Regulatory Network in Protein Phosphorylation
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Expression Analysis
In this work, the human gene expression samples of Affymetrix GeneChip Human Genome U133 Array Set HG-U133A platform (GPL96) from Gene Expression Omnibus (GEO), consisting of 22283 probe set for 12678 genes, are used to explore the co-coexpression analysis of kinase and substrate genes. However, the first problem we faced is what kind of microarray experiment should be selected for investigating the co-expression of kinase and substrate genes. Without any specific interest and limitation, we decide to focus on the experimental series of microarray with the raw data. Totally 2714 samples within 98 experiment series (GSE) were collected and normalized by RMA package.

Choose a kinase:Choose a substrate:

SeriesGSE1000
DatasetGDS562 (Bone cell tissue culture on amino acid conjugated surfaces)
DescriptionEvaluation of osteosarcoma TE85 cell tissue culture on a variety of amino acid conjugated surfaces at 6 and 32 hours. Study holds potential applications for bone tissue engineering.
Number of subset7 (10 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1133
DatasetGDS596 (Large-scale analysis of the human transcriptome (HG-U133A))
DescriptionGene atlas of human protein-encoding transcriptome. Examined gene expression profiles from 79 physiologically normal tissues obtained from various sources.
Number of subset79 (158 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1140
DatasetGDS962 (Peripheral blood mononuclear cells and the effect of exercise)
Description"Peripheral blood mononuclear cells (PBMC) were isolated from blood samples taken from healthy male subjects before, immediately after, and 60 minutes after 30 minutes of exercise. Brisk activation and deactivation of genes associated with stress, inflammation, and tissue repair observed."
Number of subset3 (15 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1295
DatasetGDS914 (Metabolic syndrome response to exercise intervention (HG-U133A))
Description"Analysis of skeletal muscle from overweight males and females with metabolic syndrome. Individuals subjected to chronic exercise training. Muscles examined prior to training, and after 1, 3, and 14 days of recovery following 9 months training. Provides insight into effects of exercise intervention."
Number of subset6 (24 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1297
DatasetGDS810 (Alzheimer's disease at various stages of severity)
Description"Expression profiling of brain hippocampi from 22 postmortem subjects with Alzheimer's disease (AD) at various stages of severity. 7, 8, and 7 subjects diagnosed with incipient, moderate, and severe AD respectively. Results provide insight into mechanisms underlying the early pathogenesis of AD."
Number of subset4 (31 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1323
DatasetGDS756 (Colon cancer progression)
Description"Comparison of gene expression in SW480, a primary tumor colon cancer cell line, to that in SW620, an isogenic metastatic colon cancer cell line. Cell lines derived from one individual. Results provide insight the progression of cancer from primary tumor growth to metastasis."
Number of subset2 (6 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1400
DatasetGDS992 (Endoplasmic reticulum membrane-associated genes in breast cancer cell line MCF-7)
DescriptionIdentification of genes whose mRNA are translated from the endoplasmic reticulum (ER) in the breast cancer cell line MCF-7. Secreted and membrane-bound proteins are preferentially translated in the ER. Results provide insight into the association of membrane-bound proteins and breast cancer.
Number of subset2 (6 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1417
DatasetGDS885 (Tumor cell response to topoisomerase poison camptothecin)
DescriptionHeLa tumor cells treated with 10 uM topoisomerase poison camptothecin (CPT) for 8 hours. This dose and time are sufficient to induce rapid apoptosis. Results identify potential targets for adjuvant cancer therapy.
Number of subset2 (7 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1420
DatasetGDS1321 (Barrett's metaplasia progression to adenocarcinoma)
Description"Expression profiling of normal esophageal epithelium, premalignant Barrett's metaplasia, and esophageal adenocarcinoma samples. Tissue samples of each type obtained from 8 patients by transhiatal esophagectomy. Results identify potential markers of disease progression."
Number of subset11 (24 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1428
DatasetGDS749 (Sarcopenia expression profiling)
DescriptionAnalysis of sarcopenia by comparing gene expression profiles in vastus lateralis muscles of 19 to 25 year old males to that of 70 to 80 year old males. Results provide insight into mechanisms underlying age-related loss of muscle mass.
Number of subset2 (22 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1460
DatasetGDS785 (CD4+ T cell differentiation (HG-133A))
Description"Analysis of CD4+ T cell differentiation by expression profiling of subpopulations of CD4+ cells representing 5 successive stages of differentiation: intrathymic T progenitors, double positive thymocytes, single positive thymocytes, naïve T cells from cord blood, and naïve T cells from adult blood."
Number of subset10 (15 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1518
DatasetGDS1317 (Umbilical vein endothelial cell response to shear stress and intraluminal pressure)
DescriptionAnalysis of endothelial cells (HUVEC) isolated from umbilical veins subjected to high shear stress or high intraluminal pressure. Umbilical veins exposed to each stimuli using a vascular ex vivo perfusion system. Results suggests that response to shear stress differs from response to pressure.
Number of subset4 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1561
DatasetGDS1329 (Molecular apocrine breast tumors)
Description"Analysis of tumors of 49 breast cancer patients. Tumors classified into luminal and basal classes, and a novel molecular apocrine class. Apocrine tumors are estrogen receptor negative (ER-) and androgen receptor positive (AR+), while luminal tumors are ER+ and AR+, and basal tumors are ER- and AR-."
Number of subset3 (49 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1577
DatasetGDS760 (T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma comparison)
DescriptionComparison of expression profiles in T-cell acute lymphoblastic leukemia (T-ALL) to that in T-cell lymphoblastic lymphoma (T-LL). Gene expression in B-precursor acute lymphoblastic leukemia also examined. Results provide insight into the molecular basis for the difference between T-ALL and T-LL.
Number of subset5 (29 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1615
DatasetGDS1050 (Valproic acid effect on theca cells (HG-U133A))
Description"Analysis of normal theca cells treated with 500 uM valproic acid (VPA), an anti-epilipetic that induces polycystic ovary syndrome (PCOS)-like symptoms. Theca cells from PCOS patients also examined. Results provide insight into the underlying mechanisms contributing to VPA-induced PCOS-like symptoms."
Number of subset4 (13 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1648
DatasetGDS738 (Intervertebral disc cells and osmotic loading)
Description"Gene expression profiles of intervertebral disc cells (IVD) exposed to iso-osmotic, hyper-osmotic and hypo-osmotic conditions. Under physiological conditions, IVD are subject to osmotic stress."
Number of subset7 (11 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1650
DatasetGDS737 (Lung tissue from smokers with severe emphysema)
DescriptionComparison of lung tissue from smokers with severe emphysema (removed at lung volume reduction surgery) and smokers with mild or no emphysema. Study provides insights into the pathogenesis of chronic obstructive pulmonary disease (COPD).
Number of subset2 (30 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1657
DatasetGDS2366 (Preadipocytes from anatomically separate fat depots (HG-U133A))
Description"Analysis of undifferentiated and differentiated preadipocytes from abdominal subcutaneous, mesenteric, and greater omental regions. Separate fat depots differ in size, function, and contribution to pathological states. Results provide insight into the contribution of preadipocytes to this variation."
Number of subset8 (24 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1729
DatasetGDS1064 (Acute myeloid leukemia subclasses)
Description"Expression profiling of bone marrow from 43 patients with various forms of acute myeloid leukemia (AML): 10 promyelocytic leukemias with t(15;17), 4 AMLs with inv(16), 7 monocytic leukemias, and 22 nonmonocytic leukemias. Results identify expression signatures unique to each AML subclass."
Number of subset8 (43 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1786
DatasetGDS1340 (Exercise effect on aged muscle)
Description"Expression profiling of vastus lateralis muscles from 6 healthy, elderly, sedentary males after 3 months of exercise at 80% of maximal capacity. Results provide insight into the molecular changes induced by exercise in sedentary skeletal muscles. "
Number of subset14 (12 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE1869
DatasetGDS1362 (Ischemic and nonischemic cardiomyopathy comparison)
Description"Analysis of myocardial tissues from nonischemic (NICM) and ischemic cardiomyopathy (ICM) patients. NICM and ICM, major forms of dilated cardiomyopathy leading to congestive heart failure, have similar presentations but differ in pathophysiology, prognosis, and response to therapy."
Number of subset3 (37 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2004
DatasetGDS1663 (Expression data from different research centers)
Description"Comparison of expression data from the Translational Genomics Research Institute to that from the Children's National Medical Center in Washington, DC. Data consists of normal kidney, liver, and spleen expression profiles. "
Number of subset6 (25 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2018
DatasetGDS999 (Bronchoalveolar lavage cells of lung transplant recipients with acute rejection)
DescriptionExpression profiling of bronchoalveolar lavage cells of lung transplant recipients with acute rejection. Rejection status determined from biopsies. Results identify possible gene markers of lung transplant rejection.
Number of subset2 (34 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2113
DatasetGDS1067 (Plasma cell dyscrasias)
Description"Expression profiling of plasma cells from patients with plasma cell dyscrasias: 7 with monoclonal gammopathy of undetermined significance, 39 with multiple myeloma (MM), and 6 with plasma cell leukemia. Results provide insight into the neoplastic transformation of plasma cells in MM. "
Number of subset3 (52 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2144
DatasetGDS1286 (Esophageal cell response to low pH: time course)
DescriptionAnalysis of esophageal cell line SKGT4 following exposure to low pH 6.5. Cells examined at various time points up to 2 hours following exposure. Results provide insight into role of gastric acid in pathogenesis of gastro-esophageal reflux disease (GORD) and esophagus adenocarcinoma.
Number of subset5 (10 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2152
DatasetGDS1476 (Uterine fibroids with fumarate hydratase mutations)
DescriptionAnalysis of 7 uterine fibroids carrying fumarate hydratase (FH) mutations. FH catalyzes hydration of fumarate in the Krebs tricarboxylic acid cycle. Results provide insight into the connection between the disruption of mitochondrial metabolic pathways and neoplasia.
Number of subset2 (22 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2175
DatasetGDS1253 (Pituitary adenoma subtypes)
Description"Expression profiling of 4 pituitary adenoma subtypes. Growth hormone (GH), prolactin (PRL), and adrenocorticotrophin (ACTH) secreting pituitary adenomas, and non-functioning pituitary adenoma examined. 5 specimens pooled and examined for each subtype. Results provide insight into tumor pathogenesis."
Number of subset5 (5 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2189
DatasetGDS1204 (Lung cancer cell line response to motexafin gadolinium: time course)
Description"Expression profiling of lung cancer cell line A549 following treatment with 50 uM of the metal cation-containing chemotherapeutic drug motexafin gadolinium (MGd). Cells examined at 4, 12, and 24 hours following treatment. Results provide insight into the mechanism of action of MGd. "
Number of subset5 (18 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2225
DatasetGDS1873 (Antiestrogen and aromatase inhibitor effect on breast cancer cells )
Description"Analysis of estrogen receptor positive, aromatase transfected MCF-7 cells after treatment with an antiestrogen (AE) or an aromatase inhibitor (AI). AEs and AIs are used to treat estrogen-dependent breast cancer. Cells also treated with androgen which is converted to estrogen by aromatase. "
Number of subset10 (18 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2240
DatasetGDS1556 (Atrial and ventricular myocardium comparison (HG-U133A))
Description"Analysis of right atria and left ventricles of hearts. While both the ventricle and atrium contract, the atrium is also a source and target for neurohumoral signals. Results provide insight into the molecular basis for the ultrastructural and functional differences between the atrium and ventricle."
Number of subset6 (25 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2248
DatasetGDS1288 (Mesenchymal precursor cells derived from embryonic stem cells)
DescriptionComparison of mesenchymal stem cells (MSC) and undifferentiated embryonic stem cells (ESC). ESC plated on a monolayer of OP9 stromal cells in the presence of 20% heat inactivated fetal bovine serum in alpha MEM medium to induce differentiation into MSC.
Number of subset3 (6 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2280
DatasetGDS1062 (Squamous cell carcinoma of the oral cavity with lymph node metastasis)
DescriptionExpression profiling of 18 primary squamous cell carcinomas of the oral cavity with or without lymph node metastasis. Expression in lymph node metastasis also examined. Results used to identify gene expression signature in primary tumors that indicates the presence of lymph node metastasis.
Number of subset4 (27 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2361
DatasetGDS1096 (Normal tissues of various types)
DescriptionExpression profiling of 36 types of normal tissue. Each RNA tissue sample pooled from several donors. Results identify tissue specific genes and provide baselines for interpreting gene expression in cancer.
Number of subset36 (36 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2395
DatasetGDS2142 (Cystic fibrosis patients with mild and severe lung disease: nasal respiratory epithelium (HG-U133A))
DescriptionAnalysis of the nasal respiratory epithelium of cystic fibrosis (CF) patients with mild or severe lung disease. CF patients have identical homozygous deltaF508 CFTR genotypes but exhibit variability in pulmonary disease severity. Results provide insight into the basis of the phenotypic difference.
Number of subset3 (19 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2443
DatasetGDS1390 (Prostate cancer progression after androgen ablation)
DescriptionAnalysis of prostate cancer progression following androgen ablation treatment. 10 treated androgen-independent primary prostate tumors compared to 10 untreated androgen-dependent primary prostate tumors. Results provide insight into progression of prostate cancer to aggressive androgen-independent
Number of subset2 (20 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2450
DatasetGDS1630 (Immortalized endothelial cell line response to atorvastatin)
Description"Analysis of EA.hy926, an immortalized umbilical vein endothelial cell (HUVEC) line, and its primary cell counterpart following treatment with HMG-CoA reductase inhibitor atorvastatin to inhibit the mevalonate pathway. Results suggest EA.hy926 cells have retained endothelial cell-specific features."
Number of subset6 (16 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2461
DatasetGDS2014 (Ulcerative colitis)
Description"Expression profiling of colonic mucosa from patients with ulcerative colitis, a chronic inflammatory bowel disease of the colon. Colonic mucosa from patients with irritable bowel syndrome used as controls. Biopsies obtained during colonoscopy from region with macroscopically normal appearing mucosa."
Number of subset4 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2485
DatasetGDS1380 (Glioblastoma pseudopalisading cells)
DescriptionAnalysis of pseudopalisading cells obtained by laser capture microdissection from glioblastoma tumors. The presence of pseudopalisading cells is associated with aggressive malignant gliomas. Results identify putative prognostic markers for glioblastoma.
Number of subset2 (18 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2487
DatasetGDS1637 (Oncogene-induced sensescence in vitro model)
DescriptionAnalysis of transformed cell lines that either exhibit oncogene-induced senescence (OIS) triggered by MEK activation or bypass OIS. Senescent cells exist in premalignant tumors but not in malignant ones. Results provide insight into the molecular basis of OIS.
Number of subset8 (10 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2509
DatasetGDS1780 (Colorectal cancer progression: polysomal mRNA profiles)
Description"Comparison of polysomal RNA from isogenic cell lines established from a colorectal cancer (CRC) patient. SW480 and SW620 cells derived from the primary tumor and a lymph node metastasis, respectively. The cell lines constitute a cellular model of CRC transition from invasive carcinoma to metastasis."
Number of subset2 (6 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2513
DatasetGDS1758 (Pterygium)
Description"Expression profiling of primary pterygium tissue. Pterygium, a common ocular surface disorder, is a fibrovascular overgrowth from the conjunctiva onto the cornea. Results provide insight into pterygium pathogenesis."
Number of subset2 (12 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2531
DatasetGDS2241 (Trophoblast cell lines)
DescriptionComparison of BeWo and JEG3 trophoblast cell lines. Trophoblast cell lines are used as surrogates for primary trophoblast cells in the study of placental function. Results provide insight into the differences between the two cell lines.
Number of subset2 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2638
DatasetGDS1543 (Tumor necrosis factor effect on microvascular endothelial cells)
DescriptionAnalysis of microvascular endothelial cells (HMEC) stimulated with tumor necrosis factor (TNF)-alpha for 5 hours. TNF is a potent inflammatory stimulus. Results provide insight into the relevance of the diversity of endothelial cell subtypes for the response to inflammatory stimuli.
Number of subset2 (6 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2639
DatasetGDS1542 (Tumor necrosis factor effect on macrovascular umbilical vein endothelial cells)
DescriptionAnalysis of macrovascular umbilical vein endothelial cells (HUVEC) stimulated with tumor necrosis factor (TNF)-alpha for 5 hours. TNF is a potent inflammatory stimulus. Results provide insight into the relevance of the diversity of endothelial cell subtypes for the response to inflammatory stimuli.
Number of subset2 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2665
DatasetGDS1618 (Lymph node and tonsil comparison)
Description"Analysis of lymph node (sinuses) and tonsil (no sinuses), highly similar secondary lymphoid organs. Metastatic tumor cells are preferentially arrested in the lymph node sinuses. Results identify signature genes that are prime candidates for mediating adhesion of tumor cells to sinusoidal cells."
Number of subset2 (20 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2666
DatasetGDS1230 (Hematopoietic stem cell and progenitor cell comparison (HG-U133A))
Description"Comparison of CD34+CD33-CD38-Rho(lo)c-kit+ cells, enriched for hematopoietic stem/progenitor cells (HSC), to CD34+CD33-CD38-Rho(hi) cells, enriched for committed hematopoietic progenitor cells (HPC). Cells obtained from umbilical cord blood and bone marrow. Provides insight into control of HSC fate."
Number of subset4 (18 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2703
DatasetGDS2110 (Adrenal gland across a 24-hour period)
Description"Analysis of whole adrenal glands collected at 4-hour intervals across a 24-hour period from adult females acclimated to a 12hr light, 12hr dark photoperiod. Results provide insight into the nature of oscillatory patterns of gene expression in the adrenal gland."
Number of subset6 (6 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2724
DatasetGDS2245 (Uterine fibroids with mutated fumarate hydratase (I))
DescriptionAnalysis of uterine fibroids with mutations in the fumarate hydratase (FH) gene. FH catalyzes the hydration of fumarate in the TCA cycle. Heterozygous germline mutations in FH cause uterine fibroids and renal cell cancer. Results provide insight into the pathogenesis of TCA cycle-related tumors.
Number of subset15 (18 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2725
DatasetGDS2246 (Uterine fibroids with mutated fumarate hydratase (II))
DescriptionAnalysis of uterine fibroids with mutations in the fumarate hydratase (FH) gene. FH catalyzes the hydration of fumarate in the TCA cycle. Heterozygous germline mutations in FH cause uterine fibroids and renal cell cancer. Results provide insight into the pathogenesis of TCA cycle-related tumors.
Number of subset5 (10 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2742
DatasetGDS1902 (Cyanobacterial metabolite apratoxin A cytotoxic effect on colon adenocarcinoma cells: time course and dose response)
DescriptionAnalysis of colon adenocarcinoma HT29 cells at various time points up to 12 hours following treatment with 2 or 10 nM of the cyanobacterial metabolite apratoxin A. Results provide insight into the molecular mechanisms underlying the cytotoxic effect of apratoxin A on tumor cells.
Number of subset16 (27 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE2815
DatasetGDS1384 (c-Myb and its oncogenic variant v-Myb)
Description"Analysis of transcriptional activity in MCF7 cells infected with control adenovirus versus adenovirus expressing c-Myb, oncogenic variant v-Myb, or a 3MutC hybrid construct. Results indicate that v-Myb is a distinct transcriptional regulator with a unique set of activities."
Number of subset4 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3167
DatasetGDS1479 (Carcinoma in situ lesions of the urinary bladder)
DescriptionAnalysis of bladder biopsies of superficial transitional cell carcinomas with or without surrounding carcinoma in situ (CIS) lesions and muscle invasive carcinomas (mTCC). CIS is a common mTCC precursor. Results provide insight into which tumors in early stage bladder cancer are likely to progress.
Number of subset6 (60 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3183
DatasetGDS2852 (Interleukin 13 effect on bronchial cell line: time course)
DescriptionAnalysis of bronchial A549 cells at various time points up to 24 hours following treatment with the cytokine interleukin 13 (IL-13). IL-13 contributes to the pathogenesis of asthma.
Number of subset6 (15 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3284
DatasetGDS1574 (Endotoxin effect on leukocytes: time course (HG-U133A))
DescriptionAnalysis of leukocytes from 8 healthy subjects intravenously administered bacterial endotoxin. Leukocytes examined at various time points up to 24 hours post-infusion. Results provide insight into the molecular mechanisms involved in the propagation and resolution of the inflammatory response.
Number of subset16 (46 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3307
DatasetGDS1956 (Various muscle diseases (HG-U133A))
DescriptionAnalysis of muscle biopsy specimens from patients with various muscle diseases. Results provide insight into the diagnosis and pathogenesis of muscle diseases.
Number of subset12 (121 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3356
DatasetGDS2021 (Coronary smooth muscle cell response to beta-1 receptor blockers metoprolol and nebivolol)
Description"Expression profiling of coronary smooth muscle cells treated with metoprolol or nebivolol. Metoprolol and nebivolol are beta 1-receptor blockers. In a study of 155 patients with hypertension, adverse effects of metoprolol were higher than nebivolol (Uhlir et al. 1991). "
Number of subset3 (9 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3407
DatasetGDS2175 (Cockayne syndrome group B protein-null fibroblast rescue (HG-U133A))
Description"Analysis of Cockayne syndrome group B (CSB) protein-null fibroblasts rescued by expression of CSB cDNA. CS, a neurodegenerative disorder, arises mostly from CSB defects. Results provide insight into how CSB defects cause CS."
Number of subset3 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3419
DatasetGDS1672 (Keratinocyte stem cell?enriched hair follicle bulge cells)
Description"Comparison of outer root sheath (ORS) cells of the hair follicle bulge with other defined ORS cell subpopulations within the follicle. Results provide insight into the biological distinctiveness of hair follicle bulge cells, suggesting the bulge is a repository for keratinocyte stem cells (KSCs). "
Number of subset7 (16 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3524
DatasetGDS1584 (Oral squamous cell carcinoma)
DescriptionAnalysis of oral squamous cell carcinoma (OSCC) cells from 16 patients. OSCC cells isolated from tumors by laser capture microdissection. Results identify a strong correlation between gene expression profile and tumor invasiveness in OSCC.
Number of subset11 (20 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3737
DatasetGDS1736 (Arachidonic acid effect on prostate cancer cells)
DescriptionAnalysis of PC-3 prostate cancer cells incubated with arachidonic acid (AA). AA is an omega-6 fatty acid shown to induce cancer cell proliferation. Results suggest AA plays an important role in stimulation of growth-related genes and proliferation via phosphatidylinositol 3-kinase (PI3K) signaling.
Number of subset2 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3846
DatasetGDS2767 (Blood response to various beverages: time course)
Description"Analysis of blood samples from 6 individuals at various time points up to 12 hours following the intake of water, ethanol, grape juice, or red wine. Results may contribute to elucidating the mechanisms underlying the cardioprotective effects of red wine."
Number of subset15 (108 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE3860
DatasetGDS1503 (Hutchinson-Gilford progeria syndrome: fibroblast (HG-U133A))
DescriptionExpression profiling of three fibroblast cell lines derived from Hutchinson-Gilford progeria syndrome (HGPS) patients. Identified changes in gene expression may provide clues to potential risk factors or factors influencing disease progression.
Number of subset8 (18 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4045
DatasetGDS2201 (Serrated and conventional adenocarcinomas)
DescriptionComparison of serrated and conventional colorectal adenocarcinoma tumor samples. Results differentiate serrated from conventional colorectal carcinomas (CRC) and provide insight into the molecular pathogenesis of serrated CRC.
Number of subset2 (37 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4127
DatasetGDS1688 (Various lung cancer cell lines)
Description"Expression profiling of a set of 29 lung cancer cell lines consisting of 10 non-small cell adenocarcinoma, 10 small cell cancer, and 9 squamous cell cancer lines. Gene expression results analyzed in relation to the sensitivity of each cell line to commonly used anti-cancer agents."
Number of subset3 (29 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4176
DatasetGDS1750 (Mantle cell lymphoma cell lines (HG-U133A))
DescriptionExpression profiling of 4 mantle cell lymphoma (MCL) cell lines. MCL has the worst prognosis among B-cell lymphomas. Gene expression results combine with genomic profiling results to identify genes that are relevant to MCL pathogenesis and that could also represent possible therapeutic targets.
Number of subset4 (5 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4271
DatasetGDS1815 (High-grade gliomas (HG-U133A))
DescriptionAnalysis of high-grade glioma (HGGs) samples from cases of WHO grade III and IV astrocytomas. Results classify HGGs into molecular subclasses with prognostic value that predict survival and disease progression. The molecular subclasses resemble key stages of neurogenesis.
Number of subset15 (100 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4412
DatasetGDS1975 (Gliomas of grades III and IV (HG-U133A))
Description"Analysis of grades III and IV gliomas of various histologic types. Results used to develop a gene-expression based, histology independent-classification scheme, and provide insight into the biology of gliomas."
Number of subset6 (85 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4485
DatasetGDS2287 (Airway epithelial cell response to Pseudomonas aeruginosa rsmA mutant infection)
DescriptionAnalysis of airway epithelial cells infected with Pseudomonas aeruginosa PAO1 or the rsmA mutant. RsmA is a small RNA-binding protein that plays a role in the regulation of virulence-related genes in P. aeruginosa. Results provide insight into the influence of RsmA-regulated functions on the host.
Number of subset5 (6 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4636
DatasetGDS2057 (Androgen receptor modulator effect: time course (HG-U133A))
Description"Analysis of LNCaP cells treated for 6 and 24 hours with RTI-018, an androgen receptor (AR) ligand with a mechanism of action different from that of canonical agonists. Results provide insight into the link between RTI-018 induced AR conformational changes and its ability to regulate gene expression."
Number of subset5 (18 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4646
DatasetGDS2332 (Neisseria meningitidis non-adherent mutant infected umbilical vein endothelial cells)
Description"Analysis of umbilical vein endothelial cells 4 hours following infection with adherent wild type, frpC-deficient mutant, or the non-adherent (delta pilD) mutant form of Neisseria meningitidis. Results provide insight into the role of adherence-mediated signaling in N. meningitidis infections."
Number of subset9 (11 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE473
DatasetGDS266 (Asthma and atopy (HG-U133A))
Description"Investigation of CD4+ lymphocytes from patients with and without atopy, in combination with asthma."
Number of subset5 (29 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE474
DatasetGDS268 (Obesity and fatty acid oxidation)
DescriptionIdentification of proteins involved in fatty acid oxidation in skeletal muscle. Fat oxidation may be reduced in morbidly obese individuals. Provides understanding of how obesity contributes to cardiovascular disease via insulin resistance.
Number of subset3 (24 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE475
DatasetGDS289 (Chronic obstructive pulmonary disease)
DescriptionStudy of the signaling mechanisms responsible for diaphragm muscle transformation from fast-to-slow fiber type in chronic obstructive pulmonary disease (COPD) patients.
Number of subset2 (7 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE4917
DatasetGDS2095 (Glucocorticoid receptor activation effect on breast cancer cells: time course (series 1))
DescriptionAnalysis of breast cancer MCF10A-Myc cells at various time points up to 24 hours following treatment with dexamethasone to activate the glucocorticoid receptor (GR). GR activation is critical in the stress response of virtually all cell types.
Number of subset18 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE5090
DatasetGDS2084 (Polycystic ovary syndrome: adipose tissue)
Description"Analysis of omental adipose tissues of morbidly obese patients with polycystic ovary syndrome (PCOS). PCOS is a common hormonal disorder among women of reproductive age, and is characterized by hyperandrogenism and chronic anovulation. PCOS is associated with obesity."
Number of subset2 (15 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE5370
DatasetGDS2153 (Dermatomyositis)
DescriptionAnalysis of skeletal muscle biopsies of 5 patients with dermatomyositis (DM). DM is an idiopathic inflammatory myopathy characterized by muscle weakness and skin lesions. Results provide insight into the pathogenic pathways responsible for muscle fiber damage and dysfunction in myositis.
Number of subset2 (9 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE5388
DatasetGDS2190 (Bipolar disorder: dorsolateral prefrontal cortex )
DescriptionAnalysis of postmortem dorsolateral prefrontal cortex from 30 adults with bipolar disorder. Results provide insight into the pathophysiology of the disease.
Number of subset2 (61 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE5389
DatasetGDS2191 (Bipolar disorder: orbitofrontal cortex)
DescriptionAnalysis of postmortem orbitofrontal cortex from 10 adults with bipolar disorder. Results provide insight into the pathophysiology of the disease.
Number of subset2 (21 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE5418
DatasetGDS2362 (Presymptomatic and symptomatic malaria: peripheral blood mononuclear cells)
Description"Comparison of peripheral blood mononuclear cells of subjects with early, presymptomatic, experimentally acquired malaria to those with acute, uncomplicated, naturally acquired malaria. Results provide insight into the immune response to malaria in these two stages of infection."
Number of subset8 (71 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE6014
DatasetGDS2444 (Dichloroacetate effect on cultured lung carcinoma and glioblastoma cells)
Description"Analysis of A549 lung carcinoma and M059K glioblastoma cells treated with dichloroacetate (DCA), an inhibitor of the mitochondrial pyruvate dehydrogenase kinase. DCA shifts metabolism from glycolysis to glucose oxidation and decreases mitochondrial membrane potential in cancer cells."
Number of subset4 (4 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE620
DatasetGDS493 (Cystic fibrosis pathology and 4-phenylbutyrate (HG-U133A))
Description"Effect of 1mM 4-phenylbutyrate (PBA) at 0, 12 and 24 hours in cystic fibrosis bronchial epithelial model cell line IB3-1. PBA modulates heat shock protein and promotes trafficking of deltaF508 cystic fibrosis transmembrane conductance regulator (CFTR)."
Number of subset3 (11 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE6236
DatasetGDS2655 (Fetal and adult reticulocytes (HG-U133A))
DescriptionAnalysis of circulating blood reticulocytes from umbilical cords and normal adults. Reticulocytes are immature red blood cells containing residual RNA. Results provide insight into the molecular basis of terminal erythroid differentiation.
Number of subset2 (28 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE6322
DatasetGDS2723 (Primary immunodeficiency syndrome: B cells)
Description"Analysis of immortalized B cells from 2 children with a primary immunodeficiency syndrome that is characterized by neutropenia, partial albinism, short stature, and B-cell and cytotoxic T-cell deficiencies. Results provide insight into the genetic basis of this syndrome."
Number of subset6 (4 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE6691
DatasetGDS2643 (Waldenstrom's macroglobulinemia: B lymphocytes and plasma cells)
Description"Analysis of B lymphocytes (BL) and plasma cells (PC) from patients with Waldenstrom's macroglobulinemia (WM), a B-lymphoproliferative disorder (BLPD). Results provide insight into differences between PC and BL from WM and their cell counterpart in chronic lymphocytic leukemia and multiple myeloma. "
Number of subset6 (56 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE6740
DatasetGDS2649 (HIV infection effect on CD4+ and CD8+ T cells)
DescriptionAnalysis of CD4+ and CD8+ T cells from HIV patients at different clinical stages and rates of disease progression. Changes in T-cell function are a hallmark of HIV infection. Results provide insight into the pathogenic mechanisms in HIV infections that lead to these changes in T-cell function.
Number of subset6 (40 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE6783
DatasetGDS2623 (Epidermal growth factor effect on cervical carcinoma cell line: time course)
DescriptionAnalysis of cervical carcinoma HeLa cells following treatment with epidermal growth factor for various time points up to 480 minutes. Results provide insight into the dynamics of growth factor signaling.
Number of subset9 (7 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE6883
DatasetGDS2617 (Tumorigenic breast cancer cells (HG-U133A))
DescriptionAnalysis of breast cancer cells that have high tumorigenic capacity. These cells express CD44 and low or undetectable levels of CD24. Results used to define a gene expression signature associated with metastasis.
Number of subset3 (12 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE7035
DatasetGDS2705 (PPARgamma agonist and platinum-based drug effect on adenocarcinoma cell line)
Description"Analysis of NSCLC adenocarcinoma cells treated with rosiglitazone, carboplatin, or both. Rosiglitazone is an agonist of the nuclear receptor PPARgamma. Results provide insight into the molecular basis of the synergy observed between rosiglitazone and platinum-based drugs in cancer models."
Number of subset4 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE7765
DatasetGDS2744 (Dioxin effect on breast cancer cell line (HG-U133A))
Description"Analysis of MCF-7 breast cancer cells treated with 100 nM dioxin. Although dioxin is causative for many types of cancers, low exposure to dioxin is associated with a decreased incidence of breast carcinoma. Results provide insight into the molecular basis of this protective effect."
Number of subset2 (6 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE781
DatasetGDS505 (Renal clear cell carcinoma (HG-U133A))
DescriptionInvestigation into mechanisms of renal clear cell carcinogenesis (RCC). Comparison of renal clear cell tumor tissue and adjacent normal tissue isolated from the same surgical samples.
Number of subset12 (17 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE873
DatasetGDS525 (Extraocular and limb muscle comparison)
DescriptionMolecular definition of extraocular muscle (EOM). Autopsy superior rectus EOM compared with biopsy limb quadriceps femoris muscle.
Number of subset2 (5 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE907
DatasetGDS556 (Extraocular muscle layer profiles (HG-U133A))
Description"Analysis of adult monkey whole medial and lateral rectus extraocular muscle (EOM), and microdissected medial rectus global and orbital EOM layers."
Number of subset4 (8 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE973
DatasetGDS649 (Inflammatory response of interleukin-1-stimulated endothelial cells)
Description"Temporal analysis of human umbilical vein endothelial cell (HUVEC) inflammatory response to interleukin-1 (IL-1) stimulation for 0, 0.5, 1, 2.5, and 6 hours. Immediate-early to early gene expression program characterized."
Number of subset5 (5 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE974
DatasetGDS558 (Myocardial remodeling in response to LVAD)
Description"Analysis of paired left ventricular apex samples harvested at implant of left ventricular assist device (LVAD) and at explant. Patients classified as ischemic, non-ischemic or acute myocardial infarction within 10 days of implant."
Number of subset24 (38 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)

SeriesGSE994
DatasetGDS534 (Smoking-induced changes in airway transcriptome)
Description"Analysis of cigarette smoking-induced changes in bronchial epithelia, and reversibility of effects when smoking is discontinued. May provide insight to molecular events leading to chronic obstructive pulmonary disease (COPD) and lung cancer."
Number of subset3 (75 samples)
PlatformGPL96 (Organism: Homo sapiens, in situ oligonucleotide)