GEO DataSets

(Submitter supplied) Human papillomavirus (HPV) integration is a critical step in cervical cancer development, while the oncogenic mechanism in genome-wide transcriptional level is still poorly understood. In this study, we employed integrative analysis on multi-omics data of cervical cancer cell lines. Through HPV integration detection, super enhancer (SE) identification, SE-associated gene expression and extrachromosomal DNA (ecDNA) investigation, we aimed to explore the genome-wide transcriptional influence of HPV integration. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing

6 related Platforms

77 Samples

Download data: BW, HIC, TXT, XLS

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

12 Samples

Download data: BW, TXT

(Submitter supplied) We identified LAMP3 as a key driver gene of anti-viral subnetwork genes in cervical cancer patients. Therefore we tested this prediction using an in vitro system. This is the first direct demonstration of LAMP3 regulatory role in interferon-dependent immune response.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5189

Platform:

GPL10558

8 Samples

Download data: TXT

(Submitter supplied) Gene expression profiling of 82 patients with cervical cancer was performed. The expression data were correlated with copy number alterations of the same patients, as assessed with array CGH in a separate study, in order to identify drivers of cervical cancer carcinogenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

82 Samples

Download data: TXT

(Submitter supplied) Cervical cancer is the one of the most common cancer type among women worldwide, with Human Papillomavirus (HPV) playing a causal role in this disease. We applied a novel integrative approach to understand the disease process and find its major drivers. We performed a meta-analysis of gene expression and chromosomal aberration studies comprising data on over 500 patients for the reconstruction of a regulatory meta-network. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL1053 GPL1052

54 Samples

Download data: TXT

Analysis of LAMP3 depleted HeLa cells following treatment with interferon-alpha for 3 or 4 days. Results provide insight into the role of LAMP3 in the immune response mediated by interferon-alpha.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 protocol, 2 time sets

Platform:

GPL10558

Series:

GSE29009

8 Samples

Download data: TXT

(Submitter supplied) A better understanding of the consequences of recurrent (epi)genetic alterations that occur during cervical carcinogenesis is essential in the search for novel biomarkers. In this study we determined genome-wide expression profiles of 10 squamous cell carcinomas (SCCs), 5 adenocarcinomas (AdCAs) and 6 normal epithelial samples. Expression patterns were subsequently combined with previously determined chromosomal profiles in the same carcinomas. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Expression profiling by genome tiling array

Platforms:

GPL3054 GPL3441

38 Samples

Download data

(Submitter supplied) Oncogenic human papillomavirus (HPV) genomes are often integrated into host chromosomes in HPV-associated cancers. HPV genomes are integrated either as a single copy, or as tandem repeats of viral DNA interspersed with, or without, host DNA. Integration occurs frequently in common fragile sites susceptible to tandem repeat formation, and the flanking or interspersed host DNA often contains transcriptional enhancer elements. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

24 Samples

Download data: BROADPEAK, BW

(Submitter supplied) Extrachromosomal DNA (ecDNA) are frequently observed in human cancers and are responsible for high levels of oncogene expression.  In glioblastoma (GBM), ecDNA copy number correlates with poor prognosis. It is hypothesized that their copy number, size and chromatin accessibility facilitate clustering of ecDNA and colocalization with transcriptional hubs, and that this underpins their elevated transcriptional activity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL28038 GPL16791

6 Samples

Download data: BED, BW