Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cited-1 deficiency suppresses intestinal tumorigenesis through the repression of the Wnt pathway- evidence for the just right model of Wnt mediated tumorigenesis

ABSTRACT: Comparison of the expression profiles of the following genetically altered murine intestinal epithelium: AhCre wildtype, AhCre Apc floxed, AhCre Cited1 null and Ahcre Apcflx/Cited1 null.

ORGANISM(S): Mus musculus

SUBMITTER: Lee Parry

PROVIDER: E-MEXP-3202 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Cited1 deficiency suppresses intestinal tumorigenesis.

Méniel Valérie V Song Fei F Phesse Toby T Young Madeleine M Poetz Oliver O Parry Lee L Jenkins John R JR Williams Geraint T GT Dunwoodie Sally L SL Watson Alastair A Clarke Alan R AR

PLoS genetics 20130801 8

Conditional deletion of Apc in the murine intestine alters crypt-villus architecture and function. This process is accompanied by multiple changes in gene expression, including upregulation of Cited1, whose role in colorectal carcinogenesis is unknown. Here we explore the relevance of Cited1 to intestinal tumorigenesis. We crossed Cited1 null mice with Apc(Min/+) and AhCre(+)Apc(fl/fl) mice and determined the impact of Cited1 deficiency on tumour growth/initiation including tumour multiplicity, ...[more]

PMID: 23935526

Similar Datasets

OsJMJ705 preferentially activates stress-responsive genes

Project description:Histone methylation is important epigenomic information for gene regulation and genome activity To evaluate genome-wide effect of OsJMJ705 on gene expression, we used the Affymetrix microarray technologies to analyze the transcriptomes of the wild type, over-expression plants and the T-DNA mutant. Gene ontology (GO) analysis revealed that up-regulated genes were significantly enriched for the categories of stress-responsive genes. To evaluate genome-wide effect of OsJMJ705 on gene expression, we used the Affymetrix microarray technologies to analyze the transcriptomes of the wild type, over-expression plants and the T-DNA mutant 14 days after germination under normal growth conditions. Two biological repeats were performed. Gene expression changes between the samples were analyzed by AffylmGUI package from the R software.

2013-12-10 | E-GEOD-48069 | biostudies-arrayexpress

Gene expression microarray analysis of whole intestine from Kaiso-/- mice

Project description:Absence of the epigenetic regulator Kaiso suppresses Wnt driven intestinal tumourigenesis. To identify genes regulated by Kaiso we generated wild type and Kaiso-/- mice for microarray expression analysis to identify genes derepressed in the absence of Kaiso.

2018-12-05 | E-MTAB-6009 | biostudies-arrayexpress

Phosphoproteomic study of TOR inhibition in Chlamydomonas reinhardtii

Project description:For further details, please refer to the publication.

2018-09-11 | PXD007221 | Pride

Cryo-slicing BN-MS of rat brain mitochondrial proteins

Project description:Blue-native gel electrophoresis (BN) is a powerful method for protein separation. Combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) it enables large-scale identification of protein complexes and their subunits. Current BN-MS approaches, however, are limited in size resolution, comprehensiveness and quantification. Here, we present a new methodology combining defined sub-mm slicing of BN gels by a cryo-microtome with high-performance LC-MS/MS and label-free quantification of proteins. Application of this cryo-slicing BN-MS approach (csBN-MS) to mitochondria from brain demonstrated a high degree of comprehensiveness, quantification accuracy and size resolution. The technique provided abundance-mass profiles for 743 mitochondrial proteins including all canonical subunits of the oxidative respiratory chain assembled into 13 distinct (super)complexes. Moreover, the data revealed COX7R as a constitutive subunit of distinct supercomplexes and identified novel assemblies of porins and TOM proteins. Together, csBN-MS enables quantitative profiling of complexomes with resolution close to the limits of native gel electrophoresis.

2015-12-01 | PXD002681 | Pride

The SILAC fly allows for accurate protein quantification in vivo

Project description:Stable isotope labeling by amino acids in cell culture (SILAC) is widely used to quantify protein abundance in tissue culture cells. Until now, the only multicellular organism completely labeled at the amino acid level was the laboratory mouse. The fruit fly Drosophila melanogaster is one of the most widely used small animal models in biology. Here, we show that feeding flies with SILAC-labeled yeast leads to almost complete labeling in the first filial generation. We used these "SILAC flies" to investigate sexual dimorphism of protein abundance in D. melanogaster. Quantitative proteome comparison of adult male and female flies revealed distinct biological processes specific for each sex. Using a tudor mutant that is defective for germ cell generation allowed us to differentiate between sex-specific protein expression in the germ line and somatic tissue. We identified many proteins with known sex-specific expression bias. In addition, several new proteins with a potential role in sexual dimorphism were identified. Collectively, our data show that the SILAC fly can be used to accurately quantify protein abundance in vivo. The approach is simple, fast, and cost-effective, making SILAC flies an attractive model system for the emerging field of in vivo quantitative proteomics.

2015-10-12 | PXD003040 | Pride

Gene expression changes in Burkholderia cenocepacia ST32

Project description:Burkholderia cenocepacia sequence type 32 (ST32) represents one of the most globally distributed strains from Bukrholderia cepacia complex (Bcc), which infected 30% of Czech cystic fibrosis (CF) patients. The aim of this study was to compare gene expression in two pairs of ST32 clinical isolates that were subjected to cultivation in two different conditions, characteristic for chronic B. cenocepacia infection in CF patients. ST32 strain is known to be a problematic epidemic strain, which caused a serious outbreak at the Prague CF centre.

2015-02-27 | E-MTAB-3133 | biostudies-arrayexpress

Nuclear substrates of the CDKL5 kinase - Phosphoproteomics

Project description:Identification of nuclear substrates of the CDKL5 kinase by quantitative phosphoproteomics

2020-12-10 | PXD022916 | Pride

Substrates of the ATR kinase - Phosphoproteomics

Project description:Identification and validation of substrates of the ATR kinase by quantitative phosphoproteomics

2024-01-15 | PXD041250 | Pride

TCUP: Typing and characterization of bacteria using bottom-up tandem mass spectrometry proteomics

Project description:Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. The generated data is however highly fragmented, making down-stream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS. TCUP compares the generated protein sequence data to reference databases and automatically finds peptides suitable for characterization of taxonomic composition and identification of expressed antimicrobial resistance genes. TCUP was evaluated using four clinically relevant bacterial species (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae), using both simulated data generated by in silico peptide digestion and experimental proteomics data generated by liquid chromatography-tandem mass spectrometry (MS/MS). The results showed that TCUP performs correct peptide classifications at rates between 90.3% and 98.5% at the species level. The method was also able to accurately estimate the relative abundances of individual species in mixed cultures. Furthermore, TCUP could identify expressed beta-lactamases in an ESBL-producing E. coli strain, even when the strain was cultivated in the absence of antibiotics on non-selective media. Finally, TCUP is computationally efficient, easy to integrate in existing bioinformatics workflows and freely available under an open source license for both Windows and Linux environments.

2017-04-20 | PXD004321 | Pride

HT-SELEX of wild-type and mutated versions of recombinant DNA binding domain of SALL4

Project description:To investigate the differences in DNA binding specificity of wild-type SALL4 C2H2 zinc finger cluster 4 (ZFC4) and disease causing mutations in SALL4 ZFC4, we performed SELEX coupled with high-throughput sequencing (HT-SELEX) using the purified wild-type SALL4 ZFC4 domain, mutated SALL4 ZFC4 (R900W) and mutated SALL4 ZFC4 (G921D) combined with no protein control experiment.

2023-01-04 | E-MTAB-11519 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data