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ProteomicsTranscription factor-SNP interactome for colorectal cancer risk loci
A core task to understand the consequences of non-coding single nucleotide polymorphisms (SNP) is to identify their genotype specific binding of transcription factor (TF). Here, we generate a large-scale TF-SNP interaction map for a selection of 116 colorectal cancer (CRC) risk loci and validated TF...
ORGANISM(S): Homo sapiens (Human) 
2017-02-23 | PXD004435 | Pride
Human Transcription factor Cancer related snp Colorectal cancer 
TranscriptomicsSNP data from genomic DNA in patient with rectal cancer
The identification of surrogate single nucleotide polymorphism (SNP) markers that can predict responses to preoperative chemoradiotherapy (CRT) in rectal cancer patients. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of tumo...
ORGANISM(S): Homo sapiens 
2012-12-31 | E-GEOD-35282 | biostudies-arrayexpress
TranscriptomicsDeep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Affymetrix SNP array data]
Background: Globally, gastric cancer is the second most common cause of cancer-related death, with the majority of the health burden borne by economically less-developed countries. Methods: Here, we report a genetic characterization of 50 gastric adenocarcinoma samples, using affymetrix SNP arrays a...
ORGANISM(S): Homo sapiens 
2012-10-25 | E-GEOD-29996 | biostudies-arrayexpress
TranscriptomicsAffymetrix 250K StyI SNP array data for gastric and esophageal adenocarcinoma cancer types
Using data from high-density genomic profiling arrays, we describe the profiles of somatic copy-number aberrations (SCNAs) in 486 adenocarcinomas across all three major digestive organs, including 296 gastric and esophageal cancers. This analysis revealed that although patterns of broad, chromosome ...
ORGANISM(S): Homo sapiens 
2012-09-04 | E-GEOD-36459 | biostudies-arrayexpress
TranscriptomicsAffymetrix SNP array data for breast cancer formation in mouse
We investigated the CNAs in a four stage tumorigenesis model. This model included copy number analyses in non-transgenic NMRI mice (normal) and in transgenic SVT/t mice: non-malignant hyperplastic mammary glands and breast cancers, as well as breast cancer derived cell lines. We focused our research...
ORGANISM(S): Mus musculus 
2012-09-04 | E-GEOD-35873 | biostudies-arrayexpress
TranscriptomicsNormalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, norma...
ORGANISM(S): Homo sapiens 
2008-10-04 | E-GEOD-11977 | biostudies-arrayexpress
TranscriptomicsAffymetrix SNP 6.0 array data from neuroendocrine primary tumor and its metastasis
Reports on common mutations in neuroendocrine tumors (NET) are rare and clonality of NET metastases has not been investigated in this tumor entity yet. We selected a NET and a the corresponding lymph node and liver metastases as well as the derivative cell lines to screen for somatic mutations in...
ORGANISM(S): Homo sapiens 
2012-07-16 | E-GEOD-39371 | biostudies-arrayexpress
TranscriptomicsAffymetrix SNP array data for hepatocellular carcinoma tissue
Genetic variations play an important role in tumor development and metastasis. Hepatocellular carcinoma (HCC) is one of leading cause of cancer-related death. Despite improvements in surveillance and clinical treatment strategies, the prognosis of HCC remains dismal. Affymetrix SNP 6.0 array were us...
ORGANISM(S): Homo sapiens 
2012-10-26 | E-GEOD-29667 | biostudies-arrayexpress
TranscriptomicsDifferential in vivo tumorigenicity of distinct subpopulations from a luminal-like breast cancer model (SNP)
The cellular heterogeneity of one patient derived orthotopic breast cancer xenograft model PDX was investigated using flow cytometry, combined with assessment of in vivo tumorigenicity and SNP genotyping array for copy number analysis. Epithelial cell adhesion molecule (EpCAM) was revealed as a high...
ORGANISM(S): Homo sapiens 
2015-05-26 | E-GEOD-54595 | biostudies-arrayexpress
TranscriptomicsAffymetrix SNP6.0 on Ollier disease-related tumors
Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier pat...
ORGANISM(S): Homo sapiens 
2011-08-26 | E-GEOD-22984 | biostudies-arrayexpress
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