| 1 |
GDC TARGET-ALL-P3 |
Acute lymphoblastic leukemia |
TARGET-ALL-P3 |
58387 |
117 |
Illumina HiSeq |
2009 |
2019 |
https://xenabrowser.net/datapages/ |
25207766 |
log2(fpkm+1) |
| 2 |
Transcription profiling by array of diagnosis and relapse specimens of paediatric patients with acute lymphoblastic leukaemia (ALL) to identify mechanisms and pathways of therapy failure |
Acute lymphoblastic leukemia |
E-MTAB-1216 |
12547 |
101 |
Affymetrix GeneChip Human Genome HG-U133A |
2012 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1216 |
NA |
RMA |
| 3 |
Transcription profiling by array of bone marrow from T-cell acute lymphoblastic leukemia pediatric patients to investigate outcome prediction |
Acute lymphoblastic leukemia |
E-MTAB-1205 |
21653 |
38 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 |
2012 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1205 |
23436797 |
RMA |
| 4 |
TARGET-AML |
Acute myeloid leukemia |
TARGET-AML |
58387 |
145 |
Illumina HiSeq |
2009 |
2019 |
https://xenabrowser.net/datapages/ |
26941285 |
log2(fpkm+2) |
| 5 |
Prognostic gene signature for normal karyotype AML |
Acute myeloid leukemia |
GSE12417_GPL570 |
21653 |
79 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2008 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12417 |
18716133 |
RMA |
| 6 |
Prognostic gene signature for normal karyotype AML |
Acute myeloid leukemia |
GSE12417_GPL96 |
12547 |
163 |
Affymetrix Human Genome U133A Array |
2008 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12417 |
18716133 |
RMA |
| 7 |
Prognostic gene signature for normal karyotype AML |
Acute myeloid leukemia |
GSE12417_GPL97 |
10603 |
163 |
Affymetrix Human Genome U133B Array |
2008 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12417 |
18716133 |
RMA |
| 8 |
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia |
Acute myeloid leukemia |
TCGA-LAML |
34849 |
117 |
HTSeq |
2013 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-LAML |
23634996 |
TPM |
| 9 |
Beta-catenin status effects in human adrenocortical carcinomas (33), adenomas (22), and normal adrenal cortex (10) |
Adrenocortical carcinoma |
GSE33371 |
21653 |
65 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33371 |
22800756 |
RMA |
| 10 |
Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma |
Adrenocortical carcinoma |
TCGA-ACC |
34849 |
79 |
HTSeq |
2016 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-ACC |
27165744 |
TPM |
| 11 |
Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas |
Adult soft tissue sarcomas |
TCGA-SARC |
34849 |
255 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-SARC |
29100075 |
TPM |
| 12 |
Transcription profiling of 32 human Anaplastic Large Cell Lymphomas (ALCL) and 5 ALCL cell lines to investigate differences between tumors expressing/not-expressing Anaplastic Lymphoma kinkase |
Anaplastic large cell lymphomas |
E-TABM-117 |
12547 |
37 |
Affymetrix GeneChip Human Genome HG-U133A |
2007 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-117 |
17077326 |
RMA |
| 13 |
Predective Value of Prognosis-Related Gene Expression Study in Primary Bladder Cancer |
Bladder cancer |
GSE13507 |
24357 |
256 |
Illumina human-6 v2.0 expression beadchip |
2008 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507 |
20059769 |
Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used. |
| 14 |
Prediction of response and survival following chemotherapy in patients with advanced bladder cancer |
Bladder cancer |
GSE5287 |
12178 |
30 |
Affymetrix Human Genome U133A Array |
2006 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5287 |
17671123 |
Intensity |
| 15 |
Waldman Bladder tumors |
Bladder cancer |
GSE1827 |
6225 |
80 |
JAKE |
2004 |
2015 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1827 |
15930339 |
Norm log2 ratio |
| 16 |
Subtype classification, grading, and outcome prediction of urothelial carcinomas by combined mRNA profiling and aCGH |
Bladder cancer |
GSE19915_GPL3883 |
10314 |
84 |
Swegene Human 27K RAP UniGene188 array |
2010 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19915 |
20406976 |
normalized log2 ratio (Cy3/Cy5) representing test/reference |
| 17 |
Subtype classification, grading, and outcome prediction of urothelial carcinomas by combined mRNA profiling and aCGH |
Bladder cancer |
GSE19915_GPL5186 |
11671 |
98 |
SWEGENE H_v3.0.1 35K |
2010 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19915 |
20406976 |
normalized log2 ratio (Cy3/Cy5) representing test/reference |
| 18 |
A Molecular Taxonomy of Urothelial Carcinoma |
Bladder cancer |
GSE32894 |
16940 |
308 |
Illumina HumanHT-12 V3.0 expression beadchip |
2011 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 |
22553347 |
normalized signal |
| 19 |
Comprehensive Transcriptional Analysis of Early Stage Urothelial Carcinoma using whole transcriptome sequencing |
Bladder cancer |
E-MTAB-4321 |
38267 |
476 |
FPKM normalized RNAseq data |
2016 |
NA |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4321 |
27321955 |
Normalized signal intensities by GenePattern Illumina module |
| 20 |
Predictive Gene Signatures as Strong Prognostic Indicators of the Effectiveness of BCG Immunotherapy |
Bladder cancer |
GSE19423 |
24357 |
48 |
Illumina human-6 v2.0 expression beadchip |
2009 |
2013 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19423 |
20233890 |
Normalized signal intensity |
| 21 |
Gene expression profiling of urothelial carcinoma |
Bladder cancer |
GSE48276 |
20818 |
116 |
Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip |
2013 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48276 |
24525232 |
quantile normalized |
| 22 |
Adrenocortical Carcinoma Gene Expression Profiling |
Bladder cancer |
GSE19750 |
21653 |
48 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19750 |
24238056 |
RMA |
| 23 |
Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer ? |
Bladder cancer |
GSE31684 |
21653 |
93 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31684 |
22228636 |
RMA |
| 24 |
Comprehensive Molecular Characterization of Urothelial Bladder Carcinoma |
Bladder cancer |
TCGA-BLCA |
34849 |
400 |
HTSeq |
2014 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-BLCA |
24476821 |
TPM |
| 25 |
Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations |
Bone cancer-Ewing sarcoma |
ICGC-BOCA-FR |
24818 |
57 |
HTSeq |
2014 |
2019 |
https://dcc.icgc.org/releases/current/Projects/BOCA-FR |
25223734 |
NA |
| 26 |
Genome and transcriptome study of the response to irinotecan and bevacizumab in recurrent glioblastomas |
Brain tumor-GBM |
E-MTAB-951 |
21653 |
23 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 |
2013 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-951 |
24804210 |
RMA |
| 27 |
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age |
Brain tumor-GBM |
GSE13041_GPL570 |
21653 |
27 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2018 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13041 |
18940004 |
RMA |
| 28 |
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age |
Brain tumor-GBM |
GSE13041_GPL8300 |
8619 |
49 |
Affymetrix Human Genome U95 Version 2 Array |
2018 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13041 |
18940004 |
RMA |
| 29 |
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age |
Brain tumor-GBM |
GSE13041_GPL96 |
12547 |
191 |
Affymetrix Human Genome U133A Array |
2018 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13041 |
18940004 |
RMA |
| 30 |
Patient specific orthotopic glioblastoma xenograft models recapitulate the histopathology and biology of human glioblastomas in situ (gene expression) |
Brain tumor-GBM |
GSE42669 |
20202 |
58 |
Affymetrix Human Gene 1.0 ST Array |
2012 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42669 |
23333277 |
RMA |
| 31 |
Glioblastoma from a homogenous cohort of patients treated within clinical trial |
Brain tumor-GBM |
GSE7696 |
21653 |
84 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2007 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7696 |
18565887 |
RMA |
| 32 |
Comprehensive genomic characterization defines human glioblastoma genes and core pathways |
Brain tumor-GBM |
TCGA-GBM |
34849 |
143 |
HTSeq |
2008 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-GBM |
18772890 |
TPM |
| 33 |
An expression profiling study of anaplastic oligodendroglioma |
Brain tumor-Glioma |
E-MTAB-2768 |
21653 |
71 |
Affymetrix GeneChip Human Genome U133 Plus 2.1 |
2015 |
2018 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2768 |
26068201 |
Bioconductor justRMA with default values for background-adjustment, normalization and log-transformation parameters |
| 34 |
Wavelet modelling of microarray data provides chromosomal pattern of expression which predicts survival in gliomas |
Brain tumor-Glioma |
GSE2817 |
21653 |
25 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2005 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2817 |
17140431 |
RMA |
| 35 |
Comprehensive and Integrative Genomic Characterization of Diffuse Lower Grade Gliomas |
Brain tumor-Glioma |
TCGA-LGG |
34849 |
495 |
HTSeq |
2015 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-LGG |
26061751 |
TPM |
| 36 |
Putamen involvement and survival outcomes in patients with insular low-grade gliomas |
Brain tumor-Glioma/GBM |
CGGA_301 |
19416 |
300 |
Agilent Whole Human Genome (Array) |
2017 |
2021 |
http://www.cgga.org.cn/download.jsp |
27564467 |
Normalized signal intensity |
| 37 |
Expression data as part of an Integrated analysis of oligodendroglial tumours |
Brain tumor-Glioma/GBM |
E-MTAB-3892 |
21653 |
175 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 |
2016 |
2018 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3892 |
27090007 |
RMA |
| 38 |
Intrinsic Gene Expression Profiles of Gliomas are a Better Predictor of Survival than Histology |
Brain tumor-Glioma/GBM |
GSE16011 |
21653 |
284 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array |
2009 |
2014 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16011 |
19920198 |
RMA |
| 39 |
Molecular subclasses of high-grade glioma: prognosis, disease progression, and neurogenesis |
Brain tumor-Glioma/GBM |
GSE4271_GPL96 |
12547 |
100 |
Affymetrix Human Genome U133B Array |
2006 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4271 |
16530701 |
RMA |
| 40 |
Molecular subclasses of high-grade glioma: prognosis, disease progression, and neurogenesis |
Brain tumor-Glioma/GBM |
GSE4271_GPL97 |
10603 |
100 |
Affymetrix Human Genome U133B Array |
2006 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4271 |
16530701 |
RMA |
| 41 |
freij-affy-human-91666 |
Brain tumor-Glioma/GBM |
GSE4412_GPL96 |
12547 |
85 |
Affymetrix Human Genome U134A Array |
2006 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4412 |
15374961 |
RMA |
| 42 |
freij-affy-human-91666 |
Brain tumor-Glioma/GBM |
GSE4412_GPL97 |
10603 |
85 |
Affymetrix Human Genome U134B Array |
2006 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4412 |
15374961 |
RMA |
| 43 |
Comprehensive RNA-seq transcriptomic profiling in the malignant progression of gliomas. |
Brain tumor-Glioma/GBM |
CGGA_325 |
24326 |
325 |
Illumina HiSeq 2000 or 2500 |
2017 |
2021 |
http://www.cgga.org.cn/download.jsp |
28291232 |
RSEM |
| 44 |
Localizing seizure-susceptible brain regions associated with low-grade gliomas using voxel-based lesion-symptom mapping |
Brain tumor-Glioma/GBM |
CGGA_693 |
23987 |
693 |
Illumina HiSeq |
2015 |
2021 |
http://www.cgga.org.cn/download.jsp |
25031032 |
RSEM |
| 45 |
Expression data from 30 medulloblastomas |
Brain tumor-Medulloblastoma |
GSE30074 |
20202 |
30 |
Affymetrix Human Gene 1.0 ST Array |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30074 |
22090452 |
RMA |
| 46 |
Novel mutations target distinct subgroups of medulloblastoma. |
Brain tumor-Medulloblastoma |
GSE37418 |
21653 |
76 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2012 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37418 |
22722829 |
RMA |
| 47 |
Genomic landscape of meningiomas: gene expression |
Brain tumor-Meningioma |
GSE16581 |
21653 |
68 |
Affymetrix GeneChip Human Genome U133 Plus 2.1 Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16581 |
20015288 |
RMA |
| 48 |
Gene expression profiling of patients from the Danish Center for Translational Breast Cancer Research program |
Breast cancer |
E-MTAB-7201 |
34729 |
94 |
Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray 039494 |
2018 |
2018 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-7201 |
28123884 |
Log2 expresion |
| 49 |
Breast Cancer Dataset |
Breast cancer |
GSE3143 |
8619 |
158 |
Affymetrix HGU95 |
2005 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3143 |
16273092 |
Affymetrix Microarray Suite version 5.0 |
| 50 |
A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes |
Breast cancer |
GSE10886_GPL1390 |
10040 |
197 |
Agilent Human 1A Oligo UNC custom Microarrays |
2008 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10886 |
19204204 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 51 |
A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes |
Breast cancer |
GSE10886_GPL887 |
16546 |
27 |
Agilent-012097 Human 1A Microarray (V2) G4110B |
2008 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10886 |
19204204 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 52 |
Phenotypic and Molecular Characterization of the Claudin-low Intrinsic Subtype of Breast Cancer |
Breast cancer |
GSE18229_GPL1390 |
10040 |
199 |
Agilent Human 1A Oligo UNC custom Microarrays |
2009 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18229 |
20813035 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 53 |
Phenotypic and Molecular Characterization of the Claudin-low Intrinsic Subtype of Breast Cancer |
Breast cancer |
GSE18229_GPL887 |
16546 |
94 |
Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version) |
2009 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18229 |
20813035 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 54 |
Heterogeneity of Response to Chemotherapy and Recurrence-free Survival in Neoadjuvant Breast Cancer: Results from the I-SPY 1 TRIAL |
Breast cancer |
GSE22226_GPL1708 |
18841 |
129 |
Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version) |
2010 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22226 |
22198468 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 55 |
Heterogeneity of Response to Chemotherapy and Recurrence-free Survival in Neoadjuvant Breast Cancer: Results from the I-SPY 2 TRIAL |
Breast cancer |
GSE22226_GPL4133 |
19749 |
20 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) |
2010 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22226 |
22198468 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 56 |
Biological Classification of Breast Cancer by Real-Time Quantitative RTPCR: Comparisons to Microarray and Histopathology |
Breast cancer |
GSE2607_GPL1390 |
10040 |
64 |
Agilent Human 1A Oligo UNC custom Microarrays |
2005 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2607 |
16626501 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 57 |
Biological Classification of Breast Cancer by Real-Time Quantitative RTPCR: Comparisons to Microarray and Histopathology |
Breast cancer |
GSE2607_GPL887 |
16546 |
50 |
Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version) |
2005 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2607 |
16626501 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 58 |
Agreement in Breast Cancer Classification between Microarray and qRT-PCR from Fresh-Frozen and Formalin-Fixed Tissues |
Breast cancer |
GSE6130_GPL1390 |
10040 |
96 |
Agilent Human 1A Oligo UNC custom Microarrays |
2006 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6130 |
17525107 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 59 |
Agreement in Breast Cancer Classification between Microarray and qRT-PCR from Fresh-Frozen and Formalin-Fixed Tissues |
Breast cancer |
GSE6130_GPL887 |
16546 |
53 |
Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version) |
2006 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6130 |
17525107 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken |
| 60 |
Molecular Characterization of Breast Cancer Subtypes Derived from Joint Analysis of High Throughput miRNA and mRNA Data |
Breast cancer |
GSE19536_GPL6480 |
19595 |
114 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) |
2009 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19536 |
21364938 |
Feature Extraction (FE) v9.5.3.1 was used to extract signals. Data were log2 transformed, non-uniform spots were excluded, and when averaging replicated probes, population outliers were excluded. Probes that are missing on more than 10 arrays were excluded. |
| 61 |
A gene-expression signature to predict survival in breast cancer across independent data sets |
Breast cancer |
Caldas-2007 |
14708 |
135 |
Agilent Human 1A 60-mer Oligo Microarray |
2007 |
2011 |
https://pubmed.ncbi.nlm.nih.gov/16936776/ |
16936776 |
Feature extraction, normalization of the raw data and data filtering were performed using the Agilent G2567AA Feature Extraction software (Agilent Technologies) and Spotfire DecisionSite 8.0 (Somerville, MA, USA) |
| 62 |
A new gene expression signature, the ClinicoMolecular Triad Classification, may improve prediction and prognostication of breast cancer at the time of diagnosis |
Breast cancer |
GSE16987 |
18196 |
161 |
Illumina humanRef-8 v2.0 expression beadchip |
2009 |
2015 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16987 |
21939527 |
Image data were processed by BeadStudio software using background subtraction and Quantile normalization. |
| 63 |
Gene expression variation to predict 10-year survival in lymph-node-negative breast cancer |
Breast cancer |
GSE12071 |
12697 |
46 |
SWEGENE H_v3.0.1 35K |
2008 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12071 |
18778486 |
Intensities were calculated by median spot - median background. Flagged spots and spots for which background adjusted intensities were <0 or >65 000 were excluded as well as spots with intensities below 20 in both channels. Intensities below 20 in one channel were set to 20 to compensate for extreme quotients. pin-based Lowess normalization were performed with 12 blocks in each group |
| 64 |
A gene expression signature predicting the recurrence of tamoxifen-treated primary breast cancer. |
Breast cancer |
GSE9893 |
14819 |
155 |
MLRG Human 21K V12.0 |
2007 |
2015 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9893 |
18347175 |
log F635 norm |
| 65 |
Estrogen receptor beta expression is associated with tamoxifen response in ER alpha-negative breast carcinoma |
Breast cancer |
GSE6577 |
6742 |
88 |
Swegene Human 27K RAP UniGene188 array |
2006 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6577 |
17404078 |
log2 ratio (tumor ch1=532nm/reference ch2=635nm) after filtering and normalization procedures. |
| 66 |
Comparison between Estrogen receptor positive and Estrogen receptor negative breast cancer samples |
Breast cancer |
GSE10510 |
19852 |
152 |
DKFZ Division of Molecular Genome Analysis Human Operon 4.0 oligo Array 35k |
2008 |
2013 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10510 |
18592372 |
log2 ratios (Cy5/Cy3) |
| 67 |
Subtype-dependent prognostic relevance of an interferon-induced pathway metagene in human node negative breast cancer |
Breast cancer |
GSE37181 |
25438 |
123 |
Illumina HumanWG-6 v3.0 expression beadchip |
2012 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37181 |
24853384 |
Log2 tranformation; Robust Spline Normalization |
| 68 |
ABI1-based 7-gene expression signature predicts breast cancer metastasis and survival |
Breast cancer |
GSE159956 |
12201 |
295 |
Rosetta (Merck) GEL Breast Tumor Profiles |
2020 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159956 |
NA |
Normalization between the channels was accomplished by normalizing each channel to the mean intensities of all genes. |
| 69 |
Genomic Subtypes of Breast Cancer Identified by Array Comparative Genomic Hybridization |
Breast cancer |
GSE22133_GPL5345 |
8427 |
359 |
SWEGENE H_v2.1.1 55K |
2010 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22133 |
20576095 |
Normalized log2 ratio (tumor/reference male DNA) |
| 70 |
Gene expression profiling of early primary breast cancer to identify prognostic markers and associated pathways |
Breast cancer |
GSE22219 |
21438 |
216 |
Illumina humanRef-8 v1.0 expression beadchip |
2010 |
2013 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22219 |
21737487 |
Normalized log2 signal intensity |
| 71 |
breast cancer / tamoxifen monotherapy (whole tissue tumor biopsies) |
Breast cancer |
GSE1379 |
11728 |
60 |
Arcturus 22k human oligonucleotide microarray |
2004 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1379 |
15193263 |
Normalized ratio of Cy5/Cy3 |
| 72 |
Internal validation cohort of breast cancers for development of ClinicoMolecular Triad Classification |
Breast cancer |
GSE45725 |
18630 |
340 |
Illumina HumanRef-8 v3.0 expression beadchip |
2013 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45725 |
24996446 |
quantile-normalized log2 ratio (intensity value/average signal in all samples) |
| 73 |
Gene expression profiles of breast cancer metastasis according to organ site |
Breast cancer |
GSE175692 |
771 |
184 |
nCounter Breast Cancer 360 Panel |
2021 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175692 |
34051058 |
Raw counts of each gene were subjected to a technical normalization using the geometric mean of five housekeeping genes (ACTB, MRPL19, PSMC4, RPLP0 and SF3A1). Normalized values were then log2 transformed. |
| 74 |
Transcription profiling of human breast cancer samples |
Breast cancer |
E-TABM-158 |
12888 |
100 |
Affymetrix High Throughput Array U133AA of Av2 |
2008 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-158 |
17157792 |
RMA |
| 75 |
The humoral immune system has a key prognostic impact in node-negative breast cancer |
Breast cancer |
GSE11121 |
12547 |
200 |
Affymetrix Human Genome U133A Array |
2008 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11121 |
18593943 |
RMA |
| 76 |
The 76-gene Signature Defines High-Risk Patients that Benefit from Adjuvant Tamoxifen Therapy |
Breast cancer |
GSE12093 |
12547 |
136 |
Affymetrix Human Genome U133A Array |
2008 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12093 |
18821012 |
RMA |
| 77 |
Expression data from primary breast tumors |
Breast cancer |
GSE12276 |
21653 |
204 |
Affymetrix HGU |
2008 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12276 |
19421193 |
RMA |
| 78 |
Gene expression of breast cancer tissue in a large population-based cohort of Swedish patients |
Breast cancer |
GSE1456_GPL96 |
12547 |
159 |
Affymetrix HGU |
2004 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1456 |
16280042 |
RMA |
| 79 |
Gene Expression Signature of Microcalcification among Taiwanese Breast Cancer |
Breast cancer |
GSE146558 |
21653 |
109 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2020 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146558 |
34387660 |
RMA |
| 80 |
Prognostic significance of interferon-γ and its signaling pathway in early breast cancer depends on the molecular subtypes |
Breast cancer |
GSE158309 |
12547 |
461 |
Affymetrix Human Genome U133A Array |
2020 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158309 |
33003293 |
RMA |
| 81 |
Multifactorial Approach to Predicting Resistance to Anthracyclines |
Breast cancer |
GSE16446 |
21653 |
120 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16446 |
21422418 |
RMA |
| 82 |
Endocrine Sensitivity Index Validation Dataset |
Breast cancer |
GSE17705 |
12547 |
298 |
Affymetrix Human Genome U133A Array |
2009 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17705 |
20697068 |
RMA |
| 83 |
Integrated genomic and function characterization of the 8q22 gain |
Breast cancer |
GSE19615 |
21653 |
115 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19615 |
20098429 |
RMA |
| 84 |
Breast cancer relapse free survival |
Breast cancer |
GSE2034 |
12547 |
286 |
Affymetrix Human Genome U134A Array |
2004 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2034 |
17420468, 15721472 |
RMA |
| 85 |
Epigenetic portraits of human breast cancers (expression data) |
Breast cancer |
GSE20711 |
21653 |
90 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2010 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20711 |
21910250 |
RMA |
| 86 |
A gene expression signature identifies two prognostic subgroups of basal breast cancer |
Breast cancer |
GSE21653 |
21653 |
266 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21653 |
20490655 |
RMA |
| 87 |
Discovery cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer |
Breast cancer |
GSE25055 |
12547 |
310 |
Affymetrix Human Genome U136A Array |
2010 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25055 |
21558518 |
RMA |
| 88 |
Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer |
Breast cancer |
GSE25065 |
12547 |
198 |
Affymetrix Human Genome U137A Array |
2010 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25065 |
21558518 |
RMA |
| 89 |
Subpopulations of MDA-MB-231 and Primary Breast Cancers |
Breast cancer |
GSE2603 |
12547 |
121 |
Affymetrix Human Genome U133A Array |
2005 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2603 |
16049480 |
RMA |
| 90 |
Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis |
Breast cancer |
GSE2990 |
12547 |
189 |
Affymetrix Human Genome U133A Array |
2006 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2990 |
16478745, 17401012 |
RMA |
| 91 |
An expression signature for p53 in breast cancer predicts mutation status, transcriptional effects, and patient survival |
Breast cancer |
GSE3494_GPL96 |
12547 |
251 |
Affymetrix Human Genome U133A Array |
2005 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3494 |
16141321 |
RMA |
| 92 |
Molecular Profiles of Human Breast Cancer and Their Association with Tumor Subtypes and Disease Prognosis (Affymetrix) |
Breast cancer |
GSE37751 |
20202 |
108 |
Affymetrix Human Gene 1.0 ST Array |
2012 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37751 |
24316975 |
RMA |
| 93 |
Breast Cancer Gene Expression Analysis |
Breast cancer |
GSE42568 |
21653 |
121 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2012 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568 |
23740839 |
RMA |
| 94 |
Expression Profiles of Breast Tumors from Singapore and Europe |
Breast cancer |
GSE45255 |
12547 |
139 |
Affymetrix Human Genome U133A Array |
2013 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45255 |
23618380 |
RMA |
| 95 |
Concurrent Gene Signatures for Han Chinese Breast Cancers |
Breast cancer |
GSE48390 |
21653 |
81 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2013 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48390 |
24098497 |
RMA |
| 96 |
Genetic Reclassification of Histologic Grade Delineates New Clinical Subtypes of Breast Cancer |
Breast cancer |
GSE4922_GPL96 |
12547 |
249 |
Affymetrix Human Genome U133A Array |
2006 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4922 |
17079448 |
RMA |
| 97 |
Gene expression profiling of human breast cancer during pregnancy |
Breast cancer |
GSE53031 |
19040 |
167 |
Affymetrix Human Genome U219 Array |
2013 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53031 |
24825746 |
RMA |
| 98 |
Breast cancer relapse free survival and lung metastasis free survival |
Breast cancer |
GSE5327 |
12547 |
58 |
Affymetrix Human Genome U134A Array |
2006 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5327 |
17420468 |
RMA |
| 99 |
Breast cancer relapse free survival and lung metastasis free survival |
Breast cancer |
GSE58644 |
20202 |
321 |
Affymetrix Gene1.0ST |
2014 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58644 |
25284793 |
RMA |
| 100 |
Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response |
Breast cancer |
GSE58812 |
21653 |
107 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2014 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58812 |
25887482 |
RMA |
| 101 |
Definition of clinically distinct molecular subtypes in estrogen receptor positive breast carcinomas using genomic grade |
Breast cancer |
GSE6532_GPL570 |
21653 |
87 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2006 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6532 |
17401012 |
RMA |
| 102 |
Definition of clinically distinct molecular subtypes in estrogen receptor positive breast carcinomas using genomic grade |
Breast cancer |
GSE6532_GPL96 |
12547 |
138 |
Affymetrix Human Genome U133A Array |
2006 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6532 |
17401012 |
RMA |
| 103 |
Strong Time Dependence of the 76-Gene Prognostic Signature |
Breast cancer |
GSE7390 |
12547 |
198 |
Affymetrix Human Genome U135A Array |
2007 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7390 |
17545524 |
RMA |
| 104 |
Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen |
Breast cancer |
GSE9195 |
21653 |
77 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2007 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9195 |
18498629 |
RMA |
| 105 |
Tumour Subtype defined by an amplification of the HER2 gene |
Breast cancer |
ICGC-BRCA-FR |
20039 |
99 |
Affymetrix Human U133 Plus 2.0 |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/BRCA-FR |
NA |
RMA |
| 106 |
Breast cancer subtype of Asian phenotype |
Breast cancer |
ICGC-BRCA-KR |
26730 |
50 |
HTSeq |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/BRCA-KR |
NA |
RSEM |
| 107 |
Prognostic value of gene signatures and proliferation in lymph node negative breast cancer |
Breast cancer |
GSE46563 |
25438 |
94 |
Illumina HumanWG-6 v3.0 expression beadchip |
2013 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46563 |
24599057 |
The data were normalised using quantile normalisation with IlluminaGUI in R |
| 108 |
Comprehensive molecular portraits of human breast tumors |
Breast cancer |
TCGA-BRCA |
34849 |
1050 |
TCGA-BRCA |
2012 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= |
23000897 |
TPM |
| 109 |
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups |
Breast cancer |
METABRIC |
25233 |
2136 |
METABRIC |
2012 |
2021 |
https://ega-archive.org/studies/EGAS00000000083 |
22522925 |
NA |
| 110 |
Breast cancer classification and prognosis based on gene expression profiles from a population-based study |
Breast cancer |
NCI |
4111 |
99 |
In-house cDNA |
2003 |
2003 |
http://www.ncbi.nlm.nih.gov/pubmed/?term=12917485 |
12917485 |
NA |
| 111 |
A gene-expression signature as a predictor of survival in breast cancer |
Breast cancer |
NKI |
13114 |
337 |
Agilent |
2002 |
2002 |
http://www.ncbi.nlm.nih.gov/pubmed/?term=12490681；http://www.ncbi.nlm.nih.gov/pubmed/?term=11823860 |
12490681, 11823860 |
NA |
| 112 |
Identification of a robust gene signature that predicts breast cancer outcome in independent data sets |
Breast cancer |
UCSF |
6497 |
162 |
In-house cDNA |
2007 |
2007 |
http://www.ncbi.nlm.nih.gov/pubmed/?term=17428335 |
17428335, 14612510 |
NA |
| 113 |
A Biologic Definition of Burkitt's Lymphoma from Transcriptional and Genomic Profiling |
Burkitt's lymphoma |
GSE4475 |
12547 |
221 |
Affymetrix Human Genome U133A Array |
2006 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4475 |
16760442 |
RMA |
| 114 |
Genetic profiling to predict recurrence of early cervical cancer |
Cervical cancer |
GSE44001 |
20818 |
300 |
Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip |
2013 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44001 |
24145113 |
quantile normalized |
| 115 |
Integrated Genomic and Molecular Characterization of Cervical Cancer |
Cervical cancer |
TCGA-CESC |
34849 |
283 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-CESC |
28112728 |
TPM |
| 116 |
Distinct immune escape mechanisms identified in intrahepatic cholangiocarcinoma by immune classification |
Cholangiocarcinoma |
E-MTAB-6389 |
25359 |
109 |
Affymetrix GeneChip HTA-2_0 - Exon Level - HTA-2_0.r1.PsrsJucs.ps probesets |
2018 |
2019 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6389 |
NA |
RMA |
| 117 |
Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles |
Cholangiocarcinoma |
TCGA-CHOL |
34849 |
36 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-CHOL |
28658632 |
TPM |
| 118 |
The Somatic Genomic Landscape Of Chromophobe Renal Cell Carcinoma |
Chromophobe renal cell carcinoma |
TCGA-KICH |
34849 |
64 |
HTSeq |
2014 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-KICH |
25155756 |
TPM |
| 119 |
An eight-gene expression signature for the prediction of survival and time to treatment in chronic lymphocytic leukemia |
Chronic lymphocytic leukemia |
GSE22762_GPL570 |
21653 |
107 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22762 |
21625232 |
RMA |
| 120 |
An eight-gene expression signature for the prediction of survival and time to treatment in chronic lymphocytic leukemia |
Chronic lymphocytic leukemia |
GSE22762_GPL96 |
12547 |
44 |
Affymetrix Human Genome U133A Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22762 |
21625232 |
RMA |
| 121 |
An eight-gene expression signature for the prediction of survival and time to treatment in chronic lymphocytic leukemia |
Chronic lymphocytic leukemia |
GSE22762_GPL97 |
10603 |
44 |
Affymetrix Human Genome U133B Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22762 |
21625232 |
RMA |
| 122 |
EMT is the dominant program in human colon cancer (Agilent) |
Colon cancer |
GSE28722 |
15240 |
125 |
Rosetta custom human 23K array |
2011 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28722 |
21251323 |
normalized log10 ratio (Cy5/Cy3) representing test/reference |
| 123 |
Transcription profiling by array of human stage II colon cancers as a prognostic training set |
Colon cancer |
E-MTAB-863 |
3102 |
212 |
Affymetrix Custom Array - Almac Diagnostics Colorectal Cancer DSATM research tool ADXCRCG2a520319 |
2011 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-863 |
22067406 |
refRMA |
| 124 |
Transcription profiling by array of human stage II colon cancers as a prognostic validation set |
Colon cancer |
E-MTAB-864 |
3102 |
144 |
Affymetrix Custom Array - Almac Diagnostics Colorectal Cancer DSATM research tool ADXCRCG2a520319 |
2011 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-864 |
22067406 |
refRMA |
| 125 |
Integrative approach for prioritizing cancer genes in sporadic colon cancer |
Colon cancer |
GSE16125_GPL5175 |
497 |
36 |
Affymetrix Human Exon 1.0 ST Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16125 |
19672874 |
RMA |
| 126 |
Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples) |
Colon cancer |
GSE17536 |
21653 |
177 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2009 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536 |
19914252 |
RMA |
| 127 |
Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (VMC Samples) |
Colon cancer |
GSE17537 |
21653 |
55 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2009 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17537 |
19914252 |
RMA |
| 128 |
mRNA and microRNA profile in colon cancer |
Colon cancer |
GSE29621 |
21653 |
65 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29621 |
22362069 |
RMA |
| 129 |
Gene Expression Profiles in Stage II and III Colon Cancer. Application of a 128-gene signature |
Colon cancer |
GSE31595 |
21653 |
37 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31595 |
22710688 |
RMA |
| 130 |
NFAT transcriptional activity is associated with metastatic capacity in colon cancer |
Colon cancer |
GSE38832 |
21653 |
122 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2012 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38832 |
25320007 |
RMA |
| 131 |
Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics |
Colon cancer |
GSE39582 |
21653 |
585 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2012 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582 |
23700391 |
RMA |
| 132 |
Comprehensive Molecular Characterization of Human Colon and Rectal Cancer |
Colon cancer |
TCGA-COAD |
34849 |
430 |
HTSeq |
2012 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-COAD |
22810696 |
TPM |
| 133 |
Expression data from colorectal cancers |
Colorectal cancer |
GSE12945 |
12547 |
62 |
Affymetrix Human Genome U134A Array |
2008 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12945 |
19399471 |
RMA |
| 134 |
Expression data from 290 primary colorectal cancers |
Colorectal cancer |
GSE14333 |
21653 |
290 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333 |
19996206 |
RMA |
| 135 |
Gene level expression profiling of colorectal cancer tissue samples (test sample series) |
Colorectal cancer |
GSE30378 |
497 |
95 |
Affymetrix Human Exon 1.0 ST Array |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30378 |
22213796 |
RMA |
| 136 |
Expression data from colorectal cancer patients |
Colorectal cancer |
GSE41258 |
12547 |
182 |
Affymetrix Human Genome U134A Array |
2012 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41258 |
19359472 |
RMA |
| 137 |
Exon level expression profiling of colorectal cancer tissue samples (test sample series). |
Colorectal cancer |
GSE24549_GPL5175 |
497 |
83 |
Affymetrix Human Exon 1.0 ST Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24549 |
21619627 |
RMA |
| 138 |
Exon level expression profiling of colorectal cancer tissue samples (validation sample series). |
Colorectal cancer |
GSE24550_GPL5175 |
497 |
90 |
Affymetrix Human Exon 1.0 ST Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24550 |
21619627 |
RMA |
| 139 |
Genomic Classification of Cutaneous Melanoma |
Cutaneous melanoma |
TCGA-SKCM |
34849 |
98 |
HTSeq |
2015 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-SKCM |
26091043 |
TPM |
| 140 |
Exon-based transcriptome profiling of high-risk DLBCL patients less than 65 years old |
Diffuse large B cell lymphoma |
E-MEXP-3488 |
20088 |
43 |
Affymetrix GeneChip Human Exon 1.0 ST Array version 1 |
2012 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3488 |
25381134 |
Multiple Exon Array Preprocessing (MEAP) algorithm |
| 141 |
Transcription profiling of human patients with diffuse large B-cell lymphoma treated with CHOP or Ritxumab-CHOP |
Diffuse large B cell lymphoma |
E-TABM-346 |
12547 |
53 |
Affymetrix GeneChip Human Genome HG-U133A |
2008 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-346 |
18615101 |
RMA |
| 142 |
Prediction of survival in diffuse large B cell lymphoma treated with chemotherapy plus Rituximab |
Diffuse large B cell lymphoma |
GSE10846 |
21653 |
420 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2008 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10846 |
19038878 |
RMA |
| 143 |
DNA methylation signatures define molecular subtypes of Diffuse Large B Cell Lymphoma |
Diffuse large B cell lymphoma |
GSE23501 |
21653 |
69 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23501 |
20610814 |
RMA |
| 144 |
Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma |
Diffuse large B cell lymphoma |
TCGA-DLBC |
34849 |
46 |
HTSeq |
2018 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-DLBC |
29641966 |
TPM |
| 145 |
Integrated Genomic Characterization of Endometrial Carcinoma |
Endometrial Carcinoma |
TCGA-UCEC |
34849 |
533 |
HTSeq |
2013 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-UCEC |
23636398 |
TPM |
| 146 |
Human esophageal adenocarcinomas |
Esophageal adenocarcinomas |
GSE19417 |
19882 |
70 |
Rosetta/Merck Human 44k 1.1 microarray |
2009 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19417 |
20621683 |
Normalized log10 ratio (Cy5/Cy3) representing test/reference |
| 147 |
Integrated Genomic Characterization of Oesophageal Carcinoma |
Esophageal adenocarcinomas |
TCGA-ESCA |
34849 |
151 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-ESCA |
28052061 |
TPM |
| 148 |
Differences Between Follicular Lymphoma With and Without Translocation t(14;18) |
Follicular lymphoma |
GSE16131_GPL96 |
12547 |
184 |
Affymetrix Human Genome U133A Array |
2009 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16131 |
19471018 |
RMA |
| 149 |
Differences Between Follicular Lymphoma With and Without Translocation t(14;19) |
Follicular lymphoma |
GSE16131_GPL97 |
10603 |
184 |
Affymetrix Human Genome U133B Array |
2009 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16131 |
19471018 |
RMA |
| 150 |
Gene expression profiling of formalin fixed paraffin embedded tumor tissue identifies gastric cancer patients who are at high risk after curative surgery plus adjuvant chemoradiotherapy |
Gastric cancer |
GSE26253 |
13509 |
432 |
Illumina HumanRef-8 WG-DASL v3.0 |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26253 |
24598828 |
quantile normalized |
| 151 |
Gastric Cancer Project '08 (Singapore Patient Cohort) |
Gastric cancer |
GSE15459 |
21653 |
192 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15459 |
19798449 |
RMA |
| 152 |
Gastric cancer subtyping (Singapore Patient Cohort, batch B) |
Gastric cancer |
GSE34942 |
21653 |
56 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2012 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34942 |
25053715 |
RMA |
| 153 |
Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study |
Gastric cancer |
GSE62254 |
21653 |
300 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2014 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62254 |
25894828 |
RMA |
| 154 |
Comprehensive Molecular Characterization of Gastric Adenocarcinoma |
Gastric cancer |
TCGA-STAD |
34849 |
348 |
HTSeq |
2019 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-STAD |
25079317 |
TPM |
| 155 |
head and neck squamous cell carcinoma samples |
Head and neck squamous cell carcinoma |
GSE10300 |
21653 |
44 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2008 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10300 |
19117988 |
gcRMA |
| 156 |
Gene expression patterns and TP53 mutations are associated with HPV RNA status, lymph node metastasis, and survival in head and neck cancer |
Head and neck squamous cell carcinoma |
GSE65858 |
22000 |
270 |
Illumina HumanHT-12 V4.0 expression beadchip |
2015 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65858 |
26095926 |
log2-transformed and normalized using RSN |
| 157 |
Methylome, transcriptome and miRNome profiling by array and high throughput sequencing of 89 patients with head and neck squamous cell carcinoma |
Head and neck squamous cell carcinoma |
E-MTAB-1328 |
21653 |
89 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2013 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1328 |
23757353 |
RMA |
| 158 |
Comprehensive Genomic Characterization of Head and Neck Squamous Cell Carcinomas |
Head and neck squamous cell carcinoma |
TCGA-HNSC |
34849 |
494 |
HTSeq |
2015 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-HNSC |
25631445 |
TPM |
| 159 |
LIVER CANCER - RIKEN, JP |
Hepatocellular Carcinoma |
ICGC-LIRI-JP |
22913 |
445 |
HTSeq |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/LIRI-JP |
NA |
FKPM |
| 160 |
Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma |
Hepatocellular Carcinoma |
GSE10141 |
6100 |
80 |
Human 6k Transcriptionally Informative Gene Panel for DASL |
2008 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10141 |
18923165 |
For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were were then normalized using the cubic spline algorithm for each DAP. |
| 161 |
Gene expression in nontumoral liver tissue and recurrence-free survival in hepatitis C virus-positive HCC |
Hepatocellular Carcinoma |
GSE17856 |
14313 |
52 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17856 |
20380719 |
Normalization and filtering were performed with UNC Microarray Database (https://genome.unc.edu/). Inter-batch normalization was carried out using Distance Weighted Discrimination procedure. |
| 162 |
Transcriptional profile of human liver tissues: hepatocellular carcinoma vs. matched noncancerousliver tissue |
Hepatocellular Carcinoma |
GSE27150 |
2348 |
81 |
State Key Lab Homo sapien 2.6K |
2011 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27150 |
NA |
normalized log2 ratio (Cy5/Cy3) representing hepatocellular carcinoma/matched noncancerousliver tissue |
| 163 |
Gene expression data of human hepatocellular carcinoma (HCC) |
Hepatocellular Carcinoma |
GSE14520 |
12742 |
221 |
Affymetrix HT Human Genome U133A Array |
2009 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520 |
21159642 |
RMA |
| 164 |
Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma |
Hepatocellular Carcinoma |
TCGA-LIHC |
34849 |
363 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-LIHC |
28622513 |
TPM |
| 165 |
Identification and validation of a multigene predictor of recurrence in primary laryngeal cancer. |
Laryngeal cancer |
GSE27020 |
12547 |
109 |
Affymetrix Human Genome U133A Array |
2011 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27020 |
23950933 |
RMA |
| 166 |
Expression profiling of 275 lung cancer specimens |
Lung cancer |
GSE41271 |
25438 |
275 |
Illumina HumanWG-6 v3.0 expression beadchip |
2019 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41271 |
23449933 |
Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed |
| 167 |
Lung Cancer Dataset |
Lung cancer |
GSE3141 |
21653 |
111 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2005 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3141 |
16273092 |
MAS5- |
| 168 |
"Off-context" gene expression in lung cancer identifies a group of metastatic-prone tumors |
Lung cancer |
GSE30219 |
21653 |
307 |
Affymetrix Human Genome U133 Plus 2.0 Array |
201 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219 |
23698379 |
RMA |
| 169 |
MSKCC-A Primary Lung Cancer Specimens |
Lung cancer |
GSE31547 |
12547 |
50 |
Affymetrix Human Genome U133A Array |
2011 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31547 |
NA |
RMA |
| 170 |
Human lung adenocarcinoma mRNA expression and gene mutations. |
Lung cancer-Lung adenocarcinoma |
GSE26939 |
17108 |
116 |
Agilent-UNC-custom-4X44K |
2011 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26939 |
22590557 |
Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma. |
| 171 |
KRAS mutation-associated gene expression, p53 and STK11 mutations, proliferation and immune surveillance in lung adenocarcinoma |
Lung cancer-Lung adenocarcinoma |
GSE72094 |
22115 |
442 |
Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray |
2015 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72094 |
26477306 |
log2 expression, IRON normalized signal |
| 172 |
Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis |
Lung cancer-Lung adenocarcinoma |
GSE13213 |
18479 |
117 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F |
2008 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13213 |
19414676 |
log2 of PRE_VALUE: Normalized ratio (Cy5/Cy3) representing sample/reference |
| 173 |
Expression Profile-Defined Classification of Lung Adenocarcinoma |
Lung cancer-Lung adenocarcinoma |
GSE11969 |
16624 |
163 |
Agilent Homo sapiens 21.6K custom array |
2008 |
2013 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11969 |
16549822 |
LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used. |
| 174 |
Expression profiling defines a recurrence signature in lung adenocarcinoma |
Lung cancer-Lung adenocarcinoma |
GSE5843 |
13111 |
48 |
PRHU05-S1-0006 (PC Human Operon v2 21k) |
2006 |
2015 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5843 |
17504995 |
Raw images were imported into Imagene V5.1 (BioDiscovery, CA, USA) to extract pixel intensities and to flag spots with poor/absent signal. |
| 175 |
Transcription profiling by array of human lung samples from patients with adenocarcinoma to identify likely drivers of cell proliferation |
Lung cancer-Lung adenocarcinoma |
E-MTAB-923 |
21653 |
103 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 |
2012 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-923 |
22914773 |
RMA |
| 176 |
Gene expression data for pathological stage I-II lung adenocarcinomas |
Lung cancer-Lung adenocarcinoma |
GSE31210 |
21653 |
246 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210 |
22080568 |
RMA |
| 177 |
caArray_jacob-00182: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study |
Lung cancer-Lung adenocarcinoma |
GSE68465 |
12547 |
462 |
Affymetrix Human Genome U133A Array |
2015 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68465 |
18641660 |
RMA |
| 178 |
caArray_beer-00153: Gene-expression profiles predict survival of patients with lung adenocarcinoma |
Lung cancer-Lung adenocarcinoma |
GSE68571 |
5249 |
96 |
Affymetrix Human Full Length HuGeneFL Array |
2015 |
2016 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68571 |
12118244 |
RMA |
| 179 |
Multi-platform Characterization of Stage I Lung Adenocarcinoma (mRNA expression) |
Lung cancer-Lung adenocarcinoma |
GSE63459 |
18630 |
65 |
Illumina HumanRef-8 v3.0 expression beadchip |
2014 |
2017 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63459 |
26134223 |
RSN-normalized |
| 180 |
Comprehensive molecular profiling of lung adenocarcinoma |
Lung cancer-Lung adenocarcinoma |
TCGA-LUAD |
34849 |
497 |
HTSeq |
2014 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-LUAD |
25079552 |
TPM |
| 181 |
Human lung squamous cell carcinoma expression profiling |
Lung cancer-Lung squamous cell carcinoma |
GSE17710 |
17108 |
56 |
Agilent-UNC-custom-4X44K |
2009 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17710 |
20643781 |
Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma. |
| 182 |
Lung squamous cell carcinomas with basaloid histology represent a specific molecular entity |
Lung cancer-Lung squamous cell carcinoma |
E-MTAB-2435 |
21653 |
93 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 |
2014 |
2018 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2435 |
25189482 |
RMA |
| 183 |
Molecular Classification and Prediction of Survival in Non-Small-Cell Lung Cancer |
Lung cancer-Non-small cell lung cancer |
GSE11117 |
9661 |
56 |
Novachip human 34.5k |
2008 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11117 |
19833826 |
The fluorescence images is analyzed by means of Array Pro (Mediacybernetics, Inc. US). |
| 184 |
Prediction of Recurrence-Free Survival in Postoperative NSCLC Patients—a Useful Prospective Clinical Practice |
Lung cancer-Non-small cell lung cancer |
GSE8894 |
21653 |
138 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2007 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8894 |
19010856 |
GCRMA |
| 185 |
Multi-institutional prospective validation of prognostic mRNA signatures in early stage squamous lung cancer (Alliance) |
Lung cancer-Non-small cell lung cancer |
GSE157009 |
21653 |
249 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2020 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157009 |
32717408 |
MAS.5 |
| 186 |
Gene expression signatures for predicting prognosis of squamous cell lung carcinomas |
Lung cancer-Non-small cell lung cancer |
GSE4573 |
12547 |
129 |
Affymetrix Human Genome U133A Array |
2006 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4573 |
16885343 |
MAS5-calculated Signal intensity after global scaling the average intensity to 600. |
| 187 |
Expression data for non-small-cell lung cancer |
Lung cancer-Non-small cell lung cancer |
GSE42127 |
25438 |
176 |
Illumina HumanWG-6 v3.0 expression beadchip |
2012 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42127 |
23357979 |
Microarray data analysis and quality control were based on the Model-Based Background Correction (MBCB) method. |
| 188 |
Prognostic and Predictive Gene Signature for Adjuvant Chemotherapy in Resected Non-Small-Cell Lung Cancer |
Lung cancer-Non-small cell lung cancer |
GSE14814 |
12547 |
133 |
Affymetrix Human Genome U133A Array |
2009 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14814 |
20823422 |
RMA |
| 189 |
Multi-institutional prospective validation of prognostic mRNA signatures in early stage squamous lung cancer (Alliance) |
Lung cancer-Non-small cell lung cancer |
GSE157010 |
21653 |
235 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2020 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157010 |
32717408 |
RMA |
| 190 |
Expression data for early stage NSCLC |
Lung cancer-Non-small cell lung cancer |
GSE19188 |
21653 |
156 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19188 |
20421987 |
RMA |
| 191 |
Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis and tissue microarray validation |
Lung cancer-Non-small cell lung cancer |
GSE37745 |
21653 |
196 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2012 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745 |
23032747 |
RMA |
| 192 |
Validation of a histology-independent prognostic gene signature for early stage, non-small cell lung cancer including stage IA patients |
Lung cancer-Non-small cell lung cancer |
GSE50081 |
21653 |
181 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2013 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50081 |
24305008 |
RMA |
| 193 |
Comprehensive genomic characterization of squamous cell lung cancers |
Lung cancer-Non-small cell lung cancer |
TCGA-LUSC |
34849 |
489 |
HTSeq |
2012 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-LUSC |
22960745 |
TPM |
| 194 |
Transcription profiling by array of cells obtained from the pleura of patients with mesothelioma |
Mesothelioma |
E-MTAB-1719 |
21653 |
38 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 |
2014 |
2018 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1719 |
24443521 |
RMA |
| 195 |
mRNA profiling by array of malignant pleural mesothelioma |
Mesothelioma |
E-MTAB-6877 |
15653 |
67 |
Affymetrix Human Gene 2.0 ST Array |
2019 |
2020 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6877 |
30902996 |
RMA |
| 196 |
Integrative Molecular Characterization of Malignant Pleural Mesothelioma |
Mesothelioma |
TCGA-MESO |
34849 |
79 |
HTSeq |
2018 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-MESO |
30322867 |
TPM |
| 197 |
Gene expression profiling and correlation with outcome in clinical trials of the proteasome inhibitor bortezomib |
Multiple myeloma |
GSE9782_GPL96 |
12547 |
264 |
Affymetrix Human Genome U133A Array |
2007 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9782 |
17185464 |
MASS5 |
| 198 |
Gene expression profiling and correlation with outcome in clinical trials of the proteasome inhibitor bortezomib |
Multiple myeloma |
GSE9782_GPL97 |
10603 |
264 |
Affymetrix Human Genome U133B Array |
2007 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9782 |
17185464 |
MASS5 |
| 199 |
Transcription profiling by array of human plasma cells from myeloma patients to study molecular signatures of centrosome abnormalities |
Multiple myeloma |
E-MTAB-1038 |
20202 |
73 |
Affymetrix GeneChip Human Gene 1.0 ST Array |
2013 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1038 |
27234807 |
RMA |
| 200 |
Transcription profiling by array of CD-138-positive plasma cells from patients with multiple myeloma |
Multiple myeloma |
E-MTAB-4032 |
20202 |
151 |
Affymetrix Human Gene 1.0 ST Array |
2016 |
2016 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4032 |
27234807 |
RMA |
| 201 |
Identifying a high-risk cellular signature in the multiple myeloma bone marrow microenvironment |
Multiple myeloma |
GSE136337 |
21653 |
426 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2019 |
2020 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136337 |
33147277 |
RMA |
| 202 |
MAQC-II Project: Multiple myeloma (MM) data set |
Multiple myeloma |
GSE24080 |
21653 |
559 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080 |
20064235 |
RMA |
| 203 |
Gene expression profiles of patients with multiple myeloma who have been treated previously |
Multiple myeloma |
GSE57317 |
21653 |
55 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2014 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57317 |
25079174 |
RMA |
| 204 |
The MMRF CoMMpasS Study |
Multiple myeloma |
MMRF-CoMMpass |
34849 |
787 |
HTSeq |
2011 |
2018 |
https://portal.gdc.cancer.gov/projects |
27417553 |
TPM |
| 205 |
Telomerase is a prognostic marker of poor outcome and a therapeutic target in neuroblastoma |
Neuroblastoma |
E-MTAB-8248 |
19860 |
223 |
Agilent-020382 Human Custom Microarray 44k |
2019 |
2019 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8248 |
32291317 |
After washing and scanning, resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1. |
| 206 |
GDC TARGET-NBL |
Neuroblastoma |
TARGET-NBL |
58387 |
142 |
Illumina HiSeq |
2009 |
2019 |
https://xenabrowser.net/datapages/ |
23334666 |
log2(fpkm+3) |
| 207 |
An Investigation of Biomarkers Derived from Legacy Microarray Data for Their Utility in the RNA-Seq Era |
Neuroblastoma |
GSE62564 |
23465 |
498 |
Illumina HiSeq 2000 (Homo sapiens) |
2014 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62564 |
25150839 |
log2RPM |
| 208 |
ORAL CANCER - IN |
Oral cancer |
ICGC-ORCA-IN |
24003 |
40 |
HTSeq |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/ORCA-IN |
NA |
FPKM |
| 209 |
TARGET-OS |
Osteosarcoma |
TARGET-OS |
58387 |
87 |
Illumina HiSeq |
2009 |
2019 |
https://xenabrowser.net/datapages/ |
29228567 |
log2(fpkm+4) |
| 210 |
Genome-wide gene expression profiling on pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5yrs (n=34) and patients who did not develop metastases within 5yrs (n=19) |
Osteosarcoma |
GSE21257 |
24996 |
53 |
Illumina human-6 v2.0 expression beadchip (using nuIDs as identifier) |
2010 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21257 |
21372215 |
Normalized signal intensity |
| 211 |
Prediction of progression-free survival in patients with advanced-stage serous ovarian cancer |
Ovarian cancer |
GSE17260 |
19595 |
110 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17260 |
20300634 |
Signal intensity per spot was generated from the scanned image with Feature Extraction Software ver8.5 (Agilent Technologies) in the default settings. Data normalization was performed in GeneSpring GX 10 (Agilent Technologies) as follows: (i) Threshold raw signals were set to 1.0. (ii) Quantile normalization was chosen as normalized algorithm. (iii) Baseline was transformed to median of all samples. |
| 212 |
OVARIAN CANCER - AU |
Ovarian cancer |
ICGC-OV-AU |
24650 |
111 |
HTSeq |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/OV-AU |
NA |
FPKM |
| 213 |
Gene expression profiling in ovarian cancer |
Ovarian cancer |
GSE73614 |
19584 |
107 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F |
2015 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73614 |
27016234 |
lowess normalized |
| 214 |
Validating the Impact of a Molecular Subtype in Epithelial Ovarian Cancer (EOC) on Progression Free and Overall Survival |
Ovarian cancer |
GSE49997 |
16751 |
204 |
ABI Human Genome Survey Microarray Version 2 |
2013 |
2016 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49997 |
22497737 |
R Package ABarray 1.4.2 (Filtering flags > 5000, quantile normalization, log-2 transformation), Batch correction as follows: subtraction of the batch-specific mean from each gene, and add the overall mean. |
| 215 |
Survival Related Profile, Pathways and Transcription Factors in Ovarian Cancer |
Ovarian cancer |
GSE13876 |
15971 |
415 |
Operon human v3 ~35K 70-mer two-color oligonucleotide microarrays |
2008 |
2013 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13876 |
19192944 |
Raw data |
| 216 |
A Prognostic Gene Expression Index in Ovarian Cancer |
Ovarian cancer |
GSE14764 |
12547 |
80 |
Affymetrix Human Genome U133A Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14764 |
19294737 |
RMA |
| 217 |
Whole-genome oligonucleotide expression analysis of papillary serous ovarian adenocarcinomas |
Ovarian cancer |
GSE18520 |
21653 |
63 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2009 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18520 |
19962670 |
RMA |
| 218 |
A gene expression profile of BRCAness that is associated with outcome in ovarian cancer |
Ovarian cancer |
GSE19829_GPL570 |
21653 |
28 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19829 |
20547991 |
RMA |
| 219 |
A gene expression profile of BRCAness that is associated with outcome in ovarian cancer |
Ovarian cancer |
GSE19829_GPL8300 |
8619 |
42 |
Affymetrix Human Genome U95 Version 2 Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19829 |
20547991 |
RMA |
| 220 |
Ovarian Cancer Dataset |
Ovarian cancer |
GSE23554 |
12547 |
28 |
Affymetrix Human Genome U133A Array |
2010 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23554 |
21849418 |
RMA |
| 221 |
A Gene Signature Predicting for Survival in Suboptimally Debulked Patients with Ovarian Cancer |
Ovarian cancer |
GSE26712 |
87 |
195 |
Affymetrix Human Genome U134A Array |
2011 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26712 |
18593951 |
RMA |
| 222 |
Genomic Multivariate Predictors of Response to Adjuvant Chemotherapy in Ovarian Carcinoma: Predicting Platinum Resistance |
Ovarian cancer |
GSE30161 |
21653 |
58 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30161 |
22348014 |
RMA |
| 223 |
Unique gene expression profile based upon pathologic response in epithelial ovarian cancer |
Ovarian cancer |
GSE31245 |
8619 |
57 |
Affymetrix Human Genome U95 Version 2 Array |
2011 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31245 |
16204010 |
RMA |
| 224 |
Gene expression profiling in ovarian cancer |
Ovarian cancer |
GSE63885 |
21653 |
101 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2014 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63885 |
24478986 |
RMA |
| 225 |
Expression profile of 285 ovarian tumour samples |
Ovarian cancer |
GSE9891 |
21653 |
285 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2007 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9891 |
18698038 |
RMA |
| 226 |
Immune-activation as a therapeutic direction for patients with high-risk ovarian cancer based on gene expression signature (1) |
Ovarian cancer |
GSE32062_GPL6480 |
19595 |
260 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32062 |
22241791 |
Signal intensity per spot was generated from the scanned image with Feature Extraction Software ver.10.1 (Agilent Technologies) in the default settings. |
| 227 |
Immune-activation as a therapeutic direction for patients with high-risk ovarian cancer based on gene expression signature (2) |
Ovarian cancer |
GSE32063 |
19595 |
40 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F |
2011 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32063 |
22241791 |
Signal intensity per spot was generated from the scanned image with Feature Extraction Software ver.9.1 (Agilent Technologies) in the default settings. |
| 228 |
Integrated genomic analyses of ovarian carcinoma |
Ovarian cancer |
TCGA-OV |
34849 |
353 |
HTSeq |
2011 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-OV |
21720365 |
TPM |
| 229 |
PANCREATIC CANCER - CA |
Pancreatic cancer endocrine neoplasms |
ICGC-PACA-CA |
25731 |
262 |
HTSeq |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/PACA-CA |
NA |
FPKM |
| 230 |
PANCREATIC CANCER ENDOCRINE NEOPLASMS - AU |
Pancreatic cancer endocrine neoplasms |
ICGC-PAEN-AU |
24650 |
33 |
HTSeq |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/PAEN-AU |
NA |
RSEM |
| 231 |
A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma |
Pancreatic ductal adenocarcinoma |
GSE21501 |
19749 |
132 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F |
2010 |
2013 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21501 |
20644708 |
Data for both channels were Lowess-normalized and then log(2) ratio was taken using Agilent Feature Extraction (v10.5) software. |
| 232 |
PANCREATIC CANCER - AU |
Pancreatic ductal adenocarcinoma |
ICGC-PACA-AU |
24650 |
92 |
HTSeq |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/PACA-AU |
21436628 |
FPKM |
| 233 |
Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes. |
Pancreatic ductal adenocarcinoma |
GSE71729 |
19749 |
357 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F |
2015 |
2015 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71729 |
26343385 |
log2 Cy5 signal was analyzed after setting negative values to zero. Probe data were collapsed by gene symbol via mean expression. Samples were quantile normalized to the subset of genes with less than 0.5 standard deviation across primary, metastatic, and normal samples. Data were processed in MATLAB R2013a. |
| 234 |
Survival in Pancreatic Cancer |
pancreatic ductal adenocarcinoma |
E-MEXP-2780 |
21653 |
26 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 |
2011 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2780 |
22615549 |
RMA |
| 235 |
mRNA profiling by array for pancreatic ductal adenocarcinoma for clinical application |
pancreatic ductal adenocarcinoma |
E-MTAB-6134 |
19040 |
309 |
Affymetrix Human Genome U219 Array |
2018 |
2018 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6134 |
30165049 |
RMA |
| 236 |
Microarray gene-expression profiles of 45 matching pairs of pancreatic tumor and adjacent non-tumor tissues from 45 patients with pancreatic ductal adenocarcinoma |
Pancreatic ductal adenocarcinoma |
GSE28735 |
20202 |
90 |
Affymetrix Human Gene 1.0 ST Array |
2011 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28735 |
22363658 |
RMA |
| 237 |
Development of a prognostic gene signature in pancreatic cancer |
Pancreatic ductal adenocarcinoma |
GSE57495 |
22115 |
63 |
Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray |
2014 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57495 |
26247463 |
RMA |
| 238 |
Microarray gene-expression profiles of 69 pancreatic tumors and 61 adjacent non-tumor tissue from patients with pancreatic ductal adenocarcinoma |
Pancreatic ductal adenocarcinoma |
GSE62452 |
20202 |
130 |
Affymetrix Human Gene 1.0 ST Array |
2014 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62452 |
27197190 |
RMA |
| 239 |
Microarray gene-expression profiles of 50 pancreatic tumors tissue from patients with pancreatic ductal adenocarcinoma |
Pancreatic ductal adenocarcinoma |
GSE78229 |
20202 |
50 |
Affymetrix Human Gene 1.0 ST Array |
2016 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78229 |
27401251 |
RMA |
| 240 |
Patients with human resected pancreatic cancer |
Pancreatic ductal adenocarcinoma |
GSE85916 |
19040 |
80 |
Affymetrix Human Genome U219 Array |
2016 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85916 |
NA |
RMA |
| 241 |
RNA-sequencing of human pancreatic adenocarcinoma cancer tissues |
Pancreatic ductal adenocarcinoma |
GSE79668 |
24658 |
51 |
Illumina HiSeq 2000 (Homo sapiens) |
2016 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79668 |
27282075 |
TPM |
| 242 |
Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma |
Pancreatic ductal adenocarcinoma |
TCGA-PAAD |
34849 |
176 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-PAAD |
28810144 |
TPM |
| 243 |
Comprehensive molecular characterization of pheochromocytoma and paraganglioma |
Pheochromocytoma and paraganglioma |
TCGA-PCPG |
34849 |
175 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-PCPG |
28162975 |
TPM |
| 244 |
Prostate cancer stratification using molecular profiles |
Prostate cancer |
GSE70768 |
22000 |
199 |
Illumina HumanHT-12 V4.0 expression beadchip |
2015 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70768 |
26501111 |
log2 transformed and quantile normalized |
| 245 |
Prostate cancer stratification using molecular profiles |
Prostate cancer |
GSE70769 |
22000 |
94 |
Illumina HumanHT-12 V4.0 expression beadchip |
2015 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70769 |
26501111 |
log2 transformed and quantile normalized |
| 246 |
Molecular Sampling of Prostate Cancer: a dilemma for predicting disease progression |
Prostate cancer |
GSE16560 |
6100 |
281 |
Human 6k Transcriptionally Informative Gene Panel for DASL |
2009 |
2013 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16560 |
20233430 |
Normalized signal intensity |
| 247 |
Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy |
Prostate cancer |
GSE26022 |
522 |
192 |
Illumina Custom Prostate Cancer DASL Panel 1.5K expression beadchip |
2010 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26022 |
NA |
The data were normalized using quantile-normalization with GenomeStudio V2010.1 |
| 248 |
Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy |
Prostate cancer |
GSE26242 |
522 |
96 |
Illumina Custom Prostate Cancer DASL Panel 1.5K expression beadchip |
2010 |
2012 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26242 |
NA |
The data were normalized using quantile-normalization with GenomeStudio V2010.1 |
| 249 |
The molecular taxonomy of primary prostate cancer |
Prostate cancer |
TCGA-PRAD |
34849 |
481 |
HTSeq |
2015 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-PRAD |
26544944 |
TPM |
| 250 |
PROSTATE CANCER - ADENOCARCINOMA |
Prostate cancer |
ICGC-PRAD-FR |
22187 |
25 |
HTSeq |
|
2019 |
https://dcc.icgc.org/releases/current/Projects/PRAD-FR |
NA |
NA |
| 251 |
Comprehensive Molecular Characterization of Human Colon and Rectal Cancer |
Rectum adenocarcinoma |
TCGA-READ |
34849 |
154 |
HTSeq |
2013 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-READ |
22810696 |
TPM |
| 252 |
Next generation sequencing of TFE3-translocation renal cell carcinoma and adjacent normal tissue transcriptomes |
Renal carcinoma |
GSE167573 |
55630 |
76 |
HiSeq X Ten (Homo sapiens) |
2021 |
2021 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167573 |
34489456 |
NA |
| 253 |
RENAL CELL CANCER - EU/FR |
Renal carcinoma |
ICGC-RECA-EU |
23698 |
136 |
HTSeq |
NA |
2019 |
https://dcc.icgc.org/releases/current/Projects/RECA-EU |
NA |
NA |
| 254 |
ccRCC_expression |
Renal carcinoma-Clear-cell renal cell carcinoma |
E-MTAB-1980 |
22682 |
101 |
Agilent Human Gene Expression 4x44K v2 Microarray 026652 G4845A |
2013 |
2014 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1980 |
23797736 |
log_quantile_normalized |
| 255 |
Agilent-012391 Whole Human Genome Oligo Microarray G4112A |
Renal carcinoma-Clear-cell renal cell carcinoma |
GSE29609 |
18841 |
39 |
Agilent-012391 Whole Human Genome Oligo Microarray G4112A |
2011 |
2018 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29609 |
22626276 |
normalized log10 ratio Cy5/Cy3 |
| 256 |
Biopsies from metastatic Clear Cell Renal Carcinoma before or after treatment with nivolumab |
Renal carcinoma-Clear-cell renal cell carcinoma |
E-MTAB-3218 |
19040 |
59 |
Affymetrix Human Genome U219 Array |
2016 |
2021 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3218 |
27169994 |
RMA |
| 257 |
Expression Profiling of Clear cell renal carcinoma |
Renal carcinoma-Clear-cell renal cell carcinoma |
E-MTAB-3267 |
20202 |
59 |
Affymetrix GeneChip Human Gene 1.0 ST Array |
2015 |
2018 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3267 |
25583177 |
RMA |
| 258 |
Comprehensive molecular characterization of clear cell renal cell carcinoma |
Renal carcinoma-Clear-cell renal cell carcinoma |
TCGA-KIRC |
34849 |
522 |
HTSeq |
2013 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-KIRC |
23792563 |
TPM |
| 259 |
Comprehensive Molecular Characterization of Papillary Renal Cell Carcinoma |
Renal carcinoma-Renal papillary cell carcinoma |
TCGA-KIRP |
34849 |
284 |
HTSeq |
2016 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-KIRP |
26536169 |
TPM |
| 260 |
Transcriptional profiling by array of primary rhabdomyosarcoma samples with different PAX3/FOXO1 fusion gene status |
Rhabdomyosarcoma |
E-TABM-1202 |
21653 |
101 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 |
2011 |
2012 |
https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-1202 |
23536298 |
RMA |
| 261 |
Integrated Molecular Characterization of Testicular Germ Cell Tumors |
Testicular germ cell tumor |
TCGA-TGCT |
34849 |
133 |
HTSeq |
2018 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-TGCT |
29898407 |
TPM |
| 262 |
The Integrated Genomic Landscape of Thymic Epithelial Tumors |
Thymoma |
TCGA-THYM |
34849 |
118 |
HTSeq |
2018 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-THYM |
29438696 |
TPM |
| 263 |
Integrated genomic characterization of papillary thyroid carcinoma |
Thyroid carcinoma |
TCGA-THCA |
34849 |
496 |
HTSeq |
2014 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-THCA |
25417114 |
TPM |
| 264 |
Integrated Molecular Characterization of Uterine Carcinosarcoma |
Uterine carcinosarcoma |
TCGA-UCS |
34849 |
54 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-UCS |
28292439 |
TPM |
| 265 |
Gene expression analysis of uveal melanoma tumor tissue |
Uveal melanoma |
GSE39717 |
21453 |
31 |
Illumina humanRef-8 v1.0 expression beadchip |
2012 |
2015 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39717 |
17332290 |
cubic spline normalized with background subtraction |
| 266 |
Expression Data from Uveal Melanoma primary tumors. |
Uveal melanoma |
GSE22138 |
21653 |
63 |
Affymetrix Human Genome U133 Plus 2.0 Array |
2010 |
2019 |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22138 |
21135111 |
RMA |
| 267 |
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma |
Uveal melanoma |
TCGA-UVM |
34849 |
77 |
HTSeq |
2017 |
2021 |
https://portal.gdc.cancer.gov/projectsTCGA-UVM |
29316429 |
TPM |
| 268 |
A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor |
Wilms tumor |
TARGET-WT |
58387 |
120 |
Illumina HiSeq |
2009 |
2019 |
https://xenabrowser.net/datapages/ |
28825729 |
log2(fpkm+5) |