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TranscriptomicsNon-coding antisense transcription detected by conventional and single-stranded cDNA microarray
Recent bioinformatic studies revealed that many mammalian protein-coding genes also transcribe their complementary strands. This phenomenon raises questions regarding the validity of data obtained from double-stranded cDNA microarrays since hybridization to both strands may occur. To analyze experim...
ORGANISM(S): Homo sapiens 
2007-09-01 | E-GEOD-7860 | biostudies-arrayexpress
TranscriptomicsThe non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs
Vault particles are conserved organelles that have been implicated in multidrug resistance and intracellular transport. They are formed by three different proteins and the non-coding vault RNAs (vRNAs). Here we show that human vRNAs produce several small RNAs (svRNAs) by mechanisms different from th...
ORGANISM(S): Homo sapiens 
2009-09-07 | E-GEOD-16060 | biostudies-arrayexpress
TranscriptomicsTasquinimod, a Quinoline-3-Carboxamide Anti-Angiogenic Agent, treated Prostate Cancer Cell Line in-vivo and in-vitro
The quinoline-3-carboxamide ABR-215050 (Tasquinimod (INN)), exhibits anti-tumor activity via inhibition of tumor angiogenesis in human and rodent tumors. To further explore the mode of action of ABR-215050, in vivo experiments with gene microarray analysis were performed using samples of LNCaP prost...
ORGANISM(S): Homo sapiens 
2011-03-01 | E-GEOD-17031 | 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
TranscriptomicsMolecular subtypes of breast cancer are associated with characteristic DNA methylation patterns
Introduction: Five different molecular subtypes of breast cancer have been identified through gene expression profiling. Each subtype has a characteristic expression pattern suggested to partly depend on cellular origin. We aimed to investigate whether the molecular subtypes also display distinct me...
ORGANISM(S): Homo sapiens 
2010-06-09 | E-GEOD-22210 | biostudies-arrayexpress
TranscriptomicsThe HER2-encoded miR-4728-3p regulates ESR1 through a non-canonical internal seed interaction
Since the early 1980s remarkable progress has been made in understanding the role of the HER2 locus in carcinogenesis, but many details of its regulatory network are still elusive. We recently reported the finding of 367 new human microRNA (miRNA) genes of which one, mir-4728, is encoded in an intro...
ORGANISM(S): Homo sapiens 
2014-08-13 | E-GEOD-55822 | biostudies-arrayexpress
TranscriptomicsCharacterization of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumors
Amplification of chromosomal region 11q13, containing the cell cycle regulatory gene CCND1, is frequently found in breast cancer and other malignancies. It is associated with the favourable oestrogen receptor (ER) positive breast tumour phenotype, but also with poor prognosis and treatment failure. ...
ORGANISM(S): Homo sapiens 
2011-11-23 | E-GEOD-32578 | biostudies-arrayexpress
TranscriptomicsIdentification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene
To comprehensively characterize microRNA (miRNA) expression in breast cancer, we performed the first extensive next-generation sequencing expression analysis of this disease. We sequenced small RNA from tumors with paired samples of normal and tumor-adjacent breast tissue. Our results indicate that ...
ORGANISM(S): Homo sapiens 
2012-07-06 | E-GEOD-39162 | biostudies-arrayexpress
TranscriptomicsHigh-resolution aCGH analyses of copy number alterations in HER2-amplified breast cancer
HER2 gene amplification and protein overexpression (HER2+) define a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. Although gene expression profiling has identified an ERBB2 molecular subtype of breast cancer, it is clear that HER2+ tumors reside in...
ORGANISM(S): Homo sapiens 
2010-04-14 | E-GEOD-21259 | biostudies-arrayexpress
TranscriptomicsIdentification of subtypes in HER2-positive breast cancer reveals a gene signature prognostic of outcome
Purpose HER2 gene amplification or protein overexpression (HER2+) defines a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. We aimed to investigate the heterogeneous biological appearance and clinical behavior of HER2+ tumors using molecular profilin...
ORGANISM(S): Homo sapiens 
2010-03-16 | E-GEOD-18328 | biostudies-arrayexpress
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