GDS datasets for cola analysis

In this collection, cola analysis was applied to 206 GDS datasets. Click following link to see how the data was processed and analyzed.

Data processing and analysis

GDS datasets were downloaded from GEO database by GEOquery package on March 12, 2019. The datasets were selected by the MESH term: "Homo sapiens"[porgn] AND 50[n_samples] : 500[n_samples] AND "gds"[Filter]. GDS1761 was removed from the analysis due to error from GEOquery. For each GDS dataset, rows where there is no microarray probe IDs were removed. If the value type for the dataset is not two-channel microarray, the distribution of expression values was tested against normal distribution by KS test. If the KS statistics is larger than 0.3, we assume the expression values do not follow normal distribution and log2(x+1) transformation is applied on. GDS2808 was additionally processed that samples with more than 25% NA values were removed. Finally, quantile normalization was applied to the samples for each dataset.

The analysis were done with cola 1.3.2. Users need to use R with version >= 3.6.0 to read the *.rds files provided in the following table.

ID Title (click for cola report) Samples Features File
GDS1048 Lymphoblastoid cell lines from CEPH/Utah families 167 23916 rds_file
GDS1059 Acute myeloid leukemia response to chemotherapy 58 12625 rds_file
GDS1067 Plasma cell dyscrasias 52 22283 rds_file
GDS1209 Sarcoma and hypoxia 54 22283 rds_file
GDS1220 Malignant pleural mesothelioma 54 22283 rds_file
GDS1284 Multiple myeloma molecular classification 50 22283 rds_file
GDS1375 Cutaneous malignant melanoma 70 22283 rds_file
GDS1402 Various normal pure cell cultures 61 19881 rds_file
GDS1412 Hormone replacement therapy effect on whole blood 89 22575 rds_file
GDS1449 HIV-1 infection effect on peripheral blood mononuclear cells 87 8793 rds_file
GDS1479 Carcinoma in situ lesions of the urinary bladder 60 22283 rds_file
GDS1597 Coronary artery atherosclerosis 51 20433 rds_file
GDS1615 Ulcerative colitis and Crohn’s disease comparison: peripheral blood mononuclear cells 127 22283 rds_file
GDS1627 Breast cancer cell lines response to chemotherapeutic drugs: time course 83 20163 rds_file
GDS181 Large-scale analysis of the human transcriptome (HG-U95A) 84 12626 rds_file
GDS1813 Glial brain tumors 53 41472 rds_file
GDS1815 High-grade gliomas (HG-U133A) 100 22283 rds_file
GDS1816 High-grade gliomas (HG-U133B) 100 22645 rds_file
GDS1875 Host cell response to HIV-1 Vpr-induced cell cycle arrest: time course 87 22242 rds_file
GDS1956 Various muscle diseases (HG-U133A) 121 22283 rds_file
GDS1962 Glioma-derived stem cell factor effect on angiogenesis in the brain 180 54675 rds_file
GDS1975 Gliomas of grades III and IV (HG-U133A) 85 22283 rds_file
GDS1976 Gliomas of grades III and IV (HG-U133B) 85 22645 rds_file
GDS2106 Lymphoblastoid cell lines from various CEPH pedigrees 100 8793 rds_file
GDS2113 Pheochromocytomas of various genetic origins 75 22283 rds_file
GDS2118 Myelodysplastic syndromes: CD34+ cells 66 54675 rds_file
GDS2190 Bipolar disorder: dorsolateral prefrontal cortex 61 22283 rds_file
GDS2255 Transmigrated neutrophils in the alveolar space of endotoxin-exposed lung 58 22283 rds_file
GDS2362 Presymptomatic and symptomatic malaria: peripheral blood mononuclear cells 71 22283 rds_file
GDS2373 Squamous cell lung carcinomas 130 22283 rds_file
GDS2384 Xenograft model of prostate carcinoma progression 52 19200 rds_file
GDS2415 Breast carcinomas and local recurrence 59 19200 rds_file
GDS2506 Recurrent squamous cell carcinoma of the lung: primary tumor 51 23232 rds_file
GDS2519 Early-stage Parkinson’s disease: whole blood 105 22283 rds_file
GDS2545 Metastatic prostate cancer (HG-U95A) 171 12625 rds_file
GDS2546 Metastatic prostate cancer (HG-U95B) 167 12620 rds_file
GDS2547 Metastatic prostate cancer (HG-U95C) 164 12646 rds_file
GDS2626 Epidermal growth factor and heregulin effect on breast cancer cell line: dose response and time course 57 22277 rds_file
GDS2643 Waldenstrom’s macroglobulinemia: B lymphocytes and plasma cells 56 22283 rds_file
GDS2733 Cytosine arabinoside effect on Ewing’s sarcoma cell line: time course and dose response 68 22944 rds_file
GDS2736 Malignant fibrous histiocytoma and various soft tissue sarcomas 105 22283 rds_file
GDS274 Hepatocellular carcinoma metastasis 87 9984 rds_file
GDS2767 Blood response to various beverages: time course 108 22283 rds_file
GDS2771 Large airway epithelial cells from cigarette smokers with suspect lung cancer 192 22283 rds_file
GDS2808 Sepsis: neutrophils 94 18664 rds_file
GDS2819 Leukemic white blood cells and various RNA preparation protocols 99 54675 rds_file
GDS2827 ERalpha-negative ERbeta-positive breast carcinoma response to tamoxifen 88 27648 rds_file
GDS2831 Primary graft dysfunction after lung transplantation 50 17635 rds_file
GDS2855 Various muscle diseases (HG-U133B) 119 22645 rds_file
GDS2926 Megakaryocytic differentiation: time course 77 22575 rds_file
GDS2947 Colorectal adenoma formation 64 54675 rds_file
GDS2954 Mycobacterium tuberculosis-derived lipopeptide effect on monocytes and dendritic cells: time course 50 22283 rds_file
GDS2960 Marfan syndrome: cultured skin fibroblasts 101 4132 rds_file
GDS3017 Cervical cancer response to chemoradiotherapy 156 56448 rds_file
GDS3057 Acute myeloid leukemia 64 22283 rds_file
GDS3085 Gram-positive and gram-negative sepsis: leukocytes 72 18664 rds_file
GDS3113 Various normal tissues 96 32878 rds_file
GDS3116 Letrozole effect on breast cancer tumors 116 22283 rds_file
GDS3233 Cervical cancer tumorigenesis 61 22283 rds_file
GDS3257 Cigarette smoking effect on lung adenocarcinoma 107 22283 rds_file
GDS3268 Colon epithelial biopsies of ulcerative colitis patients 202 44290 rds_file
GDS3289 Prostate cancer progression at the cellular level 104 20000 rds_file
GDS3297 Stage III serous ovarian adenocarcinomas 54 30000 rds_file
GDS3308 Cytogenetically normal acute myeloid leukemia_training set (HG-U133B) 163 22645 rds_file
GDS3312 Cytogenetically normal acute myeloid leukemia_training set (HG-U133A) 163 22283 rds_file
GDS3324 Stromal cells and invasive breast cancer development 66 22277 rds_file
GDS3325 Air pollution exposure effect on children and adults: peripheral blood 71 22575 rds_file
GDS3326 Periodontal therapy effect on peripheral blood monocytes: time course 59 54675 rds_file
GDS3329 Cytogenetically normal acute myeloid leukemia_test set 79 54675 rds_file
GDS3345 Various mental disorders: postmortem brains 50 12625 rds_file
GDS3356 Bronchopulmonary dysplasia: premature newborn umbilical cords 54 54675 rds_file
GDS3416 Relaxation response practice effect on blood 72 54675 rds_file
GDS3432 Osteosarcoma cell line response to activation of specific glucocorticoid receptor alpha isoforms: time course 60 44290 rds_file
GDS3459 Frontotemporal lobar degeneration with ubiquitinated inclusions and progranulin mutations: various brain regions 56 22277 rds_file
GDS3494 Cigarette smoke of light flavor brand effect on bronchial epithelial cells in vitro: time course 52 54675 rds_file
GDS3499 TREM-1 activation effect on monocytes in vitro 62 54675 rds_file
GDS3516 Nodular lymphocyte-predominant Hodgkin lymphoma: lymphocytic and histiocytic cells 67 54675 rds_file
GDS3517 Oncogenic NRAS depletion effect on melanoma cell lines: time course 51 22283 rds_file
GDS3539 Psoriasis 82 54675 rds_file
GDS3553 Monocytes and macrophages (RNG/MRC) 96 26496 rds_file
GDS3603 Renal cancer response to rapamycin analog CCI-779 treatment: time course 79 12625 rds_file
GDS3627 Non-small lung cancer subtypes: adenocarcinoma and squamous cell carcinoma 58 54675 rds_file
GDS3640 Copper effect on liver cell line: dose response and time course 98 20228 rds_file
GDS3646 Celiac disease: primary leukocytes 132 22185 rds_file
GDS3690 Atherosclerotic Coronary Artery Disease: circulating mononuclear cell types 153 20589 rds_file
GDS3704 Dietary polyunsaturated and saturated fatty acids effect on peripheral blood mononuclear cells 84 16313 rds_file
GDS3709 Cigarette smoke effect on the oral mucosa 79 54675 rds_file
GDS3713 Smoking effect on B lymphocytes in females 79 22283 rds_file
GDS3715 Insulin effect on skeletal muscle 110 12626 rds_file
GDS3793 Tobacco smoke effect on the placenta 76 22185 rds_file
GDS3795 Myelodysplastic syndrome: CD34+ hematopoietic stem cells 200 54675 rds_file
GDS3829 Fludarabine, cyclophosphamide, and rituximab chemoimmunotherapy effect on chronic lymphocytic leukemia 50 54675 rds_file
GDS3837 Non-small cell lung carcinoma in female nonsmokers 120 54675 rds_file
GDS3842 Transcription factor-induced pluripotent stem cells 51 45220 rds_file
GDS3874 Diabetic children: peripheral blood mononuclear cells (U133A) 117 22283 rds_file
GDS3875 Diabetic children: peripheral blood mononuclear cells (U133B) 117 22645 rds_file
GDS3884 Type 2 diabetic and insulin-resistant but normoglycemic cohorts: skeletal muscle 50 54675 rds_file
GDS3885 Glioblastoma stem-like cell lines, glioblastomas, and glioma cell lines 92 54675 rds_file
GDS3898 Social isolation effect on peripheral blood mononuclear cells 93 24526 rds_file
GDS3916 Recombinant human growth hormone effect on lactating mammary gland: time course 139 22185 rds_file
GDS3919 Severe influenza A infection: whole blood 81 49576 rds_file
GDS3929 Tobacco smoke effect on maternal and fetal cells 183 24526 rds_file
GDS3952 Breast cancer patients: peripheral blood mononuclear cells 162 54675 rds_file
GDS3966 Melanoma metastasis 83 22283 rds_file
GDS4056 ER-positive/HER2-negative and ER-negative/HER2-negative breast cancer biopsies (USO-02103 cohort) 61 22283 rds_file
GDS4057 ER-positive/HER2-negative and ER-negative/HER2-negative breast cancer biopsies (MDACC/IGR cohort) 103 22283 rds_file
GDS4088 Variable breast cancer tumor sample collection methods 86 22283 rds_file
GDS4102 Pancreatic Tumor and Normal tissue samples 52 54675 rds_file
GDS4103 ICF cohort: Whole-tissue pancreatic ductal adenocarcinoma 78 54675 rds_file
GDS4109 Recurrent and non-recurrent prostate cancer primary tumors 79 22283 rds_file
GDS4129 Endoplasmic reticulum stress effect on lymphoblastoid cells of unrelated individuals 120 54675 rds_file
GDS4130 Endoplasmic reticulum stress effect on lymphoblastoid cells of monozygotic twins 104 54675 rds_file
GDS4145 Subcutaneous Interferon-beta-1b treatment in relapsing-remitting multiple sclerosis (U133 A): peripheral mononuclear blood cells 125 22283 rds_file
GDS4146 Subcutaneous Interferon-beta-1b treatment in relapsing-remitting multiple sclerosis (U133 B): peripheral mononuclear blood cells 125 22645 rds_file
GDS4167 Chronic lymphocytic leukemia: peripheral blood B cells (HG-U133A) 52 22283 rds_file
GDS4168 Chronic lymphocytic leukemia: peripheral blood B cells (HG-U133B) 52 22645 rds_file
GDS4176 Chronic lymphocytic leukemia: peripheral blood, bone marrow and lymph node matched samples 62 54675 rds_file
GDS4181 WHO 2008-classified acute myeloid leukemia subgroups (Analysis I): bone marrow mononuclear cells 80 54675 rds_file
GDS4182 WHO 2008-classified acute myeloid leukemia subgroups (Analysis II): bone marrow mononuclear cells 96 54675 rds_file
GDS4185 Systemic Lupus Erythematosus: mononuclear cells 67 22283 rds_file
GDS4198 Australian patient cohort: gastric adenocarcinoma 70 54675 rds_file
GDS4206 Pediatric acute leukemia patients with early relapse: white blood cells 197 54675 rds_file
GDS4222 Classic Hodgkins lymphoma diagnostic lymph-node biopsies 130 54675 rds_file
GDS4228 HIV infection and Antiretroviral Therapy effects on mitochondria in various tissues 166 4825 rds_file
GDS4238 Bronchial epithelial cell response to influenza virus, viral RNA and interferon-beta: time course 169 22277 rds_file
GDS4262 Oxidized low-density lipoprotein effect on LOX-1 overexpressing aortic endothelial cell line HAECT: time course 54 54675 rds_file
GDS4265 Chronic obstructive pulmonary disease in ex-smokers: sputum 143 54675 rds_file
GDS4266 Tolerant renal transplant recipients: peripheral whole blood 58 54675 rds_file
GDS4267 Systemic juvenile idiopathic arthritis and non-systemic JIA subtypes: peripheral blood mononuclear cells 154 54675 rds_file
GDS4273 Pediatric age-specific host response to septic shock: whole blood 103 54675 rds_file
GDS4274 Stratification of pediatric septic shock patients: whole blood 130 54675 rds_file
GDS4278 Acute myeloid leukemia with CEBPA mutations [AMLSG cohort]: mononuclear cells 154 54675 rds_file
GDS4282 Clear-cell renal cell carcinoma tumors and tumorgrafts deficient for tumor suppressor BAP1 or PBRM1 76 54675 rds_file
GDS4284 Chronic lymphocytic leukemia response to antisense Bcl-2 inhibitor SPC2996: peripheral blood 56 54675 rds_file
GDS4296 NCI-60 cancer cell line panel 174 54675 rds_file
GDS4299 Early T-cell precursor acute lymphoblastic leukemia 52 54715 rds_file
GDS4318 Single nucleotide polymorphism rs1333049 from the 9p21.3 coronary artery disease risk locus: normal heart 108 33297 rds_file
GDS4336 Pancreatic ductal adenocarcinoma tumor and adjacent non-tumor tissue 90 33297 rds_file
GDS4337 Type 2 diabetic and hyperglycemic pancreatic islets 63 33297 rds_file
GDS4358 Two types of HIV-associated neurocognitive impairment: brain regions 72 54675 rds_file
GDS4379 Colorectal cancer tumors 62 54675 rds_file
GDS4381 Patient-derived colorectal cancer explants 64 54675 rds_file
GDS4393 Unresectable colorectal cancer primary or metastatic lesions: training set 54 54675 rds_file
GDS4395 External beam radiation therapy effect on prostate cancer patients: peripheral white blood cells 80 54675 rds_file
GDS4404 Facioscapulohumeral muscular dystrophy: bicep and deltoid muscles 50 33297 rds_file
GDS4412 Dietary fatty acid composition effect on vastus lateralis muscle 56 33297 rds_file
GDS4431 Autistic children and their father’s age: peripheral blood lymphocytes 146 54675 rds_file
GDS4456 High-risk bladder cancer 93 54675 rds_file
GDS4471 Medulloblastomas in children 76 54675 rds_file
GDS4513 Clinical outcome of stage UICC II colon cancer patients 53 54675 rds_file
GDS4516 Colorectal cancer: laser microdissected tumor tissues 104 54675 rds_file
GDS4523 Schizophrenia: postmortem anterior prefrontal cortex 51 54675 rds_file
GDS4547 Effect of ischemia and tissue procurement conditions on resected renal clear cell carcinoma 140 54675 rds_file
GDS4549 Pulmonary fibrosis with associated pulmonary hypertension: lung explants 116 33297 rds_file
GDS4562 Squamous cell carcinoma of the tongue: tumors and histologically normal surgical margins 96 17788 rds_file
GDS4587 UCSF sarcoidosis and hypersensitivity pneumonitis cohort: peripheral blood mononuclear cells 66 54675 rds_file
GDS4589 Stage I endometrial cancer: microdissected frozen uterine tumors 103 54675 rds_file
GDS4600 Psoriasis vulgaris ACCEPT cohort: paired lesional and non-lesional skin 170 54675 rds_file
GDS4602 Psoriasis lesional and non-lesional skin 180 54675 rds_file
GDS4607 Psoriasis non-lesional skin response to interferon-γ 60 22277 rds_file
GDS4758 Postmortem Alzheimer’s disease brains: Hisayama study 79 33297 rds_file
GDS4761 Breast cancer metastases from different anatomical sites: fine-needle aspiration biopsies 91 52378 rds_file
GDS4762 Fibroblast response to coculture with basal breast cancer cells 80 33297 rds_file
GDS4794 Small cell lung cancers 65 54675 rds_file
GDS4813 Melanoma cell line response to the depletion of various transcription factors and signaling proteins 51 54675 rds_file
GDS4837 Never-medicated and medicated bipolar patients: peripheral blood leukocytes 88 54675 rds_file
GDS4881 Postbariatric, morbidly obese patients with nonalcoholic fatty liver disease: liver biopsies 73 33297 rds_file
GDS4896 Asthma: white blood cells 54 33297 rds_file
GDS4906 Exercise training effect on chronic obstructive pulmonary disease patients: vastus lateralis muscle 54 54675 rds_file
GDS4926 Bisphenol A effect on endometrial cell line: time course and dose response 60 54675 rds_file
GDS4968 Monoclonal gammopathies: bone marrow plasma cells 99 33297 rds_file
GDS4971 Blood from septic patients: time course 163 49576 rds_file
GDS4975 Follicular lymphoma and higher grade diffuse large B-cell lymphoma patients: lymph node tumor biopsies 81 54675 rds_file
GDS4982 Non-Hodgkin’s lymphoma cell lines response to antibodies against CD20 or B-cell receptor 96 54675 rds_file
GDS5000 Mechanistic Indicators of Asthma (MICA) cohort: peripheral blood 131 54675 rds_file
GDS5027 NeOAdjuvant Herceptin (NOAH) trial: formalin-fixed, paraffin-embedded breast cancer biopsies 156 54675 rds_file
GDS5037 Severe asthma: bronchial epithelial cell 108 41108 rds_file
GDS5047 Cocaine abuse effect on the midbrain 60 49576 rds_file
GDS5074 First-time acute myocardial infarction: peripheral blood 52 54675 rds_file
GDS5083 Carotid artery atheroma 64 33297 rds_file
GDS5093 Acute Dengue patients: whole blood 56 54715 rds_file
GDS5176 Epidermis at various time points during the day 57 41108 rds_file
GDS5205 Long-term adult survivors of glioblastoma: primary tumors 70 54675 rds_file
GDS5217 Resistance exercise effect on MHC I and MHC IIa muscle fibers of young and old women 70 54675 rds_file
GDS5218 Resistance exercise effect on skeletal muscles of young and old adults 110 54675 rds_file
GDS5232 Early and late onset colorectal cancers 50 32878 rds_file
GDS5268 Cyclin-dependent kinase inhibitor R547 effect on colon cancer cell line: dose response and time course 74 54675 rds_file
GDS5277 Rheumatoid arthritis and response to anti-TNF therapy: blood 86 54675 rds_file
GDS531 Multiple myeloma and bone lesions 173 12625 rds_file
GDS534 Smoking-induced changes in airway transcriptome 75 22283 rds_file
GDS5363 Osteoarthritis: peripheral blood mononuclear cells 139 49576 rds_file
GDS5393 Bipolar disorder and response to lithium: blood 120 48107 rds_file
GDS5420 Psoriasis response to brodalumab: dose response and time course 99 54675 rds_file
GDS5430 Ethanol effect on lymphoblastoid cell lines from alcoholics 84 54675 rds_file
GDS5499 Pulmonary hypertensions: PBMCs 140 49576 rds_file
GDS596 Large-scale analysis of the human transcriptome (HG-U133A) 158 22283 rds_file
GDS711 Juvenile rheumatoid arthritis expression profiles in mononuclear cells 57 12625 rds_file
GDS724 Kidney transplant rejection expression profiling 62 12625 rds_file
GDS806 Estrogen positive breast cancer recurrence during tamoxifen therapy: whole tissue tumor 60 22575 rds_file
GDS807 Estrogen positive breast cancer recurrence during tamoxifen therapy: microdissected tumor 60 22575 rds_file
GDS829 Alternative pre-mRNA splicing in various tissues and cell lines (Rosetta/Merck Splicing Chip 1) 54 23107 rds_file
GDS830 Alternative pre-mRNA splicing in various tissues and cell lines (Rosetta/Merck Splicing Chip 2) 50 23107 rds_file
GDS831 Alternative pre-mRNA splicing in various tissues and cell lines (Rosetta/Merck Splicing Chip 3) 54 23107 rds_file
GDS832 Alternative pre-mRNA splicing in various tissues and cell lines (Rosetta/Merck Splicing Chip 4) 52 23107 rds_file
GDS833 Alternative pre-mRNA splicing in various tissues and cell lines (Rosetta/Merck Splicing Chip 5) 54 12961 rds_file
GDS968 Radiation therapy toxicity association with abnormal transcriptional response to DNA damage 171 12625 rds_file