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TranscriptomicsDeep-sequencing influences the results obtained in small-RNA sequencing
This study presents a comparison of small RNA sequencing libraries generated from the same cell lines but using different sequencing platforms and protocols. The samples were analyzed and compared at the level of miRNAs expression and as a population of small RNAs derived from repetitive elements. D...
ORGANISM(S): Mus musculus 
2012-03-01 | E-GEOD-35368 | biostudies-arrayexpress
TranscriptomicsGenome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP-arrays
We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by SNP arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Overall copy number assignmen...
ORGANISM(S): Homo sapiens 
2009-10-29 | E-GEOD-18799 | biostudies-arrayexpress
ModelsVerlingue2016 - Signalling pathway that control S-phase entry and geroconversion - Boolean Model
Verlingue2016 - Signalling pathway that control S-phase entry and geroconversion - Boolean Model This model is described in the article: A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion. Verlingue L, Dugourd A, Stoll G,...
2016-11-29 | MODEL1611180000 | BioModels
TranscriptomicsRestriction of LINE1 activity by RNAi correlates with mouse ES cell differentiation
Long interspersed elements 1 (LINE-1 or L1) are retrotransposons that dominate the mouse genomic landscape, and are expressed in Embryonic Stem Cells (ESCs), germ cells, and during early development. Based on clear precedents in plants and fission yeast, we investigated in this study a role for RNAi...
ORGANISM(S): Mus musculus 
2013-12-11 | E-GEOD-43110 | biostudies-arrayexpress
TranscriptomicsThe developmental dynamics and disease potential of random monoallelic gene expression
X-chromosome inactivation (XCI) in females and allelic exclusion of olfactory receptor or immunoglobulin loci, represent classic examples of random monoallelic expression (RME). RME of some single copy genes has also been reported, but the in vivo relevance of this remains unclear. Here we identify ...
ORGANISM(S): Mus musculus 
2014-02-27 | E-GEOD-54016 | biostudies-arrayexpress
ModelsCalzone2010_Cellfate_Master_Model
Attention: As this model cannot be encoded in SBML at this time, the SBML file contains the whole model in GINML , a different XML model description language, in its main annotation element. Still, the model can be loaded by GINsim as it is by just ignoring th...
2005-01-01 | MODEL0912180000 | BioModels
ModelsCalzone2008_Rb
Protein names are HUGO names or usual names. In the latter case, they are identified with a star (*) and the HUGO name is given in notes. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). To the extent possib...
2005-01-01 | MODEL4132046015 | BioModels
TranscriptomicsBeta-catenin status in pediatric medulloblastomas
Medulloblastoma is the most frequent malignant pediatric brain tumor. Considerable efforts are dedicated to identify markers that help to refine treatment strategies. The activation of the Wnt/beta-catenin pathway occurs in 10-15% of medulloblastomas and has been recently described as a marker for f...
ORGANISM(S): Homo sapiens 
2009-02-02 | E-GEOD-12992 | biostudies-arrayexpress
GenomicsSpi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia
Acute leukemia are characterized by deregulation of transcriptional networks that control the lineage specificity of gene expression. The aberrant overexpression of the Spi-1/PU.1 transcription factor leads to erythroleukemia. To determine how Spi-1 mechanistically influences the transcriptional pro...
ORGANISM(S): Mus musculus 
2012-06-30 | E-GEOD-33611 | biostudies-arrayexpress
TranscriptomicsExpression Data from Uveal Melanoma primary tumors.
A high percentage of uveal melanoma patients develop metastatic tumors that predominately occur in the liver. To identify genes associated with metastasis in this pathology, we studied 63 molecular profiles derived from gene expression microarrays performed from enuceated primary tumors. Metastasis ...
ORGANISM(S): Homo sapiens 
2010-12-14 | E-GEOD-22138 | biostudies-arrayexpress
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