125]
GSM1033006
[126]
GSM1033007
[127]
GSM1033008
[128]
GSM1033009
[129]
GSM1033010
[130]
GSM1033011
[131]
GSM1033012
[132]
GSM1033013
[133]
GSM1033014
[134]
GSM1033015
[135]
GSM1033016
[136]
GSM1033017
[137]
GSM1033018
[138]
GSM1033019
[139]
GSM1033020
[140]
GSM1033021
[141]
GSM1033022
[142]
GSM1033023
[143]
GSM1033024
[144]
GSM1033025
[145]
GSM1033026
[146]
GSM1033027
[147]
GSM1033028
[148]
GSM1033029
[149]
GSM1033030
[150]
GSM1033031
[151]
GSM1033032
[152]
GSM1033033
[153]
GSM1033034
[154]
GSM1033035
[155]
GSM1033036
[156]
GSM1033037
[157]
GSM1033038
[158]
GSM1033039
[159]
GSM1033040
[160]
GSM1033041
[161]
GSM1033042
[162]
GSM1033043
[163]
GSM1033044
[164]
GSM1033045
[165]
GSM1033046
[166]
GSM1033047
[167]
GSM1033048
[168]
GSM1033049
[169]
GSM1033050
[170]
GSM1033051
[171]
GSM1033052
[172]
GSM1033053
[173]
GSM1033054
[174]
GSM1033055
[175]
GSM1033056
sample_count
176
group_sizes
null
group_sizes_basis
null
platform
6884
taxon
Homo sapiens
title
Expression data for non-small-cell lung cancer
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[8] object · 15 fields
id
data:geo:GSE50081
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=GSE50081
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE50081
version
null
note
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
access_statement_kind
data_availability_statement
sample_accessions array · 181 items
[0]
GSM1213669
[1]
GSM1213670
[2]
GSM1213671
[3]
GSM1213672
[4]
GSM1213673
[5]
GSM1213674
[6]
GSM1213675
[7]
GSM1213676
[8]
GSM1213677
[9]
GSM1213678
[10]
GSM1213679
[11]
GSM1213680
[12]
GSM1213681
[13]
GSM1213682
[14]
GSM1213683
[15]
GSM1213684
[16]
GSM1213685
[17]
GSM1213686
[18]
GSM1213687
[19]
GSM1213688
[20]
GSM1213689
[21]
GSM1213690
[22]
GSM1213691
[23]
GSM1213692
[24]
GSM1213693
[25]
GSM1213694
[26]
GSM1213695
[27]
GSM1213696
[28]
GSM1213697
[29]
GSM1213698
[30]
GSM1213699
[31]
GSM1213700
[32]
GSM1213701
[33]
GSM1213702
[34]
GSM1213703
[35]
GSM1213704
[36]
GSM1213705
[37]
GSM1213706
[38]
GSM1213707
[39]
GSM1213708
[40]
GSM1213709
[41]
GSM1213710
[42]
GSM1213711
[43]
GSM1213712
[44]
GSM1213713
[45]
GSM1213714
[46]
GSM1213715
[47]
GSM1213716
[48]
GSM1213717
[49]
GSM1213718
[50]
GSM1213719
[51]
GSM1213720
[52]
GSM1213721
[53]
GSM1213722
[54]
GSM1213723
[55]
GSM1213724
[56]
GSM1213725
[57]
GSM1213726
[58]
GSM1213727
[59]
GSM1213728
[60]
GSM1213729
[61]
GSM1213730
[62]
GSM1213731
[63]
GSM1213732
[64]
GSM1213733
[65]
GSM1213734
[66]
GSM1213735
[67]
GSM1213736
[68]
GSM1213737
[69]
GSM1213738
[70]
GSM1213739
[71]
GSM1213740
[72]
GSM1213741
[73]
GSM1213742
[74]
GSM1213743
[75]
GSM1213744
[76]
GSM1213745
[77]
GSM1213746
[78]
GSM1213747
[79]
GSM1213748
[80]
GSM1213749
[81]
GSM1213750
[82]
GSM1213751
[83]
GSM1213752
[84]
GSM1213753
[85]
GSM1213754
[86]
GSM1213755
[87]
GSM1213756
[88]
GSM1213757
[89]
GSM1213758
[90]
GSM1213759
[91]
GSM1213760
[92]
GSM1213761
[93]
GSM1213762
[94]
GSM1213763
[95]
GSM1213764
[96]
GSM1213765
[97]
GSM1213766
[98]
GSM1213767
[99]
GSM1213768
[100]
GSM1213769
[101]
GSM1213770
[102]
GSM1213771
[103]
GSM1213772
[104]
GSM1213773
[105]
GSM1213774
[106]
GSM1213775
[107]
GSM1213776
[108]
GSM1213777
[109]
GSM1213778
[110]
GSM1213779
[111]
GSM1213780
[112]
GSM1213781
[113]
GSM1213782
[114]
GSM1213783
[115]
GSM1213784
[116]
GSM1213785
[117]
GSM1213786
[118]
GSM1213787
[119]
GSM1213788
[120]
GSM1213789
[121]
GSM1213790
[122]
GSM1213791
[123]
GSM1213792
[124]
GSM1213793
[125]
GSM1213794
[126]
GSM1213795
[127]
GSM1213796
[128]
GSM1213797
[129]
GSM1213798
[130]
GSM1213799
[131]
GSM1213800
[132]
GSM1213801
[133]
GSM1213802
[134]
GSM1213803
[135]
GSM1213804
[136]
GSM1213805
[137]
GSM1213806
[138]
GSM1213807
[139]
GSM1213808
[140]
GSM1213809
[141]
GSM1213810
[142]
GSM1213811
[143]
GSM1213812
[144]
GSM1213813
[145]
GSM1213814
[146]
GSM1213815
[147]
GSM1213816
[148]
GSM1213817
[149]
GSM1213818
[150]
GSM1213819
[151]
GSM1213820
[152]
GSM1213821
[153]
GSM1213822
[154]
GSM1213823
[155]
GSM1213824
[156]
GSM1213825
[157]
GSM1213826
[158]
GSM1213827
[159]
GSM1213828
[160]
GSM1213829
[161]
GSM1213830
[162]
GSM1213831
[163]
GSM1213832
[164]
GSM1213833
[165]
GSM1213834
[166]
GSM1213835
[167]
GSM1213836
[168]
GSM1213837
[169]
GSM1213838
[170]
GSM1213839
[171]
GSM1213840
[172]
GSM1213841
[173]
GSM1213842
[174]
GSM1213843
[175]
GSM1213844
[176]
GSM1213845
[177]
GSM1213846
[178]
GSM1213847
[179]
GSM1213848
[180]
GSM1213849
sample_count
181
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Validation of a histology-independent prognostic gene signature for early stage, non-small cell lung cancer including stage IA patients
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[9] object · 15 fields
id
data:geo:GSE68465
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=GSE68465
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE68465
version
null
note
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
access_statement_kind
data_availability_statement
sample_accessions array · 462 items
[0]
GSM1672281
[1]
GSM1672282
[2]
GSM1672283
[3]
GSM1672284
[4]
GSM1672285
[5]
GSM1672286
[6]
GSM1672287
[7]
GSM1672288
[8]
GSM1672289
[9]
GSM1672290
[10]
GSM1672291
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sample_count
462
group_sizes
null
group_sizes_basis
null
platform
96
taxon
Homo sapiens
title
caArray_jacob-00182: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[10] object · 15 fields
id
data:geo:GSE72094
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=GSE72094
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE72094
version
null
note
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
access_statement_kind
data_availability_statement
sample_accessions array · 442 items
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[204]
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[205]
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[216]
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[218]
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[219]
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[222]
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[223]
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[228]
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[232]
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[239]
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[263]
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[266]
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[267]
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[268]
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[270]
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[273]
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[274]
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[275]
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[278]
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[281]
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[282]
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[286]
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[287]
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[288]
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[289]
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[290]
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[291]
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[292]
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[293]
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[294]
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[295]
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[298]
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[299]
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[300]
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[301]
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[302]
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[303]
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[304]
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[305]
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[306]
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[307]
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[308]
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[309]
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[310]
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[311]
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[312]
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[313]
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[314]
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[315]
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[316]
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[317]
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[318]
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[319]
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[320]
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[321]
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[322]
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[323]
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[324]
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[325]
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[326]
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[327]
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[328]
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[329]
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[330]
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[331]
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[332]
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[333]
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[334]
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[335]
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[336]
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[337]
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[338]
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[339]
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[340]
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[341]
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[342]
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[343]
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[344]
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[345]
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[346]
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[347]
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[348]
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[349]
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[350]
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[351]
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[352]
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[353]
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[354]
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[355]
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[356]
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[357]
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[358]
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[359]
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[360]
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[361]
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[362]
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[363]
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[364]
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[365]
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[366]
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[367]
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[368]
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[369]
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[370]
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[371]
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[372]
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[373]
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[374]
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[375]
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[376]
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[377]
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[379]
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[380]
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[381]
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[382]
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[383]
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[386]
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[387]
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[400]
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[401]
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[402]
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[403]
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[404]
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[405]
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[406]
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[407]
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[408]
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[409]
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[410]
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[411]
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[412]
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[413]
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[414]
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[415]
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[416]
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[417]
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[418]
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[419]
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[420]
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[421]
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[422]
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[423]
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[424]
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[425]
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[426]
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[427]
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[428]
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[429]
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[430]
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[431]
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[432]
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[434]
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[435]
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[436]
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[437]
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[438]
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[439]
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[440]
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[441]
GSM1855238
sample_count
442
group_sizes
null
group_sizes_basis
null
platform
15048
taxon
Homo sapiens
title
KRAS mutation-associated gene expression, p53 and STK11 mutations, proliferation and immune surveillance in lung adenocarcinoma
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[11] object · 15 fields
id
data:geo:GSE81089
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=GSE81089
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE81089
version
null
note
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
access_statement_kind
data_availability_statement
sample_accessions array · 218 items
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[1]
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[2]
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[5]
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[6]
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[8]
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[9]
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[10]
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[11]
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[12]
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[13]
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[14]
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[15]
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[16]
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[18]
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[19]
GSM2142462
[20]
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[21]
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[22]
GSM2142465
[23]
GSM2142466
[24]
GSM2142467
[25]
GSM2142468
[26]
GSM2142469
[27]
GSM2142470
[28]
GSM2142471
[29]
GSM2142472
[30]
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[31]
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[32]
GSM2142475
[33]
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[34]
GSM2142477
[35]
GSM2142478
[36]
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[37]
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[38]
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[39]
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[40]
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[41]
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[42]
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[43]
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[44]
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[45]
GSM2142488
[46]
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[47]
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[48]
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[49]
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[50]
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[51]
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[52]
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[53]
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[54]
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[55]
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[56]
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[57]
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[58]
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[59]
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[60]
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[61]
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[62]
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[63]
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[64]
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[65]
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[66]
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[67]
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[68]
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[69]
GSM2142512
[70]
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[71]
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[72]
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[73]
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[74]
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[75]
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[76]
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[78]
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[79]
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[80]
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[89]
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[94]
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[95]
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[97]
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[98]
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[99]
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[100]
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[104]
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[106]
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[113]
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[114]
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[116]
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[117]
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[118]
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[119]
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[120]
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[123]
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[124]
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[125]
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[126]
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[127]
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[128]
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[129]
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[130]
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[200]
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[201]
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[202]
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[207]
GSM2142650
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[209]
GSM2142652
[210]
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[211]
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[212]
GSM2142655
[213]
GSM2142656
[214]
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[215]
GSM2142658
[216]
GSM2142659
[217]
GSM2142660
sample_count
218
group_sizes
null
group_sizes_basis
null
platform
16791
taxon
Homo sapiens
title
Next Generation Sequencing (RNAseq) of non-small cell lung cancer
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 22 items
[0]
asset:data:geo:GSE13213 not downloaded
[1]
asset:data:geo:GSE13213 licence not read
[2]
asset:data:geo:GSE14814 not downloaded
[3]
asset:data:geo:GSE14814 licence not read
[4]
asset:data:geo:GSE26939 not downloaded
[5]
asset:data:geo:GSE26939 licence not read
[6]
asset:data:geo:GSE30219 not downloaded
[7]
asset:data:geo:GSE30219 licence not read
[8]
asset:data:geo:GSE31210 not downloaded
[9]
asset:data:geo:GSE31210 licence not read
[10]
asset:data:geo:GSE37745 not downloaded
[11]
asset:data:geo:GSE37745 licence not read
[12]
asset:data:geo:GSE42127 not downloaded
[13]
asset:data:geo:GSE42127 licence not read
[14]
asset:data:geo:GSE50081 not downloaded
[15]
asset:data:geo:GSE50081 licence not read
[16]
asset:data:geo:GSE68465 not downloaded
[17]
asset:data:geo:GSE68465 licence not read
[18]
asset:data:geo:GSE72094 not downloaded
[19]
asset:data:geo:GSE72094 licence not read
[20]
asset:data:geo:GSE81089 not downloaded
[21]
asset:data:geo:GSE81089 licence not read
analysis object · 4 fields
state
partial
methods array · 9 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
wilcoxon
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_wilcoxon
expressible
false
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
Wilcoxon
[1] object · 10 fields
id
method-2
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
0.8
band
high
quote
Kaplan-Meier
[2] object · 10 fields
id
method-3
family
survival_analysis
specific
cox_proportional_hazards
label
Survival analysis
dsl_operations array · 1 item
[0]
cox_ph
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
0.8
band
high
quote
Cox regression
[3] object · 10 fields
id
method-4
family
differential_expression
specific
deseq2
label
Differential expression analysis
dsl_operations array · 3 items
[0]
normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
count_matrix_with_condition
evidence object · 3 fields
score
0.8
band
high
quote
DESeq2
[4] object · 10 fields
id
method-5
family
machine_learning
specific
support_vector_machine
label
Machine learning
dsl_operations array · 3 items
[0]
train_classifier
[1]
cross_validate
[2]
roc_auc
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
labelled_feature_matrix
evidence object · 3 fields
score
0.8
band
high
quote
Support Vector Machine
[5] object · 10 fields
id
method-6
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 correlation
[6] object · 10 fields
id
method-7
family
genetic_association
specific
gwas
label
Genetic association (GWAS / linkage / MR)
dsl_operations array · 1 item
[0]
gwas_locus_scan
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
genotype_phenotype_table
evidence object · 3 fields
score
0.7
band
medium
quote
genome-wide association study
[7] object · 10 fields
id
method-8
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
0.8
band
high
quote
Chi-square
[8] object · 10 fields
id
method-9
family
null
specific
null
label
Receiver Operating Characteristic (ROC) analysis
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
Receiver Operating Characteristic (ROC) analysis was applied to evaluate the predictive performance of the Artificial Intelligence-Derived Prognostic Signature (AIDPS) across 12 datasets and a meta-cohort combining all samples.
targets array · 0 items
gaps array · 2 items
[0]
method.reader_named_unmapped
[1]
method.group_comparison_wilcoxon
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
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survival_analysis
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statistical_regression
[4]
pca
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molecular_docking
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GSE14814
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GSE13213
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GSE31210
[3]
GSE37745
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GSE26939
[5]
GSE30219
[6]
GSE42127
[7]
GSE50081
[8]
GSE72094
[9]
GSE68465
[10]
GSE81089
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[0]
GSE14814
[1]
GSE13213
[2]
GSE31210
[3]
GSE37745
[4]
GSE26939
[5]
GSE30219
[6]
GSE42127
[7]
GSE50081
[8]
GSE72094
[9]
GSE68465
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GSE81089
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All datasets generated for this study are included in the article materials. The datasets analyzed for this study can be found in the GEO website (https://www.ncbi.nlm.nih.gov/geo/), TCGA website(https://portal.gdc.cancer.gov/) and MSigDB database (https://www.gsea-msigdb.org/gsea/index.jsp).
basis
The paper names GSE14814, GSE13213, GSE31210, GSE37745, GSE26939, GSE30219, GSE42127, GSE50081, GSE72094, GSE68465, GSE81089 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
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data:geo:GSE13213
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[17]
asset:data:geo:GSE68465 not downloaded
[18]
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[19]
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[20]
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39434164", "kind": "science-record", "revision": 3, "content_hash": "sha256:b1fb05301e3bca9586cabb7063352cdd7b652b5019ecf7ef21a1253129145e38", "created_at": "2026-11-01T20:29:42Z", "updated_at": "2026-11-01T22:13:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive multi-omics integration uncovers mitochondrial gene signatures for prognosis and personalized therapy in lung adenocarcinoma.", "doi": "10.1186/s12967-024-05754-y", "pmid": "39434164", "authors": ["Wenjia Zhang", "Lei Zhao", "Tiansheng Zheng", "Lihong Fan", "Kai Wang", "Guoshu Li"], "journal": "Journal of translational medicine", "year": 2024, "abstract": "The therapeutic efficacy of lung adenocarcinoma (LUAD), the most prevalent histological subtype of primary lung cancer, remains inadequate, with accurate prognostic assessment posing significant challenges. This study sought to elucidate the prognostic significance of mitochondrial-related genes in LUAD through an integrative multi-omics approach, aimed at developing personalized therapeutic strategies. Utilizing transcriptomic and single-cell RNA sequencing (scRNA-seq) data, alongside clinical information from publicly available databases, we first applied dimensionality reduction and clustering techniques to the LUAD single-cell dataset, focusing on the subclassification of fibroblasts, epithelial cells, and T cells. Mitochondrial-related prognostic genes were subsequently identified using TCGA-LUAD data, and LUAD cases were stratified into distinct molecular subtypes through consensus clustering, allowing for the exploration of gene expression profiles and clinical feature distributions across subtypes. By leveraging an ensemble of machine learning algorithms, we developed an Artificial Intelligence-Derived Prognostic Signature (AIDPS) model based on mitochondrial-related genes and validated its prognostic accuracy across multiple independent datasets. The AIDPS model demonstrated robust predictive power for LUAD patient outcomes, revealing significant differences in responses to immunotherapy and chemotherapy, as well as survival outcomes between risk groups. Furthermore, we conducted comprehensive analyses of tumor mutation burden (TMB), immune microenvironment characteristics, and genome-wide association study (GWAS) data, providing additional insights into the mechanistic roles of mitochondrial-related genes in LUAD pathogenesis. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13213"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE13213"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39434164", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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