GEO DataSets

(Submitter supplied) Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease and for many other purposes. Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data. We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16043

8 Samples

Download data: CEL, TXT

(Submitter supplied) Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease and for many other purposes. Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data. We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16043

6 Samples

Download data: CEL

(Submitter supplied) Genome-wide location analysis of transcription factor of c-Myc and Max was conducted using RenLab Hu6K array in Daudi cells. In comparison, the GWLA was also done for general transcription factor RNA polymerase II and TAF1, and sequence specific transcription factor E2F1 in the same cell line. Keywords = GWLA Keywords = RenLab Keywords = Hu6K Keywords = Myc Keywords = Max Keywords: other

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL1969

18 Samples

Download data

(Submitter supplied) This 6144-element (8 blocks, 12 rows, 64 columns) array contain spotted DNAs of promoter regions (800-1000 bp on average) typically from 650bp upstream to 250bp downstream of transcription start sites. Protocol: http://www.avivasysbio.com

Organism:

Homo sapiens

1 Series

3 Samples

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(Submitter supplied) Overexpression of c-Myc is one of the most common alterations in human cancers, yet it is not clear how this transcription factor acts to promote malignant transformation. To understand the molecular targets of c-Myc function, we have used an unbiased genome-wide location-analysis approach to examine the genomic binding sites of c-Myc in Burkitt's lymphoma cells. We find that c-Myc together with its heterodimeric partner, Max, occupy >15% of gene promoters tested in these cancer cells. more...

Organism:

Homo sapiens

1 Series

18 Samples

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(Submitter supplied) ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use conservative approaches aimed to minimize false-positive transcription factor targets. We present a model with improved sensitivity in detecting binding events from ChIP-on-chip data. Its application to human T-cells, followed by extensive biochemical validation, reveals that three transcription factor oncogenes, NOTCH1, MYC, and HES1, bind to several thousands target gene promoters, up to an order of magnitude increase over conventional analysis methods. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

20 Samples

Download data: CEL, CHP

(Submitter supplied) To evaluate the mechanisms and consequences of chromosomal aberrations in colorectal cancer (CRC), we used a combination of spectral karyotyping, array comparative genomic hybridization (aCGH), and array-based global gene expression profiling on 31 primary carcinomas and 15 established cell lines. Importantly, aCGH showed that the genomic profiles of primary tumors are recapitulated in the cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6848 GPL6480

50 Samples

Download data: TXT

(Submitter supplied) The MYC oncogene has been implicated in the regulation of up to thousands of genes involved in many cellular programs including proliferation, growth, differentiation, self-renewal, and apoptosis. MYC is thought to induce cancer through an exaggerated effect on these physiologic programs. Which of these genes are responsible for the ability of MYC to initiate and/or maintain tumorigenesis is not clear. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7205

16 Samples

Download data

(Submitter supplied) The PLZF-RARa fusion oncoprotein is overexpressed in the t(11;17) subtype of acute promyelocytic leukemia. Gene expression microarrays were used to identify genes involved in leukemic transformation. We used microarray to detect gene expression changes induced by the PLZF-RARa fusion oncoprotein in the U937 cell line

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) Parkinson disease (PD) is a neurodegenerative disease characterized by the accumulation of alpha-synuclein (SNCA) and other proteins in aggregates termed “Lewy Bodies” within neurons. PD has both genetic and environmental risk factors, and while processes leading to aberrant protein aggregation are unknown, past work points to abnormal levels of SNCA and other proteins. Although several genome-wide studies have been performed for PD, these have focused on DNA sequence variants by genome-wide association studies (GWAS) and on RNA levels (microarray transcriptomics), while genome-wide proteomics analysis has been lacking. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

73 Samples

Download data: RDATA, TXT

(Submitter supplied) The transcriptional regulator c-Myc is the most frequently deregulated oncogene in human tumors. Targeted overexpression of this gene in mice results in distinct types of lung adenocarcinomas. By using microarray technology, alterations in the expression of genes were captured based on a female transgenic mouse model in which, indeed, c-Myc overexpression in alveolar epithelium results in the development of bronchiolo-alveolar carcinoma (BAC) and papillary adenocarcinoma (PLAC). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3321

Platform:

GPL1261

8 Samples

Download data: CEL

Analysis of cancerous lungs of transgenics overexpressing the c-Myc proto-oncogene in their alveolar epithelia. This overexpression results in bronchiolo-alveolar carcinoma and papillary adenocarcinoma. Results provide insight into the molecular mechanisms by which c-Myc effects tumorigenesis.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 strain sets

Platform:

GPL1261

Series:

GSE10954

8 Samples

Download data: CEL

(Submitter supplied) Background: MYC is a transcription factor encoded by the c-MYC gene (thereafter termed MYC). MYC is key transcription factor involved in many central cellular processes including ribosomal biogenesis. MYC is overexpressed in the majority of human tumours including aggressive B-cell lymphoma especially Burkitt's lymphoma. Although Burkitt's lymphoma is a highlight example for MYC overexpression due to a chromosomal translocation, no global analysis of MYC binding sites by chromatin immunoprecipitation (ChIP) followed by global next generation sequencing (ChIP-Seq) has been conducted so far in Burkitt's lymphoma. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL96 GPL9052

22 Samples

Download data: BED, CEL, TXT

(Submitter supplied) Advances in genomic signatures have begun to dissect breast cancer heterogeneity, and application of these signatures will allow the prediction of which pathways are important in tumor development. Here we used genomic signatures to predict involvement of specific E2F transcription factors in Myc-induced tumors. We genetically tested this prediction by interbreeding Myc transgenics with mice lacking various activator E2F alleles. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4094

Platform:

GPL8321

80 Samples

Download data: CEL, CHP

Analysis of MMTV-Myc tumors generated in an E2F wild-type, E2F1 null, E2F2 null or E2F3 heterozygous background. E2Fs are Myc transcriptional activators shown to regulate proliferation and apoptosis. Results provide insight into role of E2Fs in Myc-induced breast cancer.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 4 genotype/variation sets

Platform:

GPL8321

Series:

GSE24594

80 Samples

Download data: CEL, CHP

(Submitter supplied) During development of the mammalian central nervous system (CNS), neurons and glial cells (astrocytes and oligodendrocytes) are generated from common neural precursor cells (NPCs). However, neurogenesis precedes gliogenesis, which normally commences at later stages of fetal telencephalic development. Astrocyte differentiation of mouse NPCs at embryonic day (E) 14.5 (relatively late gestation) is induced by activation of the transcription factor STAT3, whereas at E11.5 (mid-gestation) NPCs do not differentiate into astrocytes even when stimulated by STAT3-activating cytokines such as leukemia inhibitory factor (LIF). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL18959

34 Samples

Download data: TXT

(Submitter supplied) Myc is a well known transcription factor with important roles in cell cycle, apoptosis and cellular transformation. Long non-coding (lnc)RNAs have recently emerged as a important class of regulatory RNAs. Here, we show that lncRNAs are an extensive component of the Myc-regulated transcriptional program. Using the P493-6 inducible Myc model we demonstrate that both Myc-induced mRNAs and lncRNAs were significant enriched for Myc binding sites. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL18959

22 Samples

Download data: TXT

(Submitter supplied) Myc is a well known transcription factor with important roles in cell cycle, apoptosis and cellular transformation. Long non-coding (lnc)RNAs have recently emerged as a important class of regulatory RNAs. Here, we show that lncRNAs are an extensive component of the Myc-regulated transcriptional program. Using the P493-6 inducible Myc model we demonstrate that both Myc-induced mRNAs and lncRNAs were significant enriched for Myc binding sites. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL18959

4 Samples

Download data: TXT